RetrogeneDB ID: retro_hsap_4030

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 8:26236905..26238764(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000228451
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SDAD1
• Ensembl ID: ENSG00000198301
• Aliases: None
• Description: SDA1 domain containing 1 [Source:HGNC Symbol;Acc:25537]

Sequence

>retro_hsap_4030
ATTAGTTACTGCTACCCAGGGTATCTAAGTAATTTTCCTCAAGTGGTGAAAGATCTTCTGTCCTGTAATCATACTGTATT
GGATCCAGATCTTCGAATGACATTTTGCAAAGCTTTGATCTTGCTGAGAAATAAGAATCTCATCAATCCATCAAGCCTGC
TAGAACTCTTCTTTGAACTTCTCTGTTGCCATGATAAGCTTCTGCAAAAGACTTCATACACATATATCGTGACTGATATC
AAGAATATAAATGCAAAACACAAGAATAAAGTGGATGTAGTATTGTAAAATTTCATGTATACCATGTTGAGAGATAGCAA
TGCAACTGCAGCCAAGATGTCTTTAGATGTTATGATTGAACTCTACAGAAGGAACATCTGGAATGATACCAAAACTGTCA
ATGTTATCACAACTGCATGTTTCTCTTAGGTCACCAAGATATTAGTTGCTGCTTTGACATTCTTTCTTGGAAAAGATGAA
GATGAAAAACAGGCCAGTGACTCCGAATCTGAGGATGACGGACCAACAGCAAGAGACCTGCTAGCACAGTATGCTACAGG
GAACAAAGTTCCCAAAACAAGAAAAAGTTGGAAAAGGCAATGAAAGTGCTCAAGAAACAAAAGAAGAAGAAAAAACCAGA
GGTGTTTAACTTTTTAGCCGTTCACTTGATTCATGATCCCCAAGATTTTGCAGAAAAACTACTAAAGCAGCTTGAGTGCT
GTAAGGAGAGGTTGGAAGTGAAGATGATGCTCATGAACCTCATCTCAGATTGGTGGGAATTCATAAGCTCTTCCTCTTCA
ATTTCTATCACTTTTTGCGAAGGTTTCTGCAGCCCCACCAAAGAGAAGTAACAAAGAACCTTCTGTTTGCTGCACAAGCA
TCTCATCACCTAGTACACCCAGCGATTATTCAATCATTGCTTATGACTGTGGCCAACAATTTTGTTAACGACAAGAACTC
TGGAGAAGCCATGACAATAGGAATCAATGCTGTAAAAGAGACAACAGCTCAGTGTCCTCTGGCCATGACTGAAAAGCTTC
TCCAAGACCTGGCTCAGTATAAAACACACAAGGATAATAATGTAATGATGTCTGCTAGAACTTTGATTCGGCTCTTCCGA
ACACTGAATCCTCAGATGCTGCAGAAGAAATTCTGGGGTAAGCCTACAGAAGCCTCCATAGAAGCAAGAGTACAAGAATA
TGGAGAATTAGATGCTAAAGGTTACATTCCAGGAGCAGAAGTTCTGGAAGTTGAGAAAGAGGAGAGTGCTGAAAATGATG
AAGATGGATGGGAAAGTACCAGTCTCAGTGAGGAGGAGGATGCCGATGGCGAATGGGTTGATGTGCAACACTCTTCCAAT
GAAGAACAGCAAGAAATTTCCAAGAAGCTGAACACCATGCCCATGGAGGAGCAGAAAGCCAAAACTGCAGCCGTCAGCAC
CAGTCGAGTTTTAAGTTAGGAAGACTTCCAGAAAATCCGCATGGCGCAAATGAGAAAAGAACTTGACGCTGTCCCCGGGA
AATCCCAGAAGAGGAAATATATTGAAATCGACAGTGATGAAGAGCCGAGGGGTGAATTACTTTCTCTTCCGGACATTGAA
CGCCTTCATAAAAAGCCAAAATCTGACAAAGAGACAAGACTAGCAACTGCAATGGCTGGAAAGACAGACCGAAAAGAATT
TGTGAGGAAGAAAACCAAAGTGAATCCATTTTCCAGTTCAAAAAGTAAAGAGAAGAAAAAACAGAAGAACTTTATGATGA
TGTGGTATAGCCAGAATGTCTGGTCAGAAAATAAGCGTTCCTTCTGAGAAAAACAGTTGGCGCTGCGAGATGCCTTTTGA
AAAGAGAAAAAGAATGAAG

