RetrogeneDB ID: retro_pabe_2448

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:85786810..85787938(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BIN2
• Ensembl ID: ENSPPYG00000004526
• Aliases: None
• Description: bridging integrator 2 [Source:HGNC Symbol;Acc:1053]

Sequence

>retro_pabe_2448
AAACTACTAGAGGAGTTGCCTATTCTTTATAATAGTCATATTGGCTGCTATGTGACCATCTTCCAAAACATTTCCAACTT
GAGGGATGTCTTCTACAGGGAAATGAGCAAGCTGAACCACAATCTCTCTGAGGTGATGAGCAAACTGGAGAAGCAACATT
CCAGTAAAGTCTTTGTGCTGAAGGAACTATCAAGCAGCAGCAGGCACTCTTTAGTCATTTCTCCCCCAGTTCGAACATCT
ACAGTCTCCAGTCCTCTTACCTCACCTACTAGTCCCTCTACACTTTCCTCGAAGAGTAAGAGTGAATCTATCTCAGCAAC
TGAAGATCTGGCACCTGATGCAGCCCAGGGGGAAGACAATTCTGAGATCAAGGAACTCTTAGAAGATGAGGAAATAGAGA
AGGAAGGATCTGAAGCAAGCTCCTCTGAGGAAGAAGAGCCTCTACCAACCTGCAACAGCCCCTCCCAGGCCCAGCCCTCT
CCTATCATTGAGAGTACCAAGTCCCAGGAGGAAGTTCTCCCCAGCTCCCCTGCTCTATCACCAGGCAGAGCCCTAAGCCC
TTCAGGACACCCTTCATCATTTGCCACAGAAGTAGTCCTCCGAACCCGCACCACAGGTGAAGGATCTGAACAACCAAAGA
AGAGAGCCTCTATCCAGAGGACCTCAGCACCCCCTAGTAGGCCTCCTCCACCCAGAGCCACTGCAAGCCCCAGGCCCTCC
TCAGGGAACATACCCTCCAGCCCTCCAGCCTCTGGAGGGGGTTCACCCACCAGCCCTAGGGCCTCCTTGGGGACTGGGAC
TCCAAGTCCTAGGACCTCCCTAGAGGTCTCTCCTAATCCAGAACCACCAGAGAAGCCAGTAAGAACTCCTGAGGCCAAAG
AAAATGAAAACATCCACAATCAGAACTTCGAAGAACTTTGTATTTCCCCCACCTTAATGACACCTCAGATTGCTTCAGAG
CCTGGAGAGGCAAAGAAGATGGAAGACAAGGAAAATGATAATAAGCTTGTCTCAGCTGACTCCTCGGAGGGCCAAGACCA
GCTTAAAGTCTCCACAGTACCAGACAAGAGCAACCTCACAGCACCTGAACCTCAAGAAGAGGTATCTACAAGTGAAAATG
CACAACTC

Alignment

ORF - retro_pabe_2448 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.36 %
• Parental protein coverage: 76.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELLEELPILYNSRIGCYVTIFQNISNLRDVFYREMSKLNHNLYEVMSKLEKQHSNKVFVVKGLSSSSRRS
          .LLEELPILYNS.IGCYVTIFQNISNLRDVFYREMSKLNHNL.EVMSKLEKQHS.KVFV.K.LSSSSR.S
Retrocopy KLLEELPILYNSHIGCYVTIFQNISNLRDVFYREMSKLNHNLSEVMSKLEKQHSSKVFVLKELSSSSRHS

Parental  LVISPPVRTATVSSPLTSPTSPSTLSLKSESESMSATEDLAPDAAQGEDNSEIKELLEEEEIEKEGSEAS
          LVISPPVRT.TVSSPLTSPTSPSTLS.KS.SES.SATEDLAPDAAQGEDNSEIKELLE.EEIEKEGSEAS
Retrocopy LVISPPVRTSTVSSPLTSPTSPSTLSSKSKSESISATEDLAPDAAQGEDNSEIKELLEDEEIEKEGSEAS

Parental  SSEEDEPLPAFNGPAQAQPSPTTESAKSQEEVLPSSPAPSTGGALSPSGQPSSSAAEVVLRTRTASEGSE
          SSEE.EPLP..N.P.QAQPSP..ES.KSQEEVLPSSPA.S.G.ALSPSG.PSS.A.EVVLRTRT..EGSE
Retrocopy SSEEEEPLPTCNSPSQAQPSPIIESTKSQEEVLPSSPALSPGRALSPSGHPSSFATEVVLRTRTTGEGSE

Parental  QPKKRASIQRTSAPPSRPPPPRATASPRPSSGNIPSSPTASGGGSPTSPRASLGTGTPSPRTSLEVSPNP
          QPKKRASIQRTSAPPSRPPPPRATASPRPSSGNIPSSP.ASGGGSPTSPRASLGTGTPSPRTSLEVSPNP
Retrocopy QPKKRASIQRTSAPPSRPPPPRATASPRPSSGNIPSSPPASGGGSPTSPRASLGTGTPSPRTSLEVSPNP

Parental  EPPEKPVRTPEAKENENIHNQNPEELCASPTLMTSQIASEPGEAKKMEDKEEDNKLISADSSEGQDQLQV
          EPPEKPVRTPEAKENENIHNQN.EELC.SPTLMT.QIASEPGEAKKMEDKE.DNKL.SADSSEGQDQL.V
Retrocopy EPPEKPVRTPEAKENENIHNQNFEELCISPTLMTPQIASEPGEAKKMEDKENDNKLVSADSSEGQDQLKV

Parental  STVPENNNLTAPEPQEEVSTGENPQL
          STVP...NLTAPEPQEEVST.EN.QL
Retrocopy STVPDKSNLTAPEPQEEVSTSENAQL

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	3.15 RPM
SRP007412_cerebellum	0.00 RPM	0.49 RPM
SRP007412_heart	0.00 RPM	1.60 RPM
SRP007412_kidney	0.00 RPM	3.28 RPM
SRP007412_liver	0.00 RPM	9.09 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2448 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2448 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2448 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2952
Pan troglodytes	retro_ptro_2049

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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,