RetrogeneDB ID: retro_btau_1126

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 27:28120908..28121370(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPNS1
• Ensembl ID: ENSBTAG00000014872
• Aliases: CAPNS1, CAPN4
• Description: Calpain small subunit 1 [Source:UniProtKB/Swiss-Prot;Acc:P13135]

Sequence

>retro_btau_1126
CCGCCCCTTGCACGCCTCACTCCAGCCTCCAGGCCAGAAGGCGAGGAAGTCCGGCAGTTCCCGAGGATCTTTGCCTAGCT
GACTGTAGACACAGGGCACTCACTGCCACAGAACTCTCAGCCCTTCTCAACCACGTCATAACCCAACATCCTGATCTGAA
GACTGATCGTTTGGGCATTGACACCTGTCGCAGCGTGGTGGCCGTGATCGATAGTGTCACGACCAGCAAGCTGGACTTTG
AGGAATTCTAGTGCTTATGGAATGACATTCAGAAGTGGCAGGAAATATACAGTTTGACCGTTGGTGGTTTAGGGACCGTG
GGCAGCGGGGAACTCCCCAGGGACCTTTGAAGCATCAGGACTCTATTTGAATGAGGCTCTCCACGACAGTATCGTCCGAA
GCCACTCAGATAAGGGAGGAAACGTGGATGTTGACAGCTTCATCAGCTCTCTGGTCCGGCTG

Alignment

ORF - retro_btau_1126 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.32 %
• Parental protein coverage: 58.94 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PPRTHYSNIEANESEEVRQFRRLFAQLAGDD-MEVSATELMNILNKVVTRHPDLKTDGFGIDTCRSMVAV
          PP..........E.EEVRQF.R.FA.L..D......ATEL...LN.V.T.HPDLKTD..GIDTCRS.VAV
Retrocopy PPLARLTPASRPEGEEVRQFPRIFA*LTVDT<RALTATELSALLNHVITQHPDLKTDRLGIDTCRSVVAV

Parental  MDSDTTGKLGFEEFKYLWNNIKKWQAVYKQFDVDRSGTIGSSEL-PGAFEAAGFRLNEHLYNMIIRRYSD
          .DS.TT.KL.FEEF..LWN.I.KWQ..Y....V...GT.GS.EL.PG.FEA.G..LNE.L...I.R..SD
Retrocopy IDSVTTSKLDFEEF*CLWNDIQKWQEIY-SLTVGGLGTVGSGEL>PGTFEASGLYLNEALHDSIVRSHSD

Parental  EGGNMDFDNFISCLVRL
          .GGN.D.D.FIS.LVRL
Retrocopy KGGNVDVDSFISSLVRL

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
ERP005899_liver	0.00 RPM	29.49 RPM
ERP005899_muscle	0.00 RPM	192.47 RPM
SRP017611_brain	0.00 RPM	157.27 RPM
SRP017611_kidney	0.00 RPM	214.86 RPM
SRP017611_liver	0.00 RPM	51.80 RPM
SRP030211_testis	0.02 RPM	300.88 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1126 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1126 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1126 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Sus scrofa	retro_sscr_495

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Parental genes homology:

Parental genes homology involve 31 parental genes, and 43 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,
Echinops telfairi	ENSETEG00000007650	2 retrocopies	retro_etel_1190, retro_etel_60,
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,
Microcebus murinus	ENSMICG00000010255	1 retrocopy	retro_mmur_416,
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,
Oryctolagus cuniculus	ENSOCUG00000013093	1 retrocopy	retro_ocun_1095,
Otolemur garnettii	ENSOGAG00000006992	1 retrocopy	retro_ogar_1956,
Ochotona princeps	ENSOPRG00000016562	2 retrocopies	retro_opri_181, retro_opri_486,
Procavia capensis	ENSPCAG00000006353	1 retrocopy	retro_pcap_165,
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,