RetrogeneDB ID: retro_hsap_4862

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:74963062..74966746(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000215105
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TTC3
• Ensembl ID: ENSG00000182670
• Aliases: TTC3, DCRR1, RNF105, TPRDIII
• Description: tetratricopeptide repeat domain 3 [Source:HGNC Symbol;Acc:12393]

Sequence

>retro_hsap_4862
GACAATTTTGCTGAGGGAGATTTCACTATGGCGGATTATGCCTTGTTAGAAGATTGCCCTTACGTGGACGATTGTGTCTT
TGCTGCTGAATTTATGACCGATGATTATGTTCGTGTGACTCAGCTTTACTGTGATGGGGTGGGTAAGCAATATAAAGATT
ATGTCCAAAGTGAGAGGAATTTAGAATTTGACATCTGCAGTATATGGTGTAGTAAACCAATTTCTGTCCTGCAAGATTAT
TGTGATGCCATTAAAATAAACATCTTCTGGCCACTTCTGTTTCAACATCAAAACAGTTCTGTAATATCACGATTGCATCC
CTGTGTGGACGCCAACAATTCACGTGCTTCCGAGATAAATTTGAAGAGATTACAACATCTTGAGTTGATGGAAGATATTG
TGGATTTGGCAAAGAAAGCTGCTAATGATTCACTCCTTATTGGAGGCTTATTGAGAATTGGTTATAAAATAGAAAATAAA
ATCTTGGCAATGGAAGAAGCTCTGAATTGGATAAAATATGCAGGCGATGTAACAATTCTAACTAAATTAGGATCAATTGA
CAATTGTTGGCCTATGTTAAGTATTTTCTTTACTGAATACAAGTACCACATAACTAAAATTGTAATGGAAGACTGCAATT
TGCTTGAAGAACTTAAAACCCAAAGTTGTATGGATTGTATAGAGCAAGGAGAACTAATGAAAATGAAAGGAAATGAAGAG
TTTTCCAAAGAAAGATTTGATATAGCTATTATCTATTACACCAGAGCCATTGAATATAGACCTGAAAACCACCTTCTTTA
TGGTAACCGAGCTCTTTGTTTTCTTCGTACTGGACAGTTTAGAAATGCACTTGGTGATGGAAAGAGAGCCACTATTCTGA
AGAACACTTGGCCAAAGGGTCATTATCGTTATTGTGATGCTCTTTCTATGCTGGGGGAATATAACTGGGCCCTGCAAGCA
AACATAACAGCTCAAAAACTCTGTAAAAATGACCCTGAGGGAATCAAGGATCTAATTCAGCAGCATGTAAAGTTACAAAA
ACAAATAGAAGACCTACAAGGTCGAACAGCAAATAAGAATCCAATTAAAGCCTTTTATGAAAACAGGGCCTACACACCTA
GGAGTTTATCAGCACCTGTATTTAGTACTTCACTTAACTTTGTGGAGAAGGAAAGAGATTTCAGAAAAATTAATCACGAA
ATGGCTAACGGTGGTAATCAGAATCTAAAGGTGATGGATGAGGCATTGATGGTAGATGATTGTGACTGTCATCCTGAATT
TTCACCACCATCAAGTCAGCCTCCGAAACATAAAGGAAAACAAAAATCTCGAAACAATGAATCAGAAAAGTTCAGTTCTA
GTTCACAATTGACTTTACCAGCAGATTTGAAGAACATCTTGGAGAAACAGTTTTCTAAATCTTCCAGAGGTGCACACCAG
GATTTTGCTAATATAATGACAATGCTGAGAAGCTTAATTCAAGATGGCTATACAGCCTTATTGGAGCAGCGTTGCCGCAG
TGCCGCACATGCCTTTACAGAGTTGCTGAATGGTTTAGATCCTCAAAAAATAAAGCAATTGAATCTGGCCATGATTAACT
ATGTCTTGGTTGTCTATGGACTTGCCATTTCACTCCTTGGAATAGGACAGCCTGAAGAACTATCTGAAGCTGAAAACCAG
