RetrogeneDB ID: retro_pabe_448

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:139455938..139456567(-)
• Located in intron of: ENSPPYG00000001170

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPNS1
• Ensembl ID: ENSPPYG00000009898
• Aliases: None
• Description: calpain, small subunit 1 [Source:HGNC Symbol;Acc:1481]

Sequence

>retro_pabe_448
GCCTTGTGCTTCCTAGGTGGAATCATTAGCTCCATCATGGAGGTGGCTACACAGCACAACCTAGAGCCCCTGCCTCAACA
CACACATTGCTCCAACACTGAGGCCAACAAGAGTGAGGAGGTCCATCATTTCTGGAGGCTCTTGCCCAGTTGGCTGGAGA
TGACATTGAGGTCAGTGGCACAGAACTCATGAATGTTGTCAACAAGGTTGTGATCAGTAGGACTGAACTGAAGACTAATG
GTTTTGGCATTGATACATGTCAAAGCATGGTGGCCATGATGGATAGTGACACCACAGGCAAGCTGGACTTTGAGGAATTC
AAGTACCTGTGGAACAACATCAAAAAGTGACAGACAATATACAAGCAGTTTGATGTTGACCGATCCAGAACCATTTGCAG
CAGTGAACTTGCAGGGGCCTTTGAGGCACCAGGGTTCCACCTGAATGAACAACTCTACAACATAATATTCTGACACTACT
TGCATGAAGGAGAGAACATGGATTTTGGCAACTTTATCAGCTGCTTGGTCAGGCCAGATGCTTAGTTTCATGCCTTGAAA
TCTCTTTACAAAGATGACACTAGACCATTCTAAGTGAATATCCAAGAGTGGCTGCAGCTGACAATGTAT

Alignment

ORF - retro_pabe_448 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.09 %
• Parental protein coverage: 78.36 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AMRILGGVISAISEAAAQYNPEPPPPRTHYSNIEANESEEVRQFRRLF-AQLAGDDMEVSATELMNILNK
          A...LGG.IS.I.E.A.Q.N.EP.P..TH.SN.EAN.SEEV..F.RL..AQLAGDD.EVS.TELMN..NK
Retrocopy ALCFLGGIISSIMEVATQHNLEPLPQHTHCSNTEANKSEEVHHFWRLL<AQLAGDDIEVSGTELMNVVNK

Parental  VVTRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKYLWNNIKRWQAIYKQFDTDRSGTICSSELPG
          VV.....LKT.GFGIDTC.SMVA.MDSDTTGKL.FEEFKYLWNNIK..Q.IYKQFD.DRS.TICSSEL.G
Retrocopy VVISRTELKTNGFGIDTCQSMVAMMDSDTTGKLDFEEFKYLWNNIKK*QTIYKQFDVDRSRTICSSELAG

Parental  AFEAAGFHLNEHLYNMIIRRYSDESGNMDFDNFISCLVRLDAMFRAFKSLDKDGTGQIQVNIQEWLQLTM
          AFEA.GFHLNE.LYN.I...Y..E..NMDF.NFISCLVR.DA.F.A.KSL.KD.T....VNIQEWLQLTM
Retrocopy AFEAPGFHLNEQLYNIIF*HYLHEGENMDFGNFISCLVRPDA*FHALKSLYKDDTRPF*VNIQEWLQLTM

Parental  Y
          Y
Retrocopy Y

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	0.06 RPM	91.28 RPM
SRP007412_cerebellum	0.12 RPM	52.05 RPM
SRP007412_heart	0.03 RPM	59.03 RPM
SRP007412_kidney	0.13 RPM	92.84 RPM
SRP007412_liver	0.00 RPM	51.38 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_448 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_448 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_448 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000000511	1 retrocopy	retro_acar_205,
Ailuropoda melanoleuca	ENSAMEG00000001024	1 retrocopy	retro_amel_136,
Bos taurus	ENSBTAG00000014872	2 retrocopies	retro_btau_1126, retro_btau_692,
Canis familiaris	ENSCAFG00000031314	1 retrocopy	retro_cfam_942,
Callithrix jacchus	ENSCJAG00000009594	1 retrocopy	retro_cjac_2940,
Cavia porcellus	ENSCPOG00000000115	1 retrocopy	retro_cpor_1131,
Equus caballus	ENSECAG00000012210	1 retrocopy	retro_ecab_707,
Felis catus	ENSFCAG00000014149	1 retrocopy	retro_fcat_1691,
Homo sapiens	ENSG00000126247	1 retrocopy	retro_hsap_98,
Gorilla gorilla	ENSGGOG00000003699	2 retrocopies	retro_ggor_1241, retro_ggor_263,
Myotis lucifugus	ENSMLUG00000024944	1 retrocopy	retro_mluc_2336,
Macaca mulatta	ENSMMUG00000000249	2 retrocopies	retro_mmul_1334, retro_mmul_1567,
Monodelphis domestica	ENSMODG00000014179	1 retrocopy	retro_mdom_410,
Mustela putorius furo	ENSMPUG00000005617	1 retrocopy	retro_mputfur_444,
Mus musculus	ENSMUSG00000001794	1 retrocopy	retro_mmus_80,
Nomascus leucogenys	ENSNLEG00000011712	2 retrocopies	retro_nleu_1328, retro_nleu_992,
Pongo abelii	ENSPPYG00000009898	2 retrocopies	retro_pabe_1359, retro_pabe_448 ,
Pelodiscus sinensis	ENSPSIG00000012793	1 retrocopy	retro_psin_45,
Pan troglodytes	ENSPTRG00000010887	2 retrocopies	retro_ptro_1112, retro_ptro_168,
Pteropus vampyrus	ENSPVAG00000012885	3 retrocopies	retro_pvam_1375, retro_pvam_639, retro_pvam_737,
Rattus norvegicus	ENSRNOG00000045747	2 retrocopies	retro_rnor_1447, retro_rnor_2145,
Sorex araneus	ENSSARG00000004266	1 retrocopy	retro_sara_215,
Sus scrofa	ENSSSCG00000030149	2 retrocopies	retro_sscr_495, retro_sscr_73,
Ictidomys tridecemlineatus	ENSSTOG00000026235	1 retrocopy	retro_itri_342,
Vicugna pacos	ENSVPAG00000008074	1 retrocopy	retro_vpac_64,