RetrogeneDB ID: retro_pabe_607

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:70850764..70851775(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000002406
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ANXA2
• Ensembl ID: ENSPPYG00000006526
• Aliases: None
• Description: Annexin A2 [Source:UniProtKB/Swiss-Prot;Acc:Q5R5A0]

Sequence

>retro_pabe_607
ATGTATACTATTTACAAAATCCTGTGCAAGCTCAGCTTGGAGGGTGATCACTCTACACCCTCAAGTGCATATGGGTCAGT
CAAAGCCTACACCAACTTTGATGCTGAGGGGGATGCTTTGAACATTGAAAGGACCATCAGGACAAAAGGTATGGGTGAGT
TCACCATTGTCAACATTTTGACCAACAGCAGGAATGCTCGGAGACAGGATATTGCCTTTGCCTAGCAGAGAAGGACCAAA
AAGGAACTTGCATCAGCACTGAAGTCAGCCTTATTGGCCACCTGGAGACAGTCATTTTGGGCCTATTGAAGACACCTGCT
CAGTATGATGCTTCTGAGCTAAAAGCTTCCATGAAGGGGCTGGGAACGGAGGAGGACTCCCTCATTGAGATCATCTGCTC
AACAACCAACCAGGAGCTCCAGGAAATTAACAGAGTCTACAAAGAAATGTACAAAGTTGATCTGGAGAAGGACATTATTT
CGGACACATATGGTGACTTCCGCAAGCTGATGTTTGCCCTGGCAAAGGTTAGAAGACCAGAGGATGGCTCTGTCATTGAT
TATGAACTGATTGACCAAGATGCCCAGGATTTCTATGACGCTGGAGTGAAGAGGAAAAGAACTGACGTTCCCAAGTGGAT
AAGCATCATGACCGAGCAGAGCATGTCTCACCTCCAGAAAGTATTTGATAGGTACAAGAGCTACAGCCCATCAAGAGAGA
GCATCAAGAAAAAGGTTAAAGGAGACCTGGAAAATGCTTTCCTGAACCTGGTCCAGTGCATTCAGAACAAGCCCCTGTAT
TTTGCTAATTGGCTGTACTACTCCATGAAGGGCAAGGGGACTCGAGATAAGGTCCTGATCAGAATCATCATCTCCTGCAG
TGAAGTGGACATGTTGAAAATTAGGTCTGAGTTCAAGAGAAAGTATGGCATGTCCCCGTACTATTACATCCAGCAAGACA
CTAAGAGTGACTACCCAGAAAGCACTGCTGTACCTGTGTGGTGGAGATGAC

Alignment

ORF - retro_pabe_607 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.22 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSTVHEILCKLSLEGDHSTPPSAYGSVKAYTNFDAERDALNIETAIKTKGVDEVTIVNILTNRSNAQRQD
          M.T...ILCKLSLEGDHSTP.SAYGSVKAYTNFDAE.DALNIE..I.TKG..E.TIVNILTN..NA.RQD
Retrocopy MYTIYKILCKLSLEGDHSTPSSAYGSVKAYTNFDAEGDALNIERTIRTKGMGEFTIVNILTNSRNARRQD

Parental  IAFAYQRRTKKELASALKSALS-GHLETVILGLLKTPAQYDASELKASMKGLGTDEDSLIEIICSRTNQE
          IAFA.QRRTKKELASALKSAL..GHLETVILGLLKTPAQYDASELKASMKGLGT.EDSLIEIICS.TNQE
Retrocopy IAFA*QRRTKKELASALKSALL<GHLETVILGLLKTPAQYDASELKASMKGLGTEEDSLIEIICSTTNQE

Parental  LQEINRVYKEMYKTDLEKDIISDTSGDFRKLMVALAKGRRAEDGSVIDYELIDQDARDLYDAGVKRKGTD
          LQEINRVYKEMYK.DLEKDIISDT.GDFRKLM.ALAK.RR.EDGSVIDYELIDQDA.D.YDAGVKRK.TD
Retrocopy LQEINRVYKEMYKVDLEKDIISDTYGDFRKLMFALAKVRRPEDGSVIDYELIDQDAQDFYDAGVKRKRTD

Parental  VPKWISIMTERSVPHLQKVFDRYKSYSPYDMLESIRKEVKGDLENAFLNLVQCIQNKPLYFADRLYDSMK
          VPKWISIMTE.S..HLQKVFDRYKSYSP....ESI.K.VKGDLENAFLNLVQCIQNKPLYFA..LY.SMK
Retrocopy VPKWISIMTEQSMSHLQKVFDRYKSYSP--SRESIKKKVKGDLENAFLNLVQCIQNKPLYFANWLYYSMK

Parental  GKGTRDKVLIRIMVSRSEVDMLKIRSEFKRKYGKSLYYYIQQDTKGDY-QKALLYLCGGDD
          GKGTRDKVLIRI..S.SEVDMLKIRSEFKRKYG.S.YYYIQQDTK.DY.QKALLYLCGGDD
Retrocopy GKGTRDKVLIRIIISCSEVDMLKIRSEFKRKYGMSPYYYIQQDTKSDY>QKALLYLCGGDD

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	22.61 RPM
SRP007412_cerebellum	0.00 RPM	8.76 RPM
SRP007412_heart	0.03 RPM	75.11 RPM
SRP007412_kidney	0.00 RPM	89.83 RPM
SRP007412_liver	0.03 RPM	74.85 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_607 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_607 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_607 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_580

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016686	3 retrocopies	retro_cfam_1631, retro_cfam_367, retro_cfam_707,
Homo sapiens	ENSG00000182718	3 retrocopies	retro_hsap_3114, retro_hsap_4150, retro_hsap_580,
Gorilla gorilla	ENSGGOG00000009738	3 retrocopies	retro_ggor_2137, retro_ggor_2788, retro_ggor_515,
Macropus eugenii	ENSMEUG00000008980	3 retrocopies	retro_meug_1000, retro_meug_312, retro_meug_389,
Myotis lucifugus	ENSMLUG00000002464	3 retrocopies	retro_mluc_1569, retro_mluc_2223, retro_mluc_2431,
Monodelphis domestica	ENSMODG00000011604	1 retrocopy	retro_mdom_1471,
Mustela putorius furo	ENSMPUG00000000762	2 retrocopies	retro_mputfur_73, retro_mputfur_79,
Nomascus leucogenys	ENSNLEG00000011678	2 retrocopies	retro_nleu_769, retro_nleu_802,
Pongo abelii	ENSPPYG00000006526	2 retrocopies	retro_pabe_2572, retro_pabe_607 ,
Pan troglodytes	ENSPTRG00000007132	2 retrocopies	retro_ptro_2106, retro_ptro_81,