Alignment

ORF - retro_hsap_4030 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.58 %
• Parental protein coverage: 90.54 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ISHCYPEYLSNFPQEVKDLLSCNHTVLDPDLRMTFCKALILLRNKNLINPSSLLELFFELFRCHDKLLRK
          IS.CYP.YLSNFPQ.VKDLLSCNHTVLDPDLRMTFCKALILLRNKNLINPSSLLELFFEL..CHDKLL.K
Retrocopy ISYCYPGYLSNFPQVVKDLLSCNHTVLDPDLRMTFCKALILLRNKNLINPSSLLELFFELLCCHDKLLQK

Parental  TLYTHIVTDIKNINAKHKNNKVNVVLQNFMYTMLRDSNATAAKMSLDVMIELYRRNIWNDAKTVNVITTA
          T.YT.IVTDIKNINAKHKN.KV.VVL.NFMYTMLRDSNATAAKMSLDVMIELYRRNIWND.KTVNVITTA
Retrocopy TSYTYIVTDIKNINAKHKN-KVDVVL*NFMYTMLRDSNATAAKMSLDVMIELYRRNIWNDTKTVNVITTA

Parental  CFSKVTKILVAALTFFLGKDEDEKQDSDSESEDDGPTARDLLVQYATGKK-SSKNKKKLEKAMKVLKKQK
          CFS.VTKILVAALTFFLGKDEDEKQ.SDSESEDDGPTARDLL.QYATG.K.SS.NKKKLEKAMKVLKKQK
Retrocopy CFS*VTKILVAALTFFLGKDEDEKQASDSESEDDGPTARDLLAQYATGNK<SSQNKKKLEKAMKVLKKQK

Parental  KKKKPEVFNFSAIHLIHDPQDFAEKLLKQLECCKERFEVKMMLMNLIS-RLVGIHELFLFNFYPFLQRFL
          KKKKPEVFNF.A.HLIHDPQDFAEKLLKQLECCKER.EVKMMLMNLIS.RLVGIH.LFLFNFY.FL.RFL
Retrocopy KKKKPEVFNFLAVHLIHDPQDFAEKLLKQLECCKERLEVKMMLMNLIS<RLVGIHKLFLFNFYHFLRRFL

Parental  QPHQREVTKILLFAAQASHHLVPPEIIQSLLMTVANNFVTDKNSGEVMTVGINAIKEITARCPLAMTEEL
          QPHQREVTK.LLFAAQASHHLV.P.IIQSLLMTVANNFV.DKNSGE.MT.GINA.KE.TA.CPLAMTE.L
Retrocopy QPHQREVTKNLLFAAQASHHLVHPAIIQSLLMTVANNFVNDKNSGEAMTIGINAVKETTAQCPLAMTEKL

Parental  LQDLAQYKTHKDKNVMMSARTLIHLFRTLNPQMLQKKFRGKPTEASIEARVQEYGELDAKDYIPGAEVLE
          LQDLAQYKTHKD.NVMMSARTLI.LFRTLNPQMLQKKF.GKPTEASIEARVQEYGELDAK.YIPGAEVLE
Retrocopy LQDLAQYKTHKDNNVMMSARTLIRLFRTLNPQMLQKKFWGKPTEASIEARVQEYGELDAKGYIPGAEVLE

Parental  VEKEENAENDEDGWESTSLSEEEDADGEWIDVQHSSDEEQQEISKKLNSMPMEERKAKAAAISTSRVLTQ
          VEKEE.AENDEDGWESTSLSEEEDADGEW.DVQHSS.EEQQEISKKLN.MPMEE.KAK.AA.STSRVL..
Retrocopy VEKEESAENDEDGWESTSLSEEEDADGEWVDVQHSSNEEQQEISKKLNTMPMEEQKAKTAAVSTSRVLS*

Parental  EDFQKIRMAQMRKELDAAPGKSQKRKYIEIDSDEEPRGELLSLRDIERLHKKPKSDKETRLATAMAGKTD
          EDFQKIRMAQMRKELDA.PGKSQKRKYIEIDSDEEPRGELLSL.DIERLHKKPKSDKETRLATAMAGKTD
Retrocopy EDFQKIRMAQMRKELDAVPGKSQKRKYIEIDSDEEPRGELLSLPDIERLHKKPKSDKETRLATAMAGKTD

Parental  RKEFVRKKTKTNPFSSSTNKEKKKQKNFMMMRYSQNVRSKNKRSFREKQLALRDA-LLK-KRKRMK
          RKEFVRKKTK.NPFSSS..KEKKKQKNFMMM.YSQNV.S.NKRSF.EKQLALRDA.LLK.KRKRMK
Retrocopy RKEFVRKKTKVNPFSSSKSKEKKKQKNFMMMWYSQNVWSENKRSF*EKQLALRDA<LLK<KRKRMK

