RetrogeneDB ID: retro_ptro_2251

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:39634493..39635803(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BIN2
• Ensembl ID: ENSPTRG00000004954
• Aliases: None
• Description: bridging integrator 2 [Source:HGNC Symbol;Acc:1053]

Sequence

>retro_ptro_2251
TACTTCACCCAGTTCAGTGAGATTGAGGAGAGAATTGCCAAGTGGGGTTGAAAACTCATGGATTATGATGGTGCCCAACA
TCATCTGGATGCAGTACAGAATGCCAAGAAGAAAGATGAGGCCAAGACTGCCAAGGCAGAGGAAGAGTTCAACAAAGCCC
AGACTATGTTTGAAGATCTGAACCAAAAACTACTAGAGGAGCTGCCTATTCTTTATAATAGTCATGTTGGCTGCTATGTG
ACCATCTTCCAAAACATTTCCAATTTGAGGGATGTCTTCTACAGGGAAATGAGCAACCTGAACTGCAATCTCTAGGAGGT
GATGAGCAAACTGCAGAAGCAACATTCCAATAAAGTCTTTGTGGTGAAGGGACTATCAAGCAGCAGCAGGCTGTCTTTAG
TCATTTATCCCCCAGTTCAAACATCTGTAGCCTCCAGTCCTCTTACCTCACCTACTAGTCCCTCTACACTTTCCTTGAAG
AGTGAGAGTGAATCTGTCGCAACAACTGAAGATCTGGCACCTGATGCAGCCCAGGGGAAGATAATTCTGAGATCAAGGAG
CACTTAGAAGATGAGGAAATAGAGAAGGAAGGATCTGAAGCAAGCTCCTCTGAGGAAGAAGAGCCTCTACCAGCCTGCAA
TGGCCCTGCCCAGACCCAGCCCTCTCCTACCATTGGGAGTGGCAAGTCCCAGGAGGAAGTTCTCCCTAGCTCCCCAGCTC
CATCACCACGCAGAACCCTGAGCCCTTCAGGGCAGCCTTCATCATCTGCCACAGAAGTAGTCCTCCGAACCTGCACAGAA
AGTGAAGGATCTGAACAACCAAAGAAGAGAACCTATATCCAGAGGACCTCAGCACCCCCTAGTAGGCCTCCTCCACCCAG
AGCCACTCCAAGCCCCAGGCTCTCCTCAGGAAACATACCCTCCAGTCCTCCAGCCTCTGAAGAGGGTTCACCCACTGGCC
TAAGGGTCTCCTTGGGGACTGAGACTCCAAGTCCTAGGACCTCCCTAGAGTTCTCCCCTAATCCAGAACTACCAGAGAAG
CCAGTAAGAACTGAGGTCAAAGAAAATGAAAACATCCACAATCAGAACCCCGAAGAACTTTGCACTTTTCCCACCTTAAT
GACATCTCAGACTGCTTCAGAGCCTGGAGAGGCAAAGAAGATGGAAGACAAGAAAGAGGATAATAAGCTTGTCTTAGCTG
ACTCCTCGGAGGGCCAAGACCAGCTTTAAGTCTCCACAGTACCAGACAAGAGCAACCTCACAGCACCTGAACCTCAAGAA
TAGGTATCTACAAGTGAAAATGCACAACTC

Alignment

ORF - retro_ptro_2251 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.19 %
• Parental protein coverage: 81.26 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YVAQFSEIKERIAKRGRKLVDYDSARHHLEAVQNAKKKDEAKTAKAEEEFNKAQTVFEDLNQELLEELPI
          Y..QFSEI.ERIAK.G.KL.DYD.A.HHL.AVQNAKKKDEAKTAKAEEEFNKAQT.FEDLNQ.LLEELPI
Retrocopy YFTQFSEIEERIAKWG*KLMDYDGAQHHLDAVQNAKKKDEAKTAKAEEEFNKAQTMFEDLNQKLLEELPI

