RetrogeneDB ID: retro_hsap_39

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 5:112227336..112228776(+)
• Located in intron of: ENSG00000129625

Retrocopy information

• Ensembl ID: ENSG00000212643
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ZRSR2
• Ensembl ID: ENSG00000169249
• Aliases: ZRSR2, U2AF1-RS2, U2AF1L2, U2AF1RS2, URP
• Description: zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2 [Source:HGNC Symbol;Acc:23019]

Sequence

>retro_hsap_39
ATGGCTGCACTTGAGAAGATGACGTTTCCCAAGAAGATGACATTTCCAGAGAAACCAAGCCACAAAAAGTACAGGGCCGC
CCTGAAGAAGGAGAAACGAAAGAAACGTCGGCAGGAACTTGCTCGACTGAGAGACTCAGGACTCTCACAGGAGGAGGAAG
AGGACACTTTTATTGAAGAACAACAACTAGAAGAAGAGAAGCTATTGGAAAGAGAGAGGGAAAGATTACATGAGGAGTGG
TTGCTGAGGGAGCAGAAGGCACAAGAAGAATTCAGAATAAAGAAGGAAAAGGAAGAGGCGGCTAAAAAATGGCTAGAAGA
ACAAGAGAGAAAGTTAAAGGAACAATGGAAAGAACAGCAGAGGAAAGAGAGAGAAGAGGAGGAGCAGAAACAACAGGAGA
AGAAAGAAAAAGAGGAAGCTGTGCAGAAGATGCTGGATCAGGCTGAAAATGATTTAGAAAATAGTACCACATGGCAAAAC
CCAGAACCACCCGTGGATTTCAGAGTAATGGAGAAGGATCGAGCTAATTGTCCCTTCTACAGTAAAACAGGAGCTTGCAG
ATTTGGAGACAGATGTTCACGTAAACATAATTTCCCAACATCTAGTCCTACCCTTCTTATTAAGAGCATGTTTACAACGT
TTGGAATGGAGCAGTGCAGGAGGGATGACTATGACCCTGACGCAAGCCTGGAGTACAGCGAGGAAGAAACCTACCAACAG
TTCCTAGATTTCTATGAGGATGTGTTGCCCGAGTTCAAGAACGTGGGGAAAGTGATTCAGTTCAAGGTCAGCTGCAATTT
GGAACCTCACCTGAGGGGCAATGTATATGTTCAGTACCAGTCGGAAGAAGAATGCCAAGCAGCCCTTTCTCTGTTTAACG
GACGATGGTATGCAGGACGACAGCTGCAATGTGAATTCTGCCCAGTGACCCGGTGGAAAATGGCGATTTGTGGTTTATTT
GAAATACAACAATGTCCAAGAGGAAAACACTGCAACTTTCTTCATGTGTTCAGAAATCCCAACAATGAATTCTGGGAAGC
TAATAGAGACATCTACTTGTCTTCAGATCAGACTGGCTCCTCCTTTGGCAAGAACTCCGAGAGGAGGGAGAAGATGGGCC
ACCACGACCACTACTACAGCAGGCAGCGGGGAAGGAGAAACCCTAGTCCAGACCACACCTACAAAAGAAATGGGGAATCC
GAGAGAAAAAAGAGTAGTCATAGGGGGAAGAAATCTCACAAACGCACATCAAAGAGTCGGGAGAGGCACAATTCACCAAG
CAGAGGAAGAAATAGGCACCGCAGCTGGGACCAGGGCCGCCGGAGCCAGAGCCGCAGGAGCCACCGCAGCCGGAGCCAAA
GTTCCTCTAGGTGCCGAAGTCGTGGGAGGAGGAAGTCGGGTAATAGAGACAGAACTGTTCAGAGTCCCCAATCCAAATAA