TTTAAGAGGATTATTGAACACTACCACAATGAGGGACTTGATTGCTTGGCCTACTGTGGAATTGGAAAAGTATATTTGAA
AAAAAACAGATTTCTAGAAGCTCTCAATCACTTTGAGAAAGCAAGAACCTTGATTTATCGTCTTCCTGGAGTGTTAACTT
GGCCCACAAGTAATGTGATTATTGAAGAGTCTCAGCCAGAAAAAATAAAGATGCTGTTAGAGAAATTTGTTGAAGAATGC
AAGTTCCCTCCAGTGCCAGATGCCATTTGTTGCTATCAGAAGTGCTGTGGATATTCTAAGATCCAGATATACATAACTGA
TCCAGACTTTAAGGGTTTTATACGCATCAGCTGTTGCCAGTACTGTAAAATAGAATTTCACATGAATTGCTGGAAGAAGT
TAAAAACCACAACCTTTAATGATAAAATTGACAAGGATTTTCTACAAGGAATATGTCTTACCCCTGACTGTGAAGGTGTC
ATTTCTAAGATTATCATCTTCAGCAGTGGTGGTCAAGTTAAATGTGAATTTGAACACAAGGTCATAAAAGAAAAGGTTCC
TCCAAGACCTATTCTGAAACAGAAATGTTCTAGCCTAGAGAAACTAAGACTGAAAGAAGACAAAAAATTGAAGAGAAAGA
TCCAAAAAAAAGAAGCAAAAAAATTAGCACAAGAAAGAATGGAGGAGGACTTAAGAGAAAGTAATCCACCCAAAAACGAA
GAGCAGAAAGAAACTGTAGACAATGTTCAGCATTGTCAGTTCCTTGATGACAGAATTCTACAGTGTATAAAGCAGTATGC
TGACAAGATTAAATCCGGCATATGGAATACAGCCACGCTTCTCAAAGAATTACTTTCTTGGAAAGTTTTGAGCACAGAGG
ACTATACAACCTGTTTTTCAAGCAGAAATTTTCTAAATGAAGCAGTGGACTATGTTATTCGTCACTTGATTCAAGAAAAG
AACAGAGTAAAGACAAGAATATTTCTGCATGTTTTGAGTGAGCTTAAAGAAGTGGAGCCCAAATTAGCCGCCTGGATCCG
AAAACTTAATAGCTTTGGCTTAGATGCCACAGGACCTTTCTTTTCTCGGTATGAAGCATCTCTTAAACAGCTTGATTTTA
GCATCATGACTTTCCTCTGGAATGAGAAATATGGTCACAAACTAGACTCTATAGAAGGAAAGCAACTTGATTATTTCTTT
GAGCCAACATCATCGAAGGAAGCCCGCTGTTTAATATGGCTGCTAGAAGAACACAGAGACAAGTTCCCAGCATTACATAG
TGCTTTAGATGAATTCTTTGATATAATGGACAGCCGCTGTACTGTGTTAAGGAAACAAGACAGTGGCGAAGCACCGTTTA
GTTCTACCAAGGTGAAAAACAAAGGCAAGAAAAAGAAACCAAAGGATTCAAAGCCTATGTTAGTTGGGTCTGGAACAACT
TCAGTAACTCCAAATAATGAGATCATCACTTCAAGTGAAGACCATAGCAATCAAAATTCAGATACTGCAGGCCCATTTGC
AGTGCCTGACCATCTTCGGCAAGACGTAGAAGAATTTGAAGCTCTCTATGACCAACACAGTAATGAATATGTTGTCCGCA
ATAAGAAGCTATGGGACATGAACCCAAAACAAAAATGTTCAACTCTATATGATTACTTCTCTCAGTTGTTGGAGGAACAT
GGTCCCTTGGACATGAGTCACAAGATGTTCTCTGAAGAATATGAGTTTTTCCCAGAAGAAACTCGACCAATACTAGAAAA
AGCAGGAGGTTTAAAATCTTTTCTCTTGGGATGTCCCCGTTTTGTTGTGATTGACAACTGTATTGCATTGAAGAAAGTTG
CATCACGGCTCAAGAAAAAAAGAAAGAAGAAAAACATTAAAACAAAAGTAGAAGACATTTCAAAAGCAGGAGAGTATTTA
CAAGTTAAACTACCACTTAATTCAGCTGCTAGGGAATTTAAACCAGATGTAAAGTCTAAACCAGTATCAGGTTCATCTTC
AGCA

