RetrogeneDB ID: retro_ggor_506

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 10:40763312..40764769(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM161B
• Ensembl ID: ENSGGOG00000005684
• Aliases: None
• Description: None

Sequence

>retro_ggor_506
GTGTTAGGTATACAGCTGTTGTTACCATGGTGATGGCCAGTGTCATGCAGAAGATTATACCTCGCTATTCTCTTGCTCAA
TGGCTACTCTGTAATGGCAGTTTGAGGTGGTATCAACATTCTACAGTAGAAGAATCAAGAATTCTTGCAGGGAATCAGCA
AAAAGAGAAAAGCAAAAAAGATAGGAAATATAATGGTCACATTGAAAGTAAGCCATTAACCATTCCAAAGGATATTGACC
TTCGTCTAGAAACAAAGTCAGTTACAGAAGTGGATACATTAGCATTGCATTACTTTCCAGAATACCAGTGACTGGTGGAT
TTCACAGTGGCTGCTACAGTCGTGTATCTAGTAACTGAAGTCGACTACAAGTTTATGAAGCCTACACAGGAAATAAATAT
CAGTTTAGTCTGGTGCCTGCTTGTTTCGTCTTTTGCAATCGAAGTTCTATTTTCATTAATTACACACTATTTTAAAGTAG
AAGATGCTGGTGAAAGATCTGTTTGTGTCACCTTTGGATTTTTTTTCTTTGTCAAAGCAATGGCAGTGTTGATTGTAACA
GAAAATTATCTGGAATTTGGACTTGAAACAGGGTTTACAAATTTTTCAGGCAGTGTGATGCAGTTTCTTGAAAAGCAAGG
TTTAGAATCTCAGAGTCCTGTTTCAAAACTTACTTCCAAATTTTTTCCTGGCTATTTTCTGTTCACTCACTGGGGCTTTT
TACACATTTCCTGGATTACAGCTGGCTCAAATGCATCTGGATACCCTGAATTTGTCAACAGAAAAAATTACACAAACATT
ACTTCATATCAGCTTCTTGGCACATTTATTTATGGTTCTGCTCTGGGTAAAACCAGTCACCAAAGACTACATTATGAACC
CAACCTTGGGTGAAGAAAGCATCACTTTAATGACAGAAGCCACATTTGGTACTCTGCAAATCTGGTTAATAATCCTGCTG
TGTGCTTTGCGGTTGGCCATGATGCATAGTCACCTGCAAGCTTATTTAAATTTAGCCCAAAAATGTGTGGATCAGATGAA
GAAAGAAGCAGGGTGAATAATAAGTACAGCTGAGCTACAGAAAATGGTGGCTTGAGTCTTTTATTATCTTTTTGTCATTG
CACTGCAGTATGTGGTGCCTCTGGTAACGCTGTTTCACACAACTCTGCTTTTGAAAACATTAGGTAATCATTCCTGGGGT
ATTTATCCAGAATCTGTCTCTACCTTACCAGTAGATAATAGTCTACTCTACAATTCTGTTTACTCTGAATTACCATCAGC
TGAAGAGAAGATGAAGGTTACTGTTACACAAATAACAGTGGCACTGAGCAGCTTAAAAACATTTTTACACTTCTTGTTTT
TTGAGGACTTCTGTCTTTTCTGACCTGGTAGATTGCTGCTTGCCTCTTTTCTACAAGCCTTTTTGGGCTTTTTTATCACC
AGTATCTGACTGTGGCA

Alignment

ORF - retro_ggor_506 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.16 %
• Parental protein coverage: 99.59 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VIGIQL-VVTMVMASVMQKIIPHYSLARWLLCNGSLRWYQHPTEEELRILAGKQQKGKTKKDRKYNGHIE
          V.GIQL.VVTMVMASVMQKIIP.YSLA.WLLCNGSLRWYQH.T.EE.RILAG.QQK.K.KKDRKYNGHIE
Retrocopy VLGIQL<VVTMVMASVMQKIIPRYSLAQWLLCNGSLRWYQHSTVEESRILAGNQQKEKSKKDRKYNGHIE

