RetrogeneDB ID:

retro_rnor_1447

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:19:26581986..26582628(-)
Located in intron of:ENSRNOG00000016643
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Capns1
Ensembl ID:ENSRNOG00000045747
Aliases:None
Description:Calpain small subunit 1 [Source:UniProtKB/Swiss-Prot;Acc:Q64537]


Retrocopy-Parental alignment summary:






>retro_rnor_1447
ATCCTGGAAGGTGCAGATCGGGGTCTCGGAGGGGCTCTTGGAGGCCTTCTTGGAGGAGGTGGTCAGGCAGGAGCAGGTAG
GGGCAACATCGGAGGGATCATCGGAGGAATTGTCAATTTTATCAGTGAGGCCGCCGCAGCTCAGTACACCCCAGAGCCGC
CTCCCCCACAGCGGCATTTCACTGTTGTGGAGGCCTCAGAAAGTGACGAAGTCAGGCGTTTCCGGCAGCAATTTACACAG
CTGGCTGGACCCGACATGGAGGTGGGTGCCGCCGACCTGATGAACATTCTCAACAAGGTCCTCTCTAAGCACAAGGAGCT
GAAGACGGACGGTTTCAGCCTTGACACCTGCAGGAGCATCGTGTCTGTCATGGACAGTGACACGACTGGGAAACTGGGCT
TTGAGGAATTTAAGTACCTGTGGAACAACATCAAGAAATGGCAGTGTGTTTTTAAGCAGTATGACAGCGACCATTCTGGC
TTCCTCAGGAGCTCCCAGCTACACGGGGCCATGCAGGCAGCAGGCTTCCAGCTAAATGAGCAGCTTTACCTAATGATTGT
CCGTCGGTATGCTGACGAAGACGGCAGCATGGACTTTAACAACTTTATCAGCTGCCTGGTTCGCCTGGATGCCATGTTTC
GA

ORF - retro_rnor_1447 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.55 %
Parental protein coverage: 87.65 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalLISGAAGGGGGGGGGGGMGLGGGGGGGGTAMRILGGVISAISEAAA-QYNPEPPPPRSHYSNIEANESEE
...GA..G.GG..GG...G.G..G.G.G....I.GG....ISEAAA.QY.PEPPPP..H....EA.ES.E
RetrocopyILEGADRGLGGALGGLLGGGGQAGAGRGNIGGIIGGIVNFISEAAAAQYTPEPPPPQRHFTVVEASESDE
ParentalERQFRKLFVQLAGDDMEVSATELMNILNKVVTRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKYL
.R.FR..F.QLAG.DMEV.A..LMNILNKV...H..LKTDGF..DTCRS.V.VMDSDTTGKLGFEEFKYL
RetrocopyVRRFRQQFTQLAGPDMEVGAADLMNILNKVLSKHKELKTDGFSLDTCRSIVSVMDSDTTGKLGFEEFKYL
ParentalWNNIKKWQGIYKRFDTDRSGTIGSNELPGAFEAAGFHLNQHIYSMIIRRYSDETGNMDFDNFISCLVRLD
WNNIKKWQ...K..D.D.SG...S..L.GA..AAGF.LN...Y.MI.RRY.DE.G.MDF.NFISCLVRLD
RetrocopyWNNIKKWQCVFKQYDSDHSGFLRSSQLHGAMQAAGFQLNEQLYLMIVRRYADEDGSMDFNNFISCLVRLD
ParentalAMFR
AMFR
RetrocopyAMFR

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
SRP017611_brain 0 .43 RPM 0 .00 RPM
SRP017611_kidney 0 .14 RPM 0 .07 RPM
SRP017611_liver 0 .00 RPM 0 .00 RPM

ChIP-Seq - click to see more details

Rattus norvegicus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_rnor_1447 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_1447 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_1447 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
Bos taurus retro_btau_692
Sus scrofa retro_sscr_73
Canis familiaris retro_cfam_942
Equus caballus retro_ecab_707
Parental genes homology:
Parental genes homology involve 32 parental genes, and 44 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 ENSECAG000000122101 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,
Ornithorhynchus anatinus ENSOANG000000027361 retrocopy
retro_oana_113,
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 ENSRNOG00000045747 2 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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