Alignment

ORF - retro_hsap_39 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.77 %
• Parental protein coverage: 96.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAPEKMTFPEKPSHKKYRAALKKEKRKKRRQELARLRDSGLSQKEEEEDTFIEEQQLEEEKLLERERQR
          M..P.KMTFPEKPSHKKYRAALKKEKRKKRRQELARLRDSGLSQ.EEEEDTFIEEQQLEEEKLLERER.R
Retrocopy MTFPKKMTFPEKPSHKKYRAALKKEKRKKRRQELARLRDSGLSQ-EEEEDTFIEEQQLEEEKLLERERER

Parental  LHEEWLLREQKAQEEFRIKKEKEEAAKKRQEEQERKLKEQWEEQQRKEREEEEQKRQEKKEKEEALQKML
          LHEEWLLREQKAQEEFRIKKEKEEAAKK..EEQERKLKEQW.EQQRKEREEEEQK.QEKKEKEEA.QKML
Retrocopy LHEEWLLREQKAQEEFRIKKEKEEAAKKWLEEQERKLKEQWKEQQRKEREEEEQKQQEKKEKEEAVQKML

Parental  DQAENELENGTTWQNPEPPVDFRVMEKDRANCPFYSKTGACRFGDRCSRKHNFPTSSPTLLIKSMFTTFG
          DQAEN.LEN.TTWQNPEPPVDFRVMEKDRANCPFYSKTGACRFGDRCSRKHNFPTSSPTLLIKSMFTTFG
Retrocopy DQAENDLENSTTWQNPEPPVDFRVMEKDRANCPFYSKTGACRFGDRCSRKHNFPTSSPTLLIKSMFTTFG

Parental  MEQCRRDDYDPDASLEYSEEETYQQFLDFYEDVLPEFKNVGKVIQFKVSCNLEPHLRGNVYVQYQSEEEC
          MEQCRRDDYDPDASLEYSEEETYQQFLDFYEDVLPEFKNVGKVIQFKVSCNLEPHLRGNVYVQYQSEEEC
Retrocopy MEQCRRDDYDPDASLEYSEEETYQQFLDFYEDVLPEFKNVGKVIQFKVSCNLEPHLRGNVYVQYQSEEEC

Parental  QAALSLFNGRWYAGRQLQCEFCPVTRWKMAICGLFEIQQCPRGKHCNFLHVFRNPNNEFWEANRDIYLSP
          QAALSLFNGRWYAGRQLQCEFCPVTRWKMAICGLFEIQQCPRGKHCNFLHVFRNPNNEFWEANRDIYLS.
Retrocopy QAALSLFNGRWYAGRQLQCEFCPVTRWKMAICGLFEIQQCPRGKHCNFLHVFRNPNNEFWEANRDIYLSS

Parental  DRTGSSFGKNSERRERMGHHDDYYSRLRGRRNPSPDHSYKRNGESERKSSRHRGKKSHKRTSKSRERHNS
          D.TGSSFGKNSERRE.MGHHD.YYSR.RGRRNPSPDH.YKRNGESERK.S.HRGKKSHKRTSKSRERHNS
Retrocopy DQTGSSFGKNSERREKMGHHDHYYSRQRGRRNPSPDHTYKRNGESERKKSSHRGKKSHKRTSKSRERHNS

Parental  RSRGRNRDRSRDRSRGRGSRSRSRSRSRRSRRSRSQSSSRSRSRGR
          .SRGRNR.RS.D..R...SR...RSRS..S.R.RS.....S..R.R
Retrocopy PSRGRNRHRSWDQGRRSQSRRSHRSRSQSSSRCRSRGRRKSGNRDR

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	1.63 RPM	15.29 RPM
bodymap2_adrenal	2.27 RPM	18.98 RPM
bodymap2_brain	3.73 RPM	10.81 RPM
bodymap2_breast	2.63 RPM	16.36 RPM
bodymap2_colon	1.97 RPM	23.69 RPM
bodymap2_heart	1.03 RPM	6.46 RPM
bodymap2_kidney	2.59 RPM	12.76 RPM
bodymap2_liver	0.61 RPM	2.72 RPM
bodymap2_lung	1.65 RPM	13.24 RPM
bodymap2_lymph_node	2.63 RPM	20.85 RPM
bodymap2_ovary	6.96 RPM	19.82 RPM
bodymap2_prostate	1.71 RPM	15.95 RPM
bodymap2_skeletal_muscle	0.42 RPM	7.38 RPM
bodymap2_testis	4.69 RPM	11.44 RPM
bodymap2_thyroid	3.92 RPM	21.83 RPM
bodymap2_white_blood_cells	1.67 RPM	13.58 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_39 was not detected