Parental  SKPLTIPKDIDLHLETKSVTEVDTLAALHYFPEYQWLVDFTVAATVVYLVTEVYYNFMKPTQEMNISLVW
          SKPLTIPKDIDL.LETKSVTEVDTLA.LHYFPEYQ.LVDFTVAATVVYLVTEV.Y.FMKPTQE.NISLVW
Retrocopy SKPLTIPKDIDLRLETKSVTEVDTLA-LHYFPEYQ*LVDFTVAATVVYLVTEVDYKFMKPTQEINISLVW

Parental  CLLVLSFAIKVLFSLTTHYFKVEDGGERSVCVTFGFFFFVKAMAVLIVTENYLEFGLETGFTNFSDSAMQ
          CLLV.SFAI.VLFSL.THYFKVED.GERSVCVTFG...FVKAMAVLIVTENYLEFGLETGFTNFS.S.MQ
Retrocopy CLLVSSFAIEVLFSLITHYFKVEDAGERSVCVTFGXXXFVKAMAVLIVTENYLEFGLETGFTNFSGSVMQ

Parental  FLEKQGLESQSPVSKLTFK-FFLAIFCSLIGAFLTFPGLRLAQMHLDALNLATEKITQTLLHINFLAPLF
          FLEKQGLESQSPVSKLT.K.FFLAIFCSL.GAF.TFPGL.LAQMHLD.LNL.TEKITQTLLHI.FLA.LF
Retrocopy FLEKQGLESQSPVSKLTSK>FFLAIFCSLTGAFYTFPGLQLAQMHLDTLNLSTEKITQTLLHISFLAHLF

Parental  MVLLWVKPITKDYIMNPPLGKESIPLMTEATFDTLRLWLIILLCALRLAMMRSHLQAYLNLAQKCVDQMK
          MVLLWVKP.TKDYIMNP.LG.ESI.LMTEATF.TL..WLIILLCALRLAMM.SHLQAYLNLAQKCVDQMK
Retrocopy MVLLWVKPVTKDYIMNPTLGEESITLMTEATFGTLQIWLIILLCALRLAMMHSHLQAYLNLAQKCVDQMK

Parental  KEAG-RISTVELQKMVARVFYYLCVIALQYVAPLVMLLHTTLLLKTLGNHSWGIYPESISTLPVDNSLLS
          KEAG..IST.ELQKMVA.VFYYL.VIALQYV.PLV.L.HTTLLLKTLGNHSWGIYPES.STLPVDNSLL.
Retrocopy KEAG*IISTAELQKMVA*VFYYLFVIALQYVVPLVTLFHTTLLLKTLGNHSWGIYPESVSTLPVDNSLLY

Parental  NSVYSELPSAEGKMKVTVTQITVALSS-LKNIFTPLLFRGLLSFLTWWIAACLFSTSLFGLFYHQYLTVA
          NSVYSELPSAE.KMKVTVTQITVALSS.LKNIFT.L.F.GLLSFLTW.IAACLFSTSLFGLFYHQYLTVA
Retrocopy NSVYSELPSAEEKMKVTVTQITVALSS<LKNIFTLLVF*GLLSFLTW*IAACLFSTSLFGLFYHQYLTVA

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	5.99 RPM
SRP007412_cerebellum	0.00 RPM	10.36 RPM
SRP007412_heart	0.00 RPM	0.97 RPM
SRP007412_kidney	0.00 RPM	6.87 RPM
SRP007412_liver	0.00 RPM	5.96 RPM
SRP007412_testis	0.31 RPM	15.85 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_506 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_506 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_560
Pan troglodytes	retro_ptro_419

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010857	1 retrocopy	retro_cjac_2671,
Homo sapiens	ENSG00000164180	1 retrocopy	retro_hsap_560,
Gorilla gorilla	ENSGGOG00000005684	1 retrocopy	retro_ggor_506 ,
Macaca mulatta	ENSMMUG00000009319	1 retrocopy	retro_mmul_719,
Nomascus leucogenys	ENSNLEG00000013645	1 retrocopy	retro_nleu_2224,
Pan troglodytes	ENSPTRG00000017064	1 retrocopy	retro_ptro_419,
Rattus norvegicus	ENSRNOG00000032414	1 retrocopy	retro_rnor_1023,
Ictidomys tridecemlineatus	ENSSTOG00000011141	1 retrocopy	retro_itri_1420,
Ictidomys tridecemlineatus	ENSSTOG00000027831	2 retrocopies	retro_itri_1419, retro_itri_1787,