RetrogeneDB ID: retro_pabe_1359

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 16:42763877..42764603(+)
• Located in intron of: ENSPPYG00000007358

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_1359
CTATTGGAAGGAGCAGATCGAGGTCTTGGAGAAGCTCTTGGAGGCCTCTTTGGAGGAGGTGGTCAGAGAAGAGAAGGAGG
AGGAAGAAATATTGGAGGGATAGTTGGAGGAATTGTGAATTTTATCAGTGAGGCTGCAGCAGCTCAGTATACTCCAGAAC
CGCCTCCCACTCAGCAGCATTTCACCAGTGTGGAGGCCTCAGAAAGTGAGGAAGTTAGGCGATTTCGGCAACAATTTACA
CAGCTGGCTGGACCAGACATGGAGGTGGGTGCCACTGATCTGATGAATATTCTCAACAAAGTCCTTTCTAAGCACAAGGA
TCTGAAGACTGACGGTTTTAGTCTTGACACCTGCCGGAGCATTGTGTCTGTCATGGACAGTGACACGACTGGGAAGCTGG
GCTTTGAAGAATTTAAATATCTGTGGAACAACATCAAGAAATGGCAGTGTGTTTATAAGCAGTATGACAGGGACCATTCT
GGGTCTCTGGGAAGTTCTCAGCTGCGGGGAGCTCTGCAGGCCGCAGGCTTCCAGCTAAATGAACAACTTTACCAAATGAT
TGTCCGCCGGTATGCTAATGAAGATGGAGATATGGATTTTAACAATTTCATCAGCTGCTTGGTCCACCTGGATGCCATGT
TTCGTGCCTTCAAGTCTCTGGATAGAGATAGAGATGGCCTGATTCAAGTGTCTATCAAAGAATGGCTGCAGTTGACCATG
TATTCC

Alignment

ORF - retro_pabe_1359 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.36 %
• Parental protein coverage: 89.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLGGLISGAGGGGGGGGGGGGGGGGGGGGTAMRILGGVISAISEAAA-QYNPEPPPPRTHYSNIEANESE
          .L.G...G.G...GG..GGGG....GGG.....I.GG....ISEAAA.QY.PEPPP...H....EA.ESE
Retrocopy LLEGADRGLGEALGGLFGGGGQRREGGGRNIGGIVGGIVNFISEAAAAQYTPEPPPTQQHFTSVEASESE

Parental  EVRQFRRLFAQLAGDDMEVSATELMNILNKVVTRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKY
          EVR.FR..F.QLAG.DMEV.AT.LMNILNKV...H.DLKTDGF..DTCRS.V.VMDSDTTGKLGFEEFKY
Retrocopy EVRRFRQQFTQLAGPDMEVGATDLMNILNKVLSKHKDLKTDGFSLDTCRSIVSVMDSDTTGKLGFEEFKY

Parental  LWNNIKRWQAIYKQFDTDRSGTICSSELPGAFEAAGFHLNEHLYNMIIRRYSDESGNMDFDNFISCLVRL
          LWNNIK.WQ..YKQ.D.D.SG...SS.L.GA..AAGF.LNE.LY.MI.RRY..E.G.MDF.NFISCLV.L
Retrocopy LWNNIKKWQCVYKQYDRDHSGSLGSSQLRGALQAAGFQLNEQLYQMIVRRYANEDGDMDFNNFISCLVHL

Parental  DAMFRAFKSLDKDGTGQIQVNIQEWLQLTMYS
          DAMFRAFKSLD.D..G.IQV.I.EWLQLTMYS
Retrocopy DAMFRAFKSLDRDRDGLIQVSIKEWLQLTMYS

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

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1359 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1359 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1359 has 10 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_98
Pan troglodytes	retro_ptro_1112
Gorilla gorilla	retro_ggor_1241
Macaca mulatta	retro_mmul_1567
Mus musculus	retro_mmus_80
Rattus norvegicus	retro_rnor_1447
Bos taurus	retro_btau_692
Sus scrofa	retro_sscr_73
Canis familiaris	retro_cfam_942
Equus caballus	retro_ecab_707

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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,