RetrogeneDB ID: retro_ptro_419

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:37873357..37874665(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM161B
• Ensembl ID: ENSPTRG00000017064
• Aliases: None
• Description: transmembrane protein 161B [Source:HGNC Symbol;Acc:28483]

Sequence

>retro_ptro_419
GTGATAGGTGTACAGCTGTTGTTACCATGGTGATGGCCAGTGTCATGCAGAAGATTATACCTCGCTATTCTCTTGCTCAA
TGGCTACTCTGTAATGGCAGTTTGAGGTGGTATCAACATTCTACAGTAGAAGAATCAAGAATTCTTGCAGGGAATCAGCA
AAAAGAGAAAAGCAAAAAAGATAGGAAATATGATGGTCAAATTGAAAGTAAGCCATTAACCATTCCAAAGGATATTGACC
TTCGTCTAGAAACAAAGTCAGTTACAGAAGTGGATACATTAGCATTGCATTACTTTCCAGAATACCAGTGACTGGTGGAT
TTCACAGTGGCTGGTACAGTCGTGTATCTAGTAACTGAAGTCGACTACAAGTTTATGAAGCCTACACAGGAAATAAATAT
CAGCTTAGTCTGGTGCCTGCTTGTTTCGTCTTTTGCAATCGAAGTTCTATTTTCATTAATTACACACTATTTTAAAGTAG
AAGATGCTGGTGAAAGATCTGTTTGTGTCACCTTTGGATTTTTTTTCTTTGTCAAAGCAATGGCAGCGTTGATTGTAACA
GAAAATTATCTGGAATTTGGACTTGAAACAGGGTTTACAAATTTTTCAGGCAGTGCGATGCAGTTTCTTGAAAAGCAAGG
TTTAGAATCTGAGAGTCCTGTTTTAAAACTTACTTCCAAATTTTTTCCTGGCTATTTTCTGTTCACTCACTGGGGCTTTT
TTCACATTTCCTGGATTACGGCTGGCTCAAATGCATCTGGATACCCTGAATTTGGCAACAGAAAAAATTACACAAACATT
ATTTCGTATCAGCTTCTTGGCACATTTATTTATGGTTCTGCTCTGGGTAAAACCAGTCACCAAAGACTACATTATGAACC
CAACCTTGGGTGAAGAAAGCATCACTTTAATGACAGAAGCCACATTTGGTACTCTGCAAATCTGGTTAATAATCCTGCTG
TGTGCTTTGCGGTTGGCCATGATGCATAGTCACCTGCAAGCTTATTTAAATTTAGCCCAAAAATGTGTGGATCAGATGAA
GAAAGAAGCAGAGTGAATAAGTACAGTTGAGCTACAGAAAATGGTGGCTTGAGTGTTTTATTATCTTTTTGTCATTGCAC
TGCAGTATGTGGTGCCTCTGGTAACGCTGTTTCACACAACTCTGCTTTTGAAAACACTAGGTAATCATTCCTGGGGTATT
TATCCAGAATCTGTCTCTACCTTACCAGTGGATAATAGTCTACTCTACAATTCTGTTTACTCTGAATTACCATCAGCTGA
AGAGAAGATGAAGGTTACTGTTACACAA

Alignment

ORF - retro_ptro_419 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.07 %
• Parental protein coverage: 86.85 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VIGIQL-VVTMVMASVMQKIIPHYSLARWLLCNGSLRWYQHPTEEELRILAGKQQKGKTKKDRKYNGHIE
          VIG.QL.VVTMVMASVMQKIIP.YSLA.WLLCNGSLRWYQH.T.EE.RILAG.QQK.K.KKDRKY.G.IE
Retrocopy VIGVQL<VVTMVMASVMQKIIPRYSLAQWLLCNGSLRWYQHSTVEESRILAGNQQKEKSKKDRKYDGQIE

Parental  SKPLTIPKDIDLHLETKSVTEVDTLALHYFPEYQWLVDFTVAATVVYLVTEVYYNFMKPTQEMNISLVWC
          SKPLTIPKDIDL.LETKSVTEVDTLALHYFPEYQ.LVDFTVA.TVVYLVTEV.Y.FMKPTQE.NISLVWC
Retrocopy SKPLTIPKDIDLRLETKSVTEVDTLALHYFPEYQ*LVDFTVAGTVVYLVTEVDYKFMKPTQEINISLVWC

Parental  LLVLSFAIKVLFSLTTHYFKVEDGGERSVCVTFGFFFFVKAMAVLIVTENYLEFGLETGFTNFSDSAMQF
          LLV.SFAI.VLFSL.THYFKVED.GERSVCVTFG...FVKAMA.LIVTENYLEFGLETGFTNFS.SAMQF
Retrocopy LLVSSFAIEVLFSLITHYFKVEDAGERSVCVTFGXXXFVKAMAALIVTENYLEFGLETGFTNFSGSAMQF

Parental  LEKQGLESQSPVSKLTFK-FFLAIFCSFIGAFLTFPGLRLAQMHLDALNLATEKITQTLLHINFLAPLFM
          LEKQGLES.SPV.KLT.K.FFLAIFCS..GAF.TFPGLRLAQMHLD.LNLATEKITQTL..I.FLA.LFM
Retrocopy LEKQGLESESPVLKLTSK>FFLAIFCSLTGAFFTFPGLRLAQMHLDTLNLATEKITQTLFRISFLAHLFM

Parental  VLLWVKPITKDYIMNPPLGKESIPLMTEATFDTLRLWLIILLCALRLAMMRSHLQAYLNLAQKCVDQMKK
          VLLWVKP.TKDYIMNP.LG.ESI.LMTEATF.TL..WLIILLCALRLAMM.SHLQAYLNLAQKCVDQMKK
Retrocopy VLLWVKPVTKDYIMNPTLGEESITLMTEATFGTLQIWLIILLCALRLAMMHSHLQAYLNLAQKCVDQMKK

Parental  EAGRISTVELQKMVARVFYYLCVIALQYVAPLVMLLHTTLLLKTLGNHSWGIYPESISTLPVDNSLLSNS
          EA..ISTVELQKMVA.VFYYL.VIALQYV.PLV.L.HTTLLLKTLGNHSWGIYPES.STLPVDNSLL.NS
Retrocopy EAE*ISTVELQKMVA*VFYYLFVIALQYVVPLVTLFHTTLLLKTLGNHSWGIYPESVSTLPVDNSLLYNS

Parental  VYSELPSAEGKMKHNARQ
          VYSELPSAE.KMK....Q
Retrocopy VYSELPSAEEKMKVTVTQ

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	4.88 RPM
SRP007412_cerebellum	0.04 RPM	10.68 RPM
SRP007412_heart	0.00 RPM	2.54 RPM
SRP007412_kidney	0.00 RPM	5.36 RPM
SRP007412_liver	0.00 RPM	2.85 RPM
SRP007412_testis	0.00 RPM	11.91 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_ptro_419 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CB297271	37873456	37873913	95	433	23	410

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_419 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_419 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_560
Gorilla gorilla	retro_ggor_506

---

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,