RetrogeneDB ID: retro_ggor_2348

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:67609672..67610438(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUV39H2
• Ensembl ID: ENSGGOG00000028243
• Aliases: None
• Description: None

Sequence

>retro_ggor_2348
AATCTATTGGTGGACTACTTGTGTGACTACAAGGCAGTGAAAAATATGGAATTTTATCTTGTAAAATGAAAATGATGGCT
AGATTCTACAAATACTTAGGAACCTTTGCAAAATCTCAAGGGCCCATGACTGTTTCCGCAATTCTTTAATAGTGAGCATA
ATTATTTATCTCAGGTAAATAAAGGCAAAGCAATAACTCCAAAAGACAATAACAAAACTTCAAAACCTGCCATTGCCAAG
TACATTGTAAAGAAGGCCAAGCAAAGGATAGTTCTGCAGAGATGGCAAGATGAACTCAGCAGAAGACAGAATAATAAAGG
AGTGATATTTGTTGAAAATAGGGTTCACTTAGAAGGCCCACCTTCAGGCTTCTGCTATATTGATGAATACAAACCAGCTC
CTGGAATCAGCTTAGTAAATGAAGCTACCTTTGGTTGTTCATGCACAGATTGCTTCTTTGAAAAATGTTGTCTTGCTGAA
GCTGGAATTCTTTTGGCTTATAGTAAAAACCAACAAATTAAAATCCCACCTGTTACTCCCATCTATAAATGCATCTCAAG
CTGTCAATGTGGACCTCACTGTACCAATAGGATTGTACAAAAAGGCACACAGTAATTCACTTTGCATCTTTCACAGTATC
AATGACCATGGCTGGGGTGTAAAAACCCATGTGAAGATTAAAAGAATGAGTTTTGTCATGGAATAAGTTGGAAAGGTAAT
CACAAGTGATGAAGCTGAAAGATGAGGGCAGTTATATGACAACAAA

Alignment

ORF - retro_ggor_2348 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.3 %
• Parental protein coverage: 63.28 %
• 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..QF.N..HNYLSQV.KGKAITPKDN
Retrocopy NLLVDYLCDYKAVKNMEFYLVK*K*WLDSTNT*EPLQNLKGP*LFPQFFNSEHNYLSQVNKGKAITPKDN

Parental  NKTLKPAIAEYIVKKAKQRIALQRWQDELNRRKNHKGMIFVENTVDLEGPPSDFYYINEYKPAPGISLVN
          NKT.KPAIA.YIVKKAKQRI.LQRWQDEL.RR.N.KG.IFVEN.V.LEGPPS.F.YI.EYKPAPGISLVN
Retrocopy NKTSKPAIAKYIVKKAKQRIVLQRWQDELSRRQNNKGVIFVENRVHLEGPPSGFCYIDEYKPAPGISLVN

Parental  EATFGCSCTDCFFQKCCPAEAGVLLAYNKNQQIKIPPGTPIYECNSRCQCGPDCPNRIVQKGTQ-YSLCI
          EATFGCSCTDCFF.KCC.AEAG.LLAY.KNQQIKIPP.TPIY.C.S.CQCGP.C.NRIVQKGTQ..SLCI
Retrocopy EATFGCSCTDCFFEKCCLAEAGILLAYSKNQQIKIPPVTPIYKCISSCQCGPHCTNRIVQKGTQ>NSLCI

Parental  FRTSNGRGWGVKTLVKIKRMSFVMEYVGEVITSEEAERRGQFYDNK
          F...N..GWGVKT.VKIKRMSFVME.VG.VITS.EAER.GQ.YDNK
Retrocopy FHSINDHGWGVKTHVKIKRMSFVME*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
SRP007412_brain_prefrontal_cortex	0.00 RPM	3.93 RPM
SRP007412_cerebellum	0.00 RPM	5.56 RPM
SRP007412_heart	0.00 RPM	0.53 RPM
SRP007412_kidney	0.00 RPM	4.82 RPM
SRP007412_liver	0.00 RPM	3.14 RPM
SRP007412_testis	0.00 RPM	48.07 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2348 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2348 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3482
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,