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	1.23 RPM	27.29 RPM
bodymap2_adrenal	0.80 RPM	53.08 RPM
bodymap2_brain	1.36 RPM	31.83 RPM
bodymap2_breast	1.36 RPM	35.27 RPM
bodymap2_colon	2.38 RPM	29.53 RPM
bodymap2_heart	3.19 RPM	18.92 RPM
bodymap2_kidney	0.79 RPM	40.18 RPM
bodymap2_liver	0.23 RPM	19.52 RPM
bodymap2_lung	0.88 RPM	15.95 RPM
bodymap2_lymph_node	0.75 RPM	24.93 RPM
bodymap2_ovary	1.23 RPM	63.02 RPM
bodymap2_prostate	4.50 RPM	45.78 RPM
bodymap2_skeletal_muscle	2.91 RPM	41.96 RPM
bodymap2_testis	5.75 RPM	79.05 RPM
bodymap2_thyroid	2.26 RPM	72.65 RPM
bodymap2_white_blood_cells	1.04 RPM	62.02 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4030 was not detected

EST

2 EST(s) were mapped to retro_hsap_4030 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
DW436115	26237477	26237714	99.6	236	1	235
DW456662	26237671	26237821	98.7	148	2	146

TSS

No TSS is located nearby retro_hsap_4030 retrocopy 5' end.

Lab

retro_hsap_4030 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4030 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2732

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008524	2 retrocopies	retro_cpor_510, retro_cpor_994,
Homo sapiens	ENSG00000198301	2 retrocopies	retro_hsap_2412, retro_hsap_4030 ,
Gorilla gorilla	ENSGGOG00000006441	1 retrocopy	retro_ggor_1498,
Loxodonta africana	ENSLAFG00000012217	1 retrocopy	retro_lafr_980,
Macaca mulatta	ENSMMUG00000017503	1 retrocopy	retro_mmul_604,
Nomascus leucogenys	ENSNLEG00000027034	1 retrocopy	retro_nleu_2410,
Oryctolagus cuniculus	ENSOCUG00000026953	1 retrocopy	retro_ocun_547,
Pongo abelii	ENSPPYG00000014852	1 retrocopy	retro_pabe_1777,
Pan troglodytes	ENSPTRG00000024399	2 retrocopies	retro_ptro_1388, retro_ptro_2732,
Rattus norvegicus	ENSRNOG00000022229	2 retrocopies	retro_rnor_1381, retro_rnor_1967,
Tupaia belangeri	ENSTBEG00000005270	1 retrocopy	retro_tbel_2414,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	4.52 RPM
CEU_NA11843	3.07 RPM
CEU_NA11930	2.67 RPM
CEU_NA12004	1.79 RPM
CEU_NA12400	2.74 RPM
CEU_NA12751	3.45 RPM
CEU_NA12760	2.16 RPM
CEU_NA12827	2.36 RPM
CEU_NA12872	3.18 RPM
CEU_NA12873	2.14 RPM
FIN_HG00183	1.87 RPM
FIN_HG00277	2.51 RPM
FIN_HG00315	2.73 RPM
FIN_HG00321	4.44 RPM
FIN_HG00328	3.50 RPM
FIN_HG00338	3.21 RPM
FIN_HG00349	3.04 RPM
FIN_HG00375	2.86 RPM
FIN_HG00377	1.74 RPM
FIN_HG00378	2.10 RPM
GBR_HG00099	1.66 RPM
GBR_HG00111	1.91 RPM
GBR_HG00114	2.73 RPM
GBR_HG00119	3.04 RPM
GBR_HG00131	2.44 RPM
GBR_HG00133	2.29 RPM
GBR_HG00134	1.99 RPM
GBR_HG00137	2.25 RPM
GBR_HG00142	2.33 RPM
GBR_HG00143	1.56 RPM
TSI_NA20512	1.87 RPM
TSI_NA20513	1.72 RPM
TSI_NA20518	2.33 RPM
TSI_NA20532	0.92 RPM
TSI_NA20538	1.93 RPM
TSI_NA20756	2.47 RPM
TSI_NA20765	2.03 RPM
TSI_NA20771	2.13 RPM
TSI_NA20786	0.86 RPM
TSI_NA20798	2.46 RPM
YRI_NA18870	1.08 RPM
YRI_NA18907	2.18 RPM
YRI_NA18916	1.14 RPM
YRI_NA19093	0.31 RPM
YRI_NA19099	2.10 RPM
YRI_NA19114	3.01 RPM
YRI_NA19118	1.37 RPM
YRI_NA19213	3.37 RPM
YRI_NA19214	1.75 RPM
YRI_NA19223	1.69 RPM

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Indel association:

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