Parental  LYNSRIGCYVTIFQNISNLRDVFYREMSKLNHNLYEVMSKLEKQHSNKVFVVKGLSSSSRRSLVISPPVQ
          LYNS..GCYVTIFQNISNLRDVFYREMS.LN.NL.EVMSKL.KQHSNKVFVVKGLSSSSR.SLVI.PPVQ
Retrocopy LYNSHVGCYVTIFQNISNLRDVFYREMSNLNCNL*EVMSKLQKQHSNKVFVVKGLSSSSRLSLVIYPPVQ

Parental  TATVSSPLTSPTSPSTLSLKSESESVSATEDLAPDAAQ-GEDNSEIKELLEEEEIEKEGSEASSSEEDEP
          T...SSPLTSPTSPSTLSLKSESESV..TEDLAPDAAQ.GEDNSEIKE.LE.EEIEKEGSEASSSEE.EP
Retrocopy TSVASSPLTSPTSPSTLSLKSESESVATTEDLAPDAAQ<GEDNSEIKEHLEDEEIEKEGSEASSSEEEEP

Parental  LPACNGPAQAQPSPTTESAKSQEEVLPSSPAPSPGGALSPSGQPSSSAAEVVLRTRTASEGSEQPKKRAS
          LPACNGPAQ.QPSPT..S.KSQEEVLPSSPAPSP...LSPSGQPSSSA.EVVLRT.T.SEGSEQPKKR..
Retrocopy LPACNGPAQTQPSPTIGSGKSQEEVLPSSPAPSPRRTLSPSGQPSSSATEVVLRTCTESEGSEQPKKRTY

Parental  IQRTSAPPSRPPPPRATASPRPSSGNIPSSPTASGGGSPTSPRASLGTGTPSPRTSLEVSPNPEPPEKPV
          IQRTSAPPSRPPPPRAT.SPR.SSGNIPSSP.AS..GSPT..R.SLGT.TPSPRTSLE.SPNPE.PEKPV
Retrocopy IQRTSAPPSRPPPPRATPSPRLSSGNIPSSPPASEEGSPTGLRVSLGTETPSPRTSLEFSPNPELPEKPV

Parental  RTPEAKENENIHNQNPEELCTSPTLMTSQVASEPGEAKKMEDKEEDNKLISADSSEGQDQLQVFTVPENN
          RT.E.KENENIHNQNPEELCT.PTLMTSQ.ASEPGEAKKMEDK.EDNKL..ADSSEGQDQL.V.TVP...
Retrocopy RT-EVKENENIHNQNPEELCTFPTLMTSQTASEPGEAKKMEDKKEDNKLVLADSSEGQDQL*VSTVPDKS

Parental  NLTAPEPQEEVSTSENPQL
          NLTAPEPQE.VSTSEN.QL
Retrocopy NLTAPEPQE*VSTSENAQL

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	4.52 RPM
SRP007412_cerebellum	0.00 RPM	4.30 RPM
SRP007412_heart	0.00 RPM	2.71 RPM
SRP007412_kidney	0.00 RPM	9.07 RPM
SRP007412_liver	0.00 RPM	7.89 RPM
SRP007412_testis	0.00 RPM	61.65 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2251 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2251 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2251 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3192
Gorilla gorilla	retro_ggor_1336
Pongo abelii	retro_pabe_2648
Macaca mulatta	retro_mmul_2013

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000110934	2 retrocopies	retro_hsap_2952, retro_hsap_3192,
Gorilla gorilla	ENSGGOG00000009423	1 retrocopy	retro_ggor_1336,
Loxodonta africana	ENSLAFG00000002387	1 retrocopy	retro_lafr_1163,
Nomascus leucogenys	ENSNLEG00000017774	1 retrocopy	retro_nleu_1636,
Pongo abelii	ENSPPYG00000004526	2 retrocopies	retro_pabe_2448, retro_pabe_2648,
Pan troglodytes	ENSPTRG00000004954	2 retrocopies	retro_ptro_2049, retro_ptro_2251 ,