RetrogeneDB ID: retro_ptro_2651

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:124230413..124231163(-)
• Located in intron of: ENSPTRG00000019632

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF128
• Ensembl ID: ENSPTRG00000022151
• Aliases: None
• Description: ring finger protein 128, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:21153]

Sequence

>retro_ptro_2651
TCAAAGTACTCAGAGACCTGGCTTGCACTTATTGAACGGGGAGGTTGTACCTTCACACAGAAAATTAAAGTGGCAACTGA
GAAGGGAGCCAGTGGAGTGATCATCTATAACGTTCCAGGAACTGGCAACCAGGTGTTCCCCATGTTTCATCAGGCATTTG
AAGATGTCGTTGTGGTTATGATTGGTAACTTAAAAGGCACGGAAATTTTCCATTTAATTAAGAAGGGAGTTCTCATTACA
GCCGTGGTTGAGGTGGGGAGAAAGCACATCATCTGGATGAATCACTATTTGGTCTCTTTTGTGATTGTGACAACTGCTAC
CTTAGCATATTTCATCTTTTATCACATTCATAGACTTTGTTTAGCAAGGATTCAGAACCGGAGATGGCAGCGATTAACAA
CAGATCTTCAGAACGCACTTGGACAACTCCAACTTCGAGTAGTAAAAGAGGGGGATGAAGAAATAAATCCAAATGGGGAT
AGCTGCGTAATTTGCTTTGAACGCTATAAGCCTAATGACATAGTTCGTATTCTGACTTGTAAACATTTTTTCCACAAGAA
TTGCATTGACCCCTGGATTTTACCCCATGGGACATGCCCCATTTGCAAATGTGATATTCTTAAAGTTTTGGGGATTCAAG
TGGTTGTTGAAAATGGAACAGAACCTTTGCAAGTTCTAATGTCAAATGAACTGCCTGAAACCTTATCACCTAGTGAAGAG
GAGACAAATAATGAAGTTTCTCCTGCAGGA

Alignment

ORF - retro_ptro_2651 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.16 %
• Parental protein coverage: 80.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SNTKKPWIALIERGNCTFSEKIQMAYERGASGAVIFNFPGTRNEVIPMSHPGAVDIVAIMIGNLKGTKIL
          S.....W.ALIERG.CTF..KI..A.E.GASG..I.N.PGT.N.V.PM.H....D.V..MIGNLKGT.I.
Retrocopy SKYSETWLALIERGGCTFTQKIKVATEKGASGVIIYNVPGTGNQVFPMFHQAFEDVVVVMIGNLKGTEIF

Parental  QSIQRGIQVTMVIEVGKKHGPWVNHYSIFFVSVSFFIITAATVGYFIFYSARRLRNARAQSRKQRQLKAD
          ..I..G...T.V.EVG.KH..W.NHY...FV.V.....TA............RL..AR.Q.R....L..D
Retrocopy HLIKKGVLITAVVEVGRKHIIWMNHYLVSFVIVT----TATLAYFIFYH-IHRLCLARIQNRRWQRLTTD

Parental  AKKAIGRLQLRTLKQGDKEIGPDGDSCAVCIELYKPNDLVRILTCNHIFHKTCVDPWLLEHRTCPMCKCD
          ...A.G.LQLR..K.GD.EI.P.GDSC..C.E.YKPND.VRILTC.H.FHK.C.DPW.L.H.TCP.CKCD
Retrocopy LQNALGQLQLRVVKEGDEEINPNGDSCVICFERYKPNDIVRILTCKHFFHKNCIDPWILPHGTCPICKCD

Parental  ILKALGIEVDVEDGSVSLQVPVSNEISNSASSHEEDNRSETASSG
          ILK.LGI.V.VE.G...LQV..SNE.....S..EE....E....G
Retrocopy ILKVLGIQVVVENGTEPLQVLMSNELPETLSPSEEETNNEVSPAG

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	0.02 RPM	3.75 RPM
SRP007412_cerebellum	0.68 RPM	1.83 RPM
SRP007412_heart	0.06 RPM	0.00 RPM
SRP007412_kidney	0.13 RPM	17.23 RPM
SRP007412_liver	0.20 RPM	25.40 RPM
SRP007412_testis	63.23 RPM	0.63 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2651 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2651 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2651 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Oryctolagus cuniculus	retro_ocun_37
Bos taurus	retro_btau_1358
Sus scrofa	retro_sscr_597

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000022920	1 retrocopy	retro_btau_1358,
Loxodonta africana	ENSLAFG00000002816	1 retrocopy	retro_lafr_946,
Macropus eugenii	ENSMEUG00000001567	1 retrocopy	retro_meug_1139,
Mustela putorius furo	ENSMPUG00000003695	1 retrocopy	retro_mputfur_340,
Oryctolagus cuniculus	ENSOCUG00000012328	1 retrocopy	retro_ocun_37,
Pan troglodytes	ENSPTRG00000022151	1 retrocopy	retro_ptro_2651 ,
Sus scrofa	ENSSSCG00000012551	1 retrocopy	retro_sscr_597,
Ictidomys tridecemlineatus	ENSSTOG00000022922	2 retrocopies	retro_itri_1254, retro_itri_1255,
Tursiops truncatus	ENSTTRG00000007536	1 retrocopy	retro_ttru_6,