RetrogeneDB ID:

retro_ptro_1112

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:16:54618860..54619586(+)
Located in intron of:ENSPTRG00000008124
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CAPNS1
Ensembl ID:ENSPTRG00000010887
Aliases:None
Description:calpain, small subunit 1 [Source:HGNC Symbol;Acc:1481]


Retrocopy-Parental alignment summary:






>retro_ptro_1112
CTATTGGAAGGAGCAGATCGAGGTCTTGGAGAAGCTCTTGGAGGCCTCTTTGGAGGAGGTGGTCAGAGAAGAGAAGGAGG
AGGAAGAAATATTGGAGGGATAGTTGGAGGAATTGTGAATTTTATCAGTGAGGCTGCAGCAGCTCAGTATACTCCAGAAC
CGCCTCCCACTCAGCAGCATTTCACCAGTGTGGAGGCCTCAGAAAGTGAGGAAGTTAGGCGATTTCGGCAACAATTTACA
CAGCTGGCTGGACCAGACATGGAGGTGGGTGCCACTGATCTGATGAATATTCTCAACAAAGTCCTTTCTAAGCACAAAGA
TCTGAAGACTGACGGTTTTAGTCTTGACACCTGCCGGAGCATTGTGTCTGTCATGGACAGTGACACGACTGGAAAGCTGG
GCTTTGAAGAATTTAAGTATCTGTGGAACAACATCAAGAAATGGCAGTGTGTTTATAAGCAGTATGACAGGGACCATTCT
GGGTCTCTGGGAAGTTCTCAGCTGCGGGGAGCTCTGCAGGCCGCAGGCTTCCAGCTAAATGAACAACTGTACCAAATGAT
TGTCCGCCGGTATGCTAATGAAGATGGAGATATGGATTTTAACAATTTCATCAGCTGCTTGGTCCGCCTGGATGCCATGT
TTCGTGCCTTCAAGTCTCTGGATAGAGATAGAGATGGCCTGATTCAAGTGTCTATCAAAGAATGGCTGCAGTTGACCATG
TATTCC

ORF - retro_ptro_1112 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.36 %
Parental protein coverage: 88.43 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLISGAGGGGGGGGGGGGGGGGG---GGGGTAMRILGGVISAISEAAA-QYNPEPPPPRSPYPNI-ANESE
L..GA..G.G...GG..GGGG....GGG.....I.GG....ISEAAA.QY.PEPPP.........A.ESE
RetrocopyLLEGADRGLGEALGGLFGGGGQRREGGGRNIGGIVGