RetrogeneDB ID: retro_pabe_2648

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:76038273..76039586(+)
• 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_2648
TACTTCACCCAGTTCAGTGAGATTGAGGAGAGAATTGCCAAGTGGGGTTGAAAACTCGTGGATTATGACGGTGCCCAACA
TCACCTGGACGCAGTGCAGAATGCCAAGAAGAAAGATGAGGCCAAGACTGCCAAGGCAGAGGAAGAGTTCAACAAAGCCC
AGACTGTGTTTGAAGATCTGAACCAAAAACTACTTAGAGGAGCTGCCTATTCTTTATAATAGTCATGTTGGCTGCTATGT
GACCATCTTCCAAAACATTTCCAACTTGAGGGATGTCTTTTACAGGGAAATGAGCAAGCTGAACCACAATCTCTATGAGG
TGATGAGCAAACTGGAGAAGCAACATTCCAATAAAGTCTTTGTGGTGAAGGGACTATCAAGCAGCAGCAGGCGCTCTTTA
GTCATTTATCCCCCAGTTCGAACATCTATGGCCTCCAGTCCTCTTACCTCACCTACTAGTCCCTCTACACTTTCCTTGAA
GGGTGAGAGTGAATCTGCCGCAACAACTGAAGATCTGGCACCTGATGCAGCCTGGGGGAAGATAATTCTGAGATCAAAGA
GCCCTTAGAAGATGAGGAAATAGAGAAGGAAGGATCTGAAGCAAGCTTCTCTGAGGAAGAAGAGCCTCTACCAGCCTGCA
ATGGCCCTGCCCAGGCCCAGTCCTCTCCTACCATTGGGAGTGGCAAGTCCCAGGAGGAAGTTCTCCCTAGCTCCCCAGCT
CCATCACCAGGCAGAACCCTGAGCCCTTCAGGGCAGCCTTCATCATCTGCCACAGAAGTAGTCCTCCAAACCTGCACAGA
AAGTGAAGGATCTGAACAACCAAAGAAGAGAACCTATATCCAGAGGACCTCAGCACCCCCTAGTAGGCCTCCTCCACCCA
GAGCCACTCCAAGCCCAGGCCCTCCTCAGGGAACATACCCTCCAGCCCTCCAGCCTCTGGAGGGGGTTCACCCACTGGCC
CTAGGGTCTCCTTGGGGACTGAGACTCCAAGTCCTAGGACCTCCCTAGAGTTCTCTCCTAATCCAGAACTACCAGAGAAG
CCAGTAAGAGCTCCTGAGGTCAAAGAAAATGAAAACATCCACAATCAGAACCCCGAAGAACTTTGCACTTTTCCCACCTT
AATGACATCTCAGATTGCTTCAGAGCCTGGAGAGGCAAAGAAGATGGAAGACAAGAAAGGGGATAATAAGCTTGTCTTAG
CTGACTCCTCGGAGGGCCAAGACCAGCTCTAAGTCTCCACAGTACCAGACAAGAGCAACCTCACAGCACCTGAACCTCAA
GAAGAGGTATCTACAAGTGAAAATGCACAACTC

Alignment

ORF - retro_pabe_2648 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.94 %
• Parental protein coverage: 77.52 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YVAQFSEIKERIAKRGRKLVDYDSARHHLEAVQNAKKKDEAKTAKAEEEFNKAQTVFEDLNQELL-EELP
          Y..QFSEI.ERIAK.G.KLVDYD.A.HHL.AVQNAKKKDEAKTAKAEEEFNKAQTVFEDLNQ.LL.EELP
Retrocopy YFTQFSEIEERIAKWG*KLVDYDGAQHHLDAVQNAKKKDEAKTAKAEEEFNKAQTVFEDLNQKLL>EELP

Parental  ILYNSRIGCYVTIFQNISNLRDVFYREMSKLNHNLYEVMSKLEKQHSNKVFVVKGLSSSSRRSLVISPPV
          ILYNS..GCYVTIFQNISNLRDVFYREMSKLNHNLYEVMSKLEKQHSNKVFVVKGLSSSSRRSLVI.PPV
Retrocopy ILYNSHVGCYVTIFQNISNLRDVFYREMSKLNHNLYEVMSKLEKQHSNKVFVVKGLSSSSRRSLVIYPPV

Parental  RTATVSSPLTSPTSPSTLSLKSESESMSATEDLAPDAAQG-EDNSEIKELLEEEEIEKEGSEASSSEEDE
          RT...SSPLTSPTSPSTLSLK.ESES...TEDLAPDAA.G.EDNSEIKE.LE.EEIEKEGSEAS.SEE.E
Retrocopy RTSMASSPLTSPTSPSTLSLKGESESAATTEDLAPDAAWG<EDNSEIKEPLEDEEIEKEGSEASFSEEEE

Parental  PLPAFNGPAQAQPSPTTESAKSQEEVLPSSPAPSTGGALSPSGQPSSSAAEVVLRTRTASEGSEQPKKRA
          PLPA.NGPAQAQ.SPT..S.KSQEEVLPSSPAPS.G..LSPSGQPSSSA.EVVL.T.T.SEGSEQPKKR.
Retrocopy PLPACNGPAQAQSSPTIGSGKSQEEVLPSSPAPSPGRTLSPSGQPSSSATEVVLQTCTESEGSEQPKKRT

Parental  SIQRTSAPPSRPPPPRATASP-RPSSGNIPSSPTASGGGSPTSPRASLGTGTPSPRTSLEVSPNPEPPEK
          .IQRTSAPPSRPPPPRAT.SP.RPSSGNIPSSP.ASGGGSPT.PR.SLGT.TPSPRTSLE.SPNPE.PEK
Retrocopy YIQRTSAPPSRPPPPRATPSP<RPSSGNIPSSPPASGGGSPTGPRVSLGTETPSPRTSLEFSPNPELPEK

Parental  PVRTPEAKENENIHNQNPEELCASPTLMTSQIASEPGEAKKMEDKEEDNKLISADSSEGQDQLQVSTVPE
          PVR.PE.KENENIHNQNPEELC..PTLMTSQIASEPGEAKKMEDK..DNKL..ADSSEGQDQL.VSTVP.
Retrocopy PVRAPEVKENENIHNQNPEELCTFPTLMTSQIASEPGEAKKMEDKKGDNKLVLADSSEGQDQL*VSTVPD

Parental  NNNLTAPEPQEEVSTGENPQL
          ..NLTAPEPQEEVST.EN.QL
Retrocopy KSNLTAPEPQEEVSTSENAQL

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_2648 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2648 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2648 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3192
Pan troglodytes	retro_ptro_2251
Gorilla gorilla	retro_ggor_1336
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,