Alignment

ORF - retro_hsap_4862 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.08 %
• Parental protein coverage: 60.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DNFAEGDFTVADYALLEDCPHVDDCVFAAEFMSNDYVRVTQLYCDGVGVQYKDYIQSERNLEFDICSIWC
          DNFAEGDFT.ADYALLEDCP.VDDCVFAAEFM..DYVRVTQLYCDGVG.QYKDY.QSERNLEFDICSIWC
Retrocopy DNFAEGDFTMADYALLEDCPYVDDCVFAAEFMTDDYVRVTQLYCDGVGKQYKDYVQSERNLEFDICSIWC

Parental  SKPISVLQDYCDAIKINIFWPLLFQHQNSSVISRLHPCVDANNSRASEINLKKLQHLELMEDIVDLAKKV
          SKPISVLQDYCDAIKINIFWPLLFQHQNSSVISRLHPCVDANNSRASEINLK.LQHLELMEDIVDLAKK.
Retrocopy SKPISVLQDYCDAIKINIFWPLLFQHQNSSVISRLHPCVDANNSRASEINLKRLQHLELMEDIVDLAKKA

Parental  ANDSFLIGGLLRIGCKIENKILAMEEALNWIKYAGDVTILTKLGSIDNCWPMLSIFFTEYKYHITKIVME
          ANDS.LIGGLLRIG.KIENKILAMEEALNWIKYAGDVTILTKLGSIDNCWPMLSIFFTEYKYHITKIVME
Retrocopy ANDSLLIGGLLRIGYKIENKILAMEEALNWIKYAGDVTILTKLGSIDNCWPMLSIFFTEYKYHITKIVME

Parental  DCNLLEELKTQSCMDCIEEGELMKMKGNEEFSKERFDIAIIYYTRAIEYRPENYLLYGNRALCFLRTGQF
          DCNLLEELKTQSCMDCIE.GELMKMKGNEEFSKERFDIAIIYYTRAIEYRPEN.LLYGNRALCFLRTGQF
Retrocopy DCNLLEELKTQSCMDCIEQGELMKMKGNEEFSKERFDIAIIYYTRAIEYRPENHLLYGNRALCFLRTGQF

Parental  RNALGDGKRATILKNTWPKGHYRYCDALSMLGEYDWALQANIKAQKLCKNDPEGIKDLIQQHVKLQKQIE
          RNALGDGKRATILKNTWPKGHYRYCDALSMLGEY.WALQANI.AQKLCKNDPEGIKDLIQQHVKLQKQIE
Retrocopy RNALGDGKRATILKNTWPKGHYRYCDALSMLGEYNWALQANITAQKLCKNDPEGIKDLIQQHVKLQKQIE

Parental  DLQGRTANKDPIKAFYENRAYTPRSLSAPIFTTSLNFVEKERDFRKINHEMANGGNQNLKVADEALKVDD
          DLQGRTANK.PIKAFYENRAYTPRSLSAP.F.TSLNFVEKERDFRKINHEMANGGNQNLKV.DEAL.VDD
Retrocopy DLQGRTANKNPIKAFYENRAYTPRSLSAPVFSTSLNFVEKERDFRKINHEMANGGNQNLKVMDEALMVDD

Parental  CDCHPEFSPPSSQPPKHKGKQKSRNNESEKFSSSSPLTLPADLKNILEKQFSKSSRAAHQDFANIMKMLR
          CDCHPEFSPPSSQPPKHKGKQKSRNNESEKFSSSS.LTLPADLKNILEKQFSKSSR.AHQDFANIM.MLR
Retrocopy CDCHPEFSPPSSQPPKHKGKQKSRNNESEKFSSSSQLTLPADLKNILEKQFSKSSRGAHQDFANIMTMLR

Parental  SLIQDGYMALLEQRCRSAAQAFTELLNGLDPQKIKQLNLAMINYVLVVYGLAISLLGIGQPEELSEAENQ
          SLIQDGY.ALLEQRCRSAA.AFTELLNGLDPQKIKQLNLAMINYVLVVYGLAISLLGIGQPEELSEAENQ
Retrocopy SLIQDGYTALLEQRCRSAAHAFTELLNGLDPQKIKQLNLAMINYVLVVYGLAISLLGIGQPEELSEAENQ

Parental  FKRIIEHYPSEGLDCLAYCGIGKVYLKKNRFLEALNHFEKARTLIYRLPGVLTWPTSNVIIEESQPQKIK
          FKRIIEHY..EGLDCLAYCGIGKVYL...RFLEALNHFEKARTLIYRLPGVLTWPTSNVIIEESQP.KIK
Retrocopy FKRIIEHYHNEGLDCLAYCGIGKVYLXXXRFLEALNHFEKARTLIYRLPGVLTWPTSNVIIEESQPEKIK

