RetrogeneDB ID: retro_pabe_2877

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:68250346..68251233(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: SUV39H2
• Ensembl ID: ENSPPYG00000002106
• Aliases: None
• Description: suppressor of variegation 3-9 homolog 2 (Drosophila) [Source:HGNC Symbol;Acc:17287]

Sequence

>retro_pabe_2877
ATGGCAGCAGCTGGGGGTAAGGCACAAACGAGCTTGGTATGGTGCCTTGGCTAGTTACACTTGATATTCTTCAGGAAATA
TGCAGAAAAGAAAAGCACACATGTAAATAGATTGGAATCACCAATCTATTGGTGGACTACTTGTGTGACTACAAGGCAGT
GAAGAATGTGGAATTTTATCTTGTAAAATGAAAATGATGGCTAGATTCTACAAATACTTAGGAGCCTTTGCAAAATCTCA
AGGGACTATGACTGTTTCAGCAATTCTTTAATAGTGAGCATAATTATTTATTTCAGGTAAATAAAGGCAAAGCAATAACT
CCAAAAGACAATAACACAGCTTCGAAATCTGCCATTGCCGAGTACATTGTAAAGAAGGCCAAACAAAGGATAGTTCTGCA
GAGATGGCAAGATGAACTCAGCAGAAGACAGAATAATAAAGGAGTGATATTTGTTGAAAATAGGGTTCACTTAGAAGGCC
CACCTTCAGACTTCTGCTATATTGATGAATACAAACCAGCTCCTGGAATCAGCTTAGTAAATGAAGCTACCTTTGGTTGT
TCATGCACAGATTGCTTCTTTGAAAAATGTCCTGCTGAAGCTGGAATTCTTTTGGCTTATAGTAAAAACCAACAAATTAA
AATCCCACCTGCTACTCCCATCTATAAATGCATCTCAAGCTGTCAATGTGGACCTCACTTTACCAATAGGATTGTACAAA
AAGGCACACAGTAATTCACTTTGCATCTTTCACAGTATCAACGACCATGGCTGGGTGTAAAAACCCATGTGAAGATTAAA
AGAATGAGTTTTGTCATGGAATAAGTTGGAAAGGTAATCACAAGTGACGAAGCTGAAAGATGAGGGCAGTTATAGGACAA
CAAAGGA

Alignment

ORF - retro_pabe_2877 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.11 %
• Parental protein coverage: 73.41 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAAVGAEA-RGAW-CVPCLVSLDTLQELCRKEKLTCKSIGITKRNLNNYEVEYLCDYKVVKDMEYYLVKW
          MAA.G..A...AW..VP.LV.LD.LQE.CRKEK.TCK.IGIT...L..Y...Y....K.VK..E.YLVK.
Retrocopy MAAAGGKA>KRAW>MVPWLVTLDILQEICRKEKHTCK*IGITNL-LVDYLCDY----KAVKNVEFYLVK*

Parental  KGWPDSTNTWEPLQNLKCPLLLQQFSNDKHNYLSQVKKGKAITPKDNNKTLKPAIAEYIVKKAKQRIALQ
          K.W.DSTNT.EPLQNLK...L.QQF.N..HNYL.QV.KGKAITPKDNN...K.AIAEYIVKKAKQRI.LQ
Retrocopy K*WLDSTNT*EPLQNLKGL*LFQQFFNSEHNYLFQVNKGKAITPKDNNTASKSAIAEYIVKKAKQRIVLQ

Parental  RWQDELNRRKNHKGMIFVENSVDLEGPPSDFYYINEYKPAPGISLVNEATFGCSCTDCFFQKCCPAEAGV
          RWQDEL.RR.N.KG.IFVEN.V.LEGPPSDF.YI.EYKPAPGISLVNEATFGCSCTDCFF.K.CPAEAG.
Retrocopy RWQDELSRRQNNKGVIFVENRVHLEGPPSDFCYIDEYKPAPGISLVNEATFGCSCTDCFFEK-CPAEAGI

Parental  LLAYNKNQQIKIPPGTPIYECNSRCQCGPDCPNRIVQKGTQ-YSLCIFRTSNGRGW-GVKTLVKIKRMSF
          LLAY.KNQQIKIPP.TPIY.C.S.CQCGP...NRIVQKGTQ..SLCIF...N..GW.GVKT.VKIKRMSF
Retrocopy LLAYSKNQQIKIPPATPIYKCISSCQCGPHFTNRIVQKGTQ>NSLCIFHSINDHGW<GVKTHVKIKRMSF

Parental  VMEYVGEVITSEEAERRGQFYDNKG
          VME.VG.VITS.EAER.GQ..DNKG
Retrocopy VME*VGKVITSDEAER*GQL*DNKG

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	4.64 RPM
SRP007412_cerebellum	0.00 RPM	11.19 RPM
SRP007412_heart	0.00 RPM	2.23 RPM
SRP007412_kidney	0.40 RPM	4.41 RPM
SRP007412_liver	0.34 RPM	3.46 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2877 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2877 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2877 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3482
Gorilla gorilla	retro_ggor_2348

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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,