EST

7 EST(s) were mapped to retro_hsap_39 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AW371109	112227415	112227722	98.7	301	4	295
AW866867	112227266	112227652	100	386	0	386
AW876898	112228023	112228159	100	136	0	136
AW888783	112227735	112228139	98.8	398	5	392
AW938127	112228023	112228172	100	148	0	147
BG985951	112228070	112228172	100	102	0	102
BG985994	112228050	112228172	99.2	120	0	117

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_147714	1367 libraries	421 libraries	36 libraries	2 libraries	3 libraries

The graphical summary, for retro_hsap_39 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_39 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_39 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_25

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000009333	1 retrocopy	retro_fcat_44,
Homo sapiens	ENSG00000160201	2 retrocopies	retro_hsap_1478, retro_hsap_790,
Homo sapiens	ENSG00000169249	1 retrocopy	retro_hsap_39 ,
Gorilla gorilla	ENSGGOG00000011962	1 retrocopy	retro_ggor_1422,
Macaca mulatta	ENSMMUG00000014054	1 retrocopy	retro_mmul_2030,
Mus musculus	ENSMUSG00000031370	1 retrocopy	retro_mmus_233,
Nomascus leucogenys	ENSNLEG00000009496	1 retrocopy	retro_nleu_1,
Pan troglodytes	ENSPTRG00000021693	1 retrocopy	retro_ptro_25,
Rattus norvegicus	ENSRNOG00000033176	1 retrocopy	retro_rnor_176,
Tarsius syrichta	ENSTSYG00000005278	1 retrocopy	retro_tsyr_1826,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	1.52 RPM
CEU_NA11843	1.25 RPM
CEU_NA11930	2.09 RPM
CEU_NA12004	2.17 RPM
CEU_NA12400	1.05 RPM
CEU_NA12751	2.04 RPM
CEU_NA12760	1.12 RPM
CEU_NA12827	1.46 RPM
CEU_NA12872	1.17 RPM
CEU_NA12873	2.07 RPM
FIN_HG00183	1.07 RPM
FIN_HG00277	1.59 RPM
FIN_HG00315	2.10 RPM
FIN_HG00321	1.39 RPM
FIN_HG00328	1.56 RPM
FIN_HG00338	1.17 RPM
FIN_HG00349	1.74 RPM
FIN_HG00375	1.54 RPM
FIN_HG00377	1.84 RPM
FIN_HG00378	1.98 RPM
GBR_HG00099	1.51 RPM
GBR_HG00111	1.89 RPM
GBR_HG00114	2.37 RPM
GBR_HG00119	1.96 RPM
GBR_HG00131	1.52 RPM
GBR_HG00133	1.74 RPM
GBR_HG00134	1.94 RPM
GBR_HG00137	1.29 RPM
GBR_HG00142	1.89 RPM
GBR_HG00143	2.23 RPM
TSI_NA20512	1.36 RPM
TSI_NA20513	1.60 RPM
TSI_NA20518	2.00 RPM
TSI_NA20532	2.14 RPM
TSI_NA20538	1.70 RPM
TSI_NA20756	1.25 RPM
TSI_NA20765	2.86 RPM
TSI_NA20771	1.67 RPM
TSI_NA20786	1.67 RPM
TSI_NA20798	1.84 RPM
YRI_NA18870	1.22 RPM
YRI_NA18907	2.01 RPM
YRI_NA18916	1.92 RPM
YRI_NA19093	1.72 RPM
YRI_NA19099	0.77 RPM
YRI_NA19114	1.28 RPM
YRI_NA19118	2.36 RPM
YRI_NA19213	1.24 RPM
YRI_NA19214	2.19 RPM
YRI_NA19223	2.35 RPM

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Indel association:

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