RetrogeneDB ID:

retro_ecab_707

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:3:7730203..7730914(+)
Located in intron of:ENSECAG00000009649
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CAPNS1
Ensembl ID:ENSECAG00000012210
Aliases:None
Description:calpain, small subunit 1 [Source:HGNC Symbol;Acc:1481]


Retrocopy-Parental alignment summary:






>retro_ecab_707
AATGGAGGCCTTGGAGAAGCTCTTGGAGGCCTTCTTGGAGGAGGCGGTCAGAAAAGAGGAGGAGGAGGAAATATTGGAGC
GATAGTTGGGGGAATTATGAATTTTATCAGTGAGGCTGCAGCAGCCCAGTATACCCCCGAGCCGCCGCCATCCACTCAGC
AGCATTTCACCACCGTGGAGGCCAACGAAAGTGAGGAGGTGCGGCAGTTTCGGCAACAGTTTGCGCGACTGGCTGGACCC
GACATGGAGGTGGGTGCCACTGACCTGATGAACATTCTCAACAAAGTCCTCGCTAAGCACAAGGATCTGAAGTCGGACGG
CTTCAGTCTTGACACCTGCCGGAGCATTGTATCCGTTATGGACAGTGACACGAATGGGAAGCTGGGCTTTGAAGAATTTA
AGTACTTCTGGAACAACATCAAGAAGTGGCAGTGTGTTTTCAGGCAACATGACACGGACCGTTCCGGGTCTCTGAGGAGT
TCCCAGCTGAAGGGGGCTCTGCAGGCGGCAGGTTTCCAGCTAAACGAGCAGCTCTACCGAATGATCGTCCGCCGCTACGC
CGATGAGAATGGAAGCATGGATTTTAACAACTTCATCAGCTGCCTGGTCCGCCTGGATGCCATGTTCCGTGCCTTCAAAT
CTCTGGATAGAAATGCAAGTGGCCTGATTGAGGTGTCTATCCAGGAGTGGCTGCAGCTGACCATGTACTCC

ORF - retro_ecab_707 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.35 %
Parental protein coverage: 87.92 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalSGGGGGGGGG--GGGGGGGGGGGTAMRILGGVISAISEAAA-QYNPEPPP-PRTHYSNIEANESEEVRQF
.GG.G...GG..GGGG...GGGG....I.GG....ISEAAA.QY.PEPPP....H....EANESEEVRQF
RetrocopyNGGLGEALGGLLGGGGQKRGGGGNIGAIVGGIMNFISEAAAAQYTPEPPPSTQQHFTTVEANESEEVRQF
ParentalRRLFAQLAGDDMEVSPTELMNILNKIVTRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKYLWNNI
R..FA.LAG.DMEV..T.LMNILNK....H.DLK.DGF..DTCRS.V.VMDSDT.GKLGFEEFKY.WNNI
RetrocopyRQQFARLAGPDMEVGATDLMNILNKVLAKHKDLKSDGFSLDTCRSIVSVMDSDTNGKLGFEEFKYFWNNI
ParentalKKWQAIYKQFDMDRSGTIGSSELPGAFQAAGFHLNEHLYNMIIRRYSDEGGNMDFDNFISCLVRMDAMFR
KKWQ....Q.D.DRSG...SS.L.GA.QAAGF.LNE.LY.MI.RRY.DE.G.MDF.NFISCLVR.DAMFR
RetrocopyKKWQCVFRQHDTDRSGSLRSSQLKGALQAAGFQLNEQLYRMIVRRYADENGSMDFNNFISCLVRLDAMFR
ParentalAFKSLDKDGSGQIQVNIQEWLQLTMYS
AFKSLD...SG.I.V.IQEWLQLTMYS
RetrocopyAFKSLDRNASGLIEVSIQEWLQLTMYS

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP021940_articular_cartilage 0 .00 RPM 162 .45 RPM
SRP021940_cerebellum 0 .05 RPM 151 .12 RPM
SRP021940_embryo 1 .10 RPM 157 .09 RPM
SRP021940_placental_villous 9 .67 RPM 367 .38 RPM
SRP021940_synovial_membrane 0 .14 RPM 378 .95 RPM
SRP021940_testis 0 .06 RPM 515 .32 RPM

ChIP-Seq - click to see more details

Equus caballus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ecab_707 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_707 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_707 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
Pongo abelii retro_pabe_1359
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
Parental genes homology:
Parental genes homology involve 31 parental genes, and 43 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000005111 retrocopy
retro_acar_205,
Ailuropoda melanoleuca ENSAMEG000000010241 retrocopy
retro_amel_136,
Bos taurus ENSBTAG000000148722 retrocopies
retro_btau_1126, retro_btau_692,
Canis familiaris ENSCAFG000000313141 retrocopy
retro_cfam_942,
Callithrix jacchus ENSCJAG000000095941 retrocopy
retro_cjac_2940,
Cavia porcellus ENSCPOG000000001151 retrocopy
retro_cpor_1131,
Equus caballus ENSECAG00000012210 1 retrocopy
retro_ecab_707 ,
Echinops telfairi ENSETEG000000076502 retrocopies
retro_etel_1190, retro_etel_60,
Felis catus ENSFCAG000000141491 retrocopy
retro_fcat_1691,
Homo sapiens ENSG000001262471 retrocopy
retro_hsap_98,
Gorilla gorilla ENSGGOG000000036992 retrocopies
retro_ggor_1241, retro_ggor_263,
Microcebus murinus ENSMICG000000102551 retrocopy
retro_mmur_416,
Myotis lucifugus ENSMLUG000000249441 retrocopy
retro_mluc_2336,
Macaca mulatta ENSMMUG000000002492 retrocopies
retro_mmul_1334, retro_mmul_1567,
Monodelphis domestica ENSMODG000000141791 retrocopy
retro_mdom_410,
Mustela putorius furoENSMPUG000000056171 retrocopy
retro_mputfur_444,
Mus musculus ENSMUSG000000017941 retrocopy
retro_mmus_80,
Nomascus leucogenys ENSNLEG000000117122 retrocopies
retro_nleu_1328, retro_nleu_992,
Oryctolagus cuniculus ENSOCUG000000130931 retrocopy
retro_ocun_1095,
Otolemur garnettii ENSOGAG000000069921 retrocopy
retro_ogar_1956,
Ochotona princeps ENSOPRG000000165622 retrocopies
retro_opri_181, retro_opri_486,
Procavia capensis ENSPCAG000000063531 retrocopy
retro_pcap_165,
Pongo abelii ENSPPYG000000098982 retrocopies
retro_pabe_1359, retro_pabe_448,
Pelodiscus sinensis ENSPSIG000000127931 retrocopy
retro_psin_45,
Pan troglodytes ENSPTRG000000108872 retrocopies
retro_ptro_1112, retro_ptro_168,
Pteropus vampyrus ENSPVAG000000128853 retrocopies
retro_pvam_1375, retro_pvam_639, retro_pvam_737,
Rattus norvegicus ENSRNOG000000457472 retrocopies
retro_rnor_1447, retro_rnor_2145,
Sorex araneus ENSSARG000000042661 retrocopy
retro_sara_215,
Sus scrofa ENSSSCG000000301492 retrocopies
retro_sscr_495, retro_sscr_73,
Ictidomys tridecemlineatus ENSSTOG000000262351 retrocopy
retro_itri_342,
Vicugna pacos ENSVPAG000000080741 retrocopy
retro_vpac_64,


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