RetrogeneDB ID: retro_ocun_1095

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:48985614..48986093(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPNS1
• Ensembl ID: ENSOCUG00000013093
• Aliases: None
• Description: calpain, small subunit 1 (CAPNS1), mRNA [Source:RefSeq mRNA;Acc:NM_001082264]

Sequence

>retro_ocun_1095
TTTGCCAAGCTGGCTGGCGATAGCATCAGTGCCACAGATTCCATGAACATTCTCAATGAAGTTGTGATCCAATACCCTGA
TCTACGGCTGACAGATTTGGCATTGACACATGGTAAAGTCTGGTTCCCATGATGGATAGTGACACCCCAGGCAAGCTGGG
CCTGGAGGAGTTCAAGTACCTGTGGGATAACATCAAAAAGCGGTAGGTCATACACAAACATTTAGATCTTGAGCAATCTG
GGTGCATCTGTAGCGGTGAACTGCTGGAGGCCTTTGAGGCAGCAGAGTTCCACCGCAATGATCATCTCTGAACATGAGCA
TCTGACGCTGTCCAGCTGAGGGAAGGCACCTGGAATTTTGACAGCTTCATCAGCTGCGTGGCCACATTGGACCCCATGCT
CTGTCCCTGCAAATCTCTTGACAACAATAGCACTGAACAAATCCAGGTGAATATCCAGGAGTGCCTTCAGCTGACTATG

Alignment

ORF - retro_ocun_1095 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60. %
• Parental protein coverage: 60.9 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FAQLAGDDMEVSATELMNILNKVVTRHPDLK-TDGFGLDTCRSMVAVMDSDTTGKLGFEEFKYLWNNIKK
          FA.LAGD....SAT..MNILN.VV...PDL...D.FG.DT..S.V..MDSDT.GKLG.EEFKYLW.NIKK
Retrocopy FAKLAGDS--ISATDSMNILNEVVIQYPDLR<ADRFGIDTW*SLVPMMDSDTPGKLGLEEFKYLWDNIKK

Parental  WQAIYKQFDVDRSGTICSRELPGAFEAAGFHLNEHL-YNMIIRRYSDEA-GNMDFDNFISCLVRLDAMFR
          ...I.K..D...SG.ICS.EL..AFEAA.FH.N.HL..NM.I.R...E..G...FD.FISC...LD.M..
Retrocopy R*VIHKHLDLEQSGCICSGELLEAFEAAEFHRNDHL<LNMSI*RCPAEG>GTWNFDSFISCVATLDPMLC

Parental  AFKSLDKDGTGQIQVNIQEWLQLTM
          ..KSLD...T.QIQVNIQE.LQLTM
Retrocopy PCKSLDNNSTEQIQVNIQECLQLTM

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
SRP017611_brain	0.00 RPM	169.65 RPM
SRP017611_kidney	0.00 RPM	198.86 RPM
SRP017611_liver	0.00 RPM	30.68 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1095 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1095 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1095 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 30 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,
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,
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,
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,
Pelodiscus sinensis	ENSPSIG00000012793	1 retrocopy	retro_psin_45,
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,
Vicugna pacos	ENSVPAG00000008074	1 retrocopy	retro_vpac_64,