RetrogeneDB ID: retro_hsap_3482

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:68643493..68644259(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000270509
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SUV39H2
• Ensembl ID: ENSG00000152455
• Aliases: SUV39H2, KMT1B
• Description: suppressor of variegation 3-9 homolog 2 (Drosophila) [Source:HGNC Symbol;Acc:17287]

Sequence

>retro_hsap_3482
AATCTATTGGTGGACTACTTGTGTGACTACAAGGCAGTGAAGCATATGGAATTTTATCTTGTAAAATGAAAATGATGGCT
AGATTCTACAAATACTTAGGAACCTTTGCAAAATCTCAAGGGCCCATGACTGTTTCAGCAATTCTTTAATAGTGAGCATA
ATTATTTATCTCAGGTAAATAAAGGCAAAGCAATAATTCCAAAAGACAATAACAAAACTTCAAAACCTGCCATTGCCAAG
TACATTGTAAAGAAGGCCAAACAAAGGATAGTTCTGCAGAGATGGCAAGATGAACTCAGCAGAAGACAGAATAATAAAGG
AGTGATATTTGTTGAAAATAGGGTTCACTTAGAAGGCCCACCTTCAGACTTCTGCTATATTGATGAATACAAACCAGCTC
CTGGAATCAGCTTAGTAAATGAAGCTACCTTTTGTTGTTCATGCACAGATTGCTTCTTTGAAAAATGTTGTCTTGGTGAA
GCTGGAATTCTTTTGGCTTATAGTAAAAACCAACAAATTAAAATCCCACCTGTTACTCCCATCTATAAATGCATCTCAAT
CTGTCAATGTGGACCTCACTGTACCAATAGGATTGTACAAAAAGGCACACAGTAATTCACTTTGCATCTTTCACAGTATC
AATGACCATGGCTGGGGTGTAAAAACCCATGTGAAGATTAAAAGAATAAGTTTTGTCATGGAATAAGTTGGAAAGGTAAT
CACAAGTGACGAAGCTGAAAGATGAGGGCAGTTATATGACAACAAA

Alignment

ORF - retro_hsap_3482 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.52 %
• Parental protein coverage: 62.2 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NYEVEYLCDYKVVKDMEYYLVKWKGWPDSTNTWEPLQNLKCPLLLQQFSNDKHNYLSQVKKGKAITPKDN
          N..V.YLCDYK.VK.ME.YLVK.K.W.DSTNT.EPLQNLK.P.L.QQF.N..HNYLSQV.KGKAI.PKDN
Retrocopy NLLVDYLCDYKAVKHMEFYLVK*K*WLDSTNT*EPLQNLKGP*LFQQFFNSEHNYLSQVNKGKAIIPKDN

Parental  NKTLKPAIAEYIVKKAKQRIALQRWQDELNRRKNHKGMIFVENTVDLEGPPSDFYYINEYKPAPGISLVN
          NKT.KPAIA.YIVKKAKQRI.LQRWQDEL.RR.N.KG.IFVEN.V.LEGPPSDF.YI.EYKPAPGISLVN
Retrocopy NKTSKPAIAKYIVKKAKQRIVLQRWQDELSRRQNNKGVIFVENRVHLEGPPSDFCYIDEYKPAPGISLVN

Parental  EATFGCSCTDCFFQKCCPAEAGVLLAYNKNQQIKIPPGTPIYECNSRCQCGPDCPNRIVQKGTQ-YSLCI
          EATF.CSCTDCFF.KCC..EAG.LLAY.KNQQIKIPP.TPIY.C.S.CQCGP.C.NRIVQKGTQ..SLCI
Retrocopy EATFCCSCTDCFFEKCCLGEAGILLAYSKNQQIKIPPVTPIYKCISICQCGPHCTNRIVQKGTQ>NSLCI

Parental  FRTSNGRGWGVKTLVKIKRMSFVMEYVGEVITSEEAERRGQFYDNK
          F...N..GWGVKT.VKIKR.SFVME.VG.VITS.EAER.GQ.YDNK
Retrocopy FHSINDHGWGVKTHVKIKRISFVME*VGKVITSDEAER*GQLYDNK

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	0.00 RPM	4.37 RPM
bodymap2_adrenal	0.00 RPM	7.45 RPM
bodymap2_brain	0.00 RPM	4.55 RPM
bodymap2_breast	0.00 RPM	6.05 RPM
bodymap2_colon	0.00 RPM	6.11 RPM
bodymap2_heart	0.00 RPM	3.10 RPM
bodymap2_kidney	0.00 RPM	7.20 RPM
bodymap2_liver	0.00 RPM	3.23 RPM
bodymap2_lung	0.00 RPM	3.55 RPM
bodymap2_lymph_node	0.00 RPM	5.57 RPM
bodymap2_ovary	0.00 RPM	13.51 RPM
bodymap2_prostate	0.00 RPM	7.00 RPM
bodymap2_skeletal_muscle	0.00 RPM	2.07 RPM
bodymap2_testis	0.00 RPM	52.88 RPM
bodymap2_thyroid	0.00 RPM	8.51 RPM
bodymap2_white_blood_cells	0.00 RPM	4.29 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3482 was not detected

EST

No EST(s) were mapped for retro_hsap_3482 retrocopy.

TSS

No TSS is located nearby retro_hsap_3482 retrocopy 5' end.

Lab

retro_hsap_3482 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3482 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2348
Pongo abelii	retro_pabe_2877

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004696	1 retrocopy	retro_cfam_574,
Cavia porcellus	ENSCPOG00000008492	1 retrocopy	retro_cpor_1546,
Homo sapiens	ENSG00000152455	1 retrocopy	retro_hsap_3482 ,
Gorilla gorilla	ENSGGOG00000028243	1 retrocopy	retro_ggor_2348,
Microcebus murinus	ENSMICG00000002803	1 retrocopy	retro_mmur_340,
Nomascus leucogenys	ENSNLEG00000012108	1 retrocopy	retro_nleu_2202,
Oryctolagus cuniculus	ENSOCUG00000015090	1 retrocopy	retro_ocun_1408,
Ochotona princeps	ENSOPRG00000009465	1 retrocopy	retro_opri_1005,
Pongo abelii	ENSPPYG00000002106	1 retrocopy	retro_pabe_2877,
Tupaia belangeri	ENSTBEG00000006477	4 retrocopies	retro_tbel_2646, retro_tbel_3572, retro_tbel_852, retro_tbel_993,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

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