Parental  MLLEKFVEECKFPPVPDAICCYQKCHGYSKIQIYITDPDFKGFIRISCCQYCKIEFHMNCWKKLKTTTFN
          MLLEKFVEECKFPPVPDAICCYQKC.GYSKIQIYITDPDFKGFIRISCCQYCKIEFHMNCWKKLKTTTFN
Retrocopy MLLEKFVEECKFPPVPDAICCYQKCCGYSKIQIYITDPDFKGFIRISCCQYCKIEFHMNCWKKLKTTTFN

Parental  DKIDKDFLQGICLTPDCEGVISKIIIFSSGGEVKCEFEHKVIKEKVPPRPILKQKCSSLEKLRLKEDKKL
          DKIDKDFLQGICLTPDCEGVISKIIIFSSGG.VKCEFEHKVIKEKVPPRPILKQKCSSLEKLRLKED...
Retrocopy DKIDKDFLQGICLTPDCEGVISKIIIFSSGGQVKCEFEHKVIKEKVPPRPILKQKCSSLEKLRLKEDXXX

Parental  KRKIQKKEAKKLAQERMEEDLRESNPPKNEEQKETVDNVQRCQFLDDRILQCIKQYADKIKSGIQNTAML
          ...........LAQERMEEDLRESNPPKNEEQKETVDNVQ.CQFLDDRILQCIKQYADKIKSGI.NTA.L
Retrocopy XXXXXXXXXXXLAQERMEEDLRESNPPKNEEQKETVDNVQHCQFLDDRILQCIKQYADKIKSGIWNTATL

Parental  LKELLSWKVLSTEDYTTCFSSRNFLNEAVDYVIRHLIQENNRVKTRIFLHVLSELKEVEPKLAAWIQKLN
          LKELLSWKVLSTEDYTTCFSSRNFLNEAVDYVIRHLIQE.NRVKTRIFLHVLSELKEVEPKLAAWI.KLN
Retrocopy LKELLSWKVLSTEDYTTCFSSRNFLNEAVDYVIRHLIQEKNRVKTRIFLHVLSELKEVEPKLAAWIRKLN

Parental  SFGLDATGTFFSRYGASLKLLDFSIMTFLWNEKYGHKLDSIEGKQLDYFSEPASLKEARCLIWLLEEHRD
          SFGLDATG.FFSRY.ASLK.LDFSIMTFLWNEKYGHKLDSIEGKQLDYF.EP.S.KEARCLIWLLEEHRD
Retrocopy SFGLDATGPFFSRYEASLKQLDFSIMTFLWNEKYGHKLDSIEGKQLDYFFEPTSSKEARCLIWLLEEHRD

Parental  KFPALHSALDEFFDIMDSRCTVLRKQDSGEAPFSSTKVKNKSKKKKPKDSKPMLVGSGTTSVTSNNEIIT
          KFPALHSALDEFFDIMDSRCTVLRKQDSGEAPFSSTKVKNK.KKKKPKDSKPMLVGSGTTSVT.NNEIIT
Retrocopy KFPALHSALDEFFDIMDSRCTVLRKQDSGEAPFSSTKVKNKGKKKKPKDSKPMLVGSGTTSVTPNNEIIT

Parental  SSEDHSNRNSDSAGPFAVPDHLRQDVEEFEALYDQHSNEYVVRNKKLWDMNPKQKCSTLYDYFSQFLEEH
          SSEDHSN.NSD.AGPFAVPDHLRQDVEEFEALYDQHSNEYVVRNKKLWDMNPKQKCSTLYDYFSQ.LEEH
Retrocopy SSEDHSNQNSDTAGPFAVPDHLRQDVEEFEALYDQHSNEYVVRNKKLWDMNPKQKCSTLYDYFSQLLEEH

Parental  GPLDMSNKMFSAEYEFFPEETRQILEKAGGLKPFLLGCPRFVVIDNCIALKKVASRLKKKRKKKNIKTKV
          GPLDMS.KMFS.EYEFFPEETR.ILEKAGGLK.FLLGCPRFVVIDNCIALKKVASRL.............
Retrocopy GPLDMSHKMFSEEYEFFPEETRPILEKAGGLKSFLLGCPRFVVIDNCIALKKVASRLXXXXXXXXXXXXX

Parental  EEISKAGEYVRVKLQLNPAAREFKPDVKSKPVSDSSSA
          E.ISKAGEY..VKL.LN.AAREFKPDVKSKPVS.SSSA
Retrocopy EDISKAGEYLQVKLPLNSAAREFKPDVKSKPVSGSSSA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
bodymap2_adipose	4.61 RPM	211.78 RPM
bodymap2_adrenal	3.21 RPM	139.29 RPM
bodymap2_brain	8.79 RPM	304.25 RPM
bodymap2_breast	6.75 RPM	285.63 RPM
bodymap2_colon	4.76 RPM	156.27 RPM
bodymap2_heart	2.92 RPM	70.37 RPM
bodymap2_kidney	3.12 RPM	126.58 RPM
bodymap2_liver	0.46 RPM	96.34 RPM
bodymap2_lung	2.32 RPM	98.17 RPM
bodymap2_lymph_node	2.19 RPM	144.00 RPM
bodymap2_ovary	10.27 RPM	292.72 RPM
bodymap2_prostate	3.78 RPM	216.24 RPM
bodymap2_skeletal_muscle	0.38 RPM	47.09 RPM
bodymap2_testis	6.88 RPM	245.15 RPM
bodymap2_thyroid	6.55 RPM	194.43 RPM
bodymap2_white_blood_cells	0.39 RPM	140.49 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4862 was not detected

EST

15 EST(s) were mapped to retro_hsap_4862 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA470510	74963205	74963587	99.3	379	3	376
AA470557	74963367	74963779	99.8	410	1	408
AA502576	74963237	74963592	99.2	355	0	354
AA554904	74963213	74963693	98.8	474	5	467
AI678227	74963212	74963806	100	589	0	585
AU117751	74964281	74964986	99.2	695	6	689
AU127587	74964451	74965056	99.5	597	2	593
AU144640	74964410	74964956	99.5	539	3	534
BM701975	74963702	74964250	99.9	547	1	546
BU729641	74963205	74963862	99.9	653	1	651
BX495640	74963822	74964327	97.9	503	2	497
DA200641	74964721	74965296	100	575	0	575
DA494480	74964305	74964851	100	545	0	544
DA509421	74964256	74964836	100	580	0	580
DB355669	74963215	74963709	98.6	479	3	468

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_201219	866 libraries	572 libraries	358 libraries	31 libraries	2 libraries

The graphical summary, for retro_hsap_4862 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_4862 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4862 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_3032

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000182670	2 retrocopies	retro_hsap_4862 , retro_hsap_886,
Gorilla gorilla	ENSGGOG00000011116	1 retrocopy	retro_ggor_3032,
Nomascus leucogenys	ENSNLEG00000004545	1 retrocopy	retro_nleu_12,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.26 RPM
CEU_NA11843	0.09 RPM
CEU_NA11930	0.16 RPM
CEU_NA12004	0.23 RPM
CEU_NA12400	0.14 RPM
CEU_NA12751	0.61 RPM
CEU_NA12760	0.27 RPM
CEU_NA12827	0.09 RPM
CEU_NA12872	0.49 RPM
CEU_NA12873	0.19 RPM
FIN_HG00183	0.27 RPM
FIN_HG00277	0.44 RPM
FIN_HG00315	0.28 RPM
FIN_HG00321	0.36 RPM
FIN_HG00328	0.28 RPM
FIN_HG00338	0.19 RPM
FIN_HG00349	0.11 RPM
FIN_HG00375	0.22 RPM
FIN_HG00377	0.05 RPM
FIN_HG00378	0.28 RPM
GBR_HG00099	0.20 RPM
GBR_HG00111	0.13 RPM
GBR_HG00114	0.21 RPM
GBR_HG00119	0.29 RPM
GBR_HG00131	0.34 RPM
GBR_HG00133	0.29 RPM
GBR_HG00134	0.52 RPM
GBR_HG00137	0.11 RPM
GBR_HG00142	0.08 RPM
GBR_HG00143	0.06 RPM
TSI_NA20512	0.11 RPM
TSI_NA20513	0.58 RPM
TSI_NA20518	0.50 RPM
TSI_NA20532	0.37 RPM
TSI_NA20538	0.41 RPM
TSI_NA20756	0.20 RPM
TSI_NA20765	0.31 RPM
TSI_NA20771	0.23 RPM
TSI_NA20786	0.34 RPM
TSI_NA20798	0.19 RPM
YRI_NA18870	0.30 RPM
YRI_NA18907	0.35 RPM
YRI_NA18916	0.36 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.19 RPM
YRI_NA19114	0.29 RPM
YRI_NA19118	0.25 RPM
YRI_NA19213	0.31 RPM
YRI_NA19214	0.44 RPM
YRI_NA19223	0.32 RPM

---

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).