RetrogeneDB ID: retro_nleu_2202

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397334.1:1549329..1550221(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUV39H2
• Ensembl ID: ENSNLEG00000012108
• Aliases: None
• Description: None

Sequence

>retro_nleu_2202
ATGGCAGCAGCTGGGGGTAAGGCACAAAGGAGCTTGGTATGGTGCCTTGGCTAGTTATACTTGATATTCTTCAGGAAATA
TGCAGAAAAGAAAAGCACACATGTAAATAGATTGGAATCACCAATCTATTGGTGGACTACTTGTGTGACTACAAGGCAGT
GAAGAATATGGAATGTTATCTTGTAAAATGAAAATGATGGCTAGATTCTAAAAATACTTAGGAAACTTTGCAAAATCTCA
AGGGCCCATGACTGTTTCAGCAATTCTTTAATAGTAAGCATAATTATTTATCTCAGGTAAATGAAGGCAAAGCAATAACT
CCAAAAGACAATAACAAAACTTCGAAACCTGCTATTGCCGAGCACATTGTAAAGAAGGCCAAACAAAGGATAGTTCTGCA
GAGATGGCAAGATTAACTCAGCAGAAGACAGAATAATAAAGGAGTGATATTTGTTGAAAATAGGGTTCACTTAGAAGGCT
CACCTTCAGACTTCTGCTATATTGATGAATACAAACCAGCTCCTGGAATCAGCTTAGTAAACGAAGCTATCTTTGGTTGT
TCATGCACAGATTGCTTCTTTGAAAAATGTTCTCCTGCTGAAGCTGGAGTTCTTTTGGCTTGTAGTAAAAAGCAACAAAT
TAAAATCCCACCTGTTACTCCCATCTACAAATGCATCTCAAGCTGTCAATGTGGACCTCACTGTACCAATAGGATTGTAC
AAAAAGGCACACAGTAATTCACTTTGCATCTTTTCACAGTATCAATGACCATGGCTTGGGTGTAAAAACCCATGTGAAGA
TTAAAAGAATGAGTTTTGTCATGGAATAAGTTGGAAAGGTAATCACAAGTGATGAAACTGAAAGATGAGGGCAGTTATAT
GACCACAAAGGA

Alignment

ORF - retro_nleu_2202 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.46 %
• 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..GAW..VP.LV.LD.LQE.CRKEK.TCK.IGIT...L..Y...Y....K.VK.ME.YLVK.
Retrocopy MAAAGGKA>KGAW>MVPWLVILDILQEICRKEKHTCK*IGITNL-LVDYLCDY----KAVKNMECYLVK*

Parental  KGWPDSTNTWEPLQNLKCPLLLQQFSNDKHNYLSQVKKGKAITPKDNNKTLKPAIAEYIVKKAKQRIALQ
          K.W.DS.NT.E.LQNLK.P.L.QQF.N.KHNYLSQV..GKAITPKDNNKT.KPAIAE.IVKKAKQRI.LQ
Retrocopy K*WLDSKNT*ETLQNLKGP*LFQQFFNSKHNYLSQVNEGKAITPKDNNKTSKPAIAEHIVKKAKQRIVLQ

Parental  RWQDELNRRKNHKGMIFVENTVDLEGPPSDFYYINEYKPAPGISLVNEATFGCSCTDCFFQKCCPAEAGV
          RWQD.L.RR.N.KG.IFVEN.V.LEG.PSDF.YI.EYKPAPGISLVNEA.FGCSCTDCFF.KC.PAEAGV
Retrocopy RWQD*LSRRQNNKGVIFVENRVHLEGSPSDFCYIDEYKPAPGISLVNEAIFGCSCTDCFFEKCSPAEAGV

Parental  LLAYNKNQQIKIPPGTPIYECNSRCQCGPDCPNRIVQKGTQ-YSLCI-FRTSNGRGWGVKTLVKIKRMRF
          LLA..K.QQIKIPP.TPIY.C.S.CQCGP.C.NRIVQKGTQ..SLCI.F...N..G.GVKT.VKIKRM.F
Retrocopy LLACSKKQQIKIPPVTPIYKCISSCQCGPHCTNRIVQKGTQ>NSLCI>FHSINDHGLGVKTHVKIKRMSF

Parental  VMEYVGEVITSEEAERRGQFYDNKG
          VME.VG.VITS.E.ER.GQ.YD.KG
Retrocopy VME*VGKVITSDETER*GQLYDHKG

Legend:

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

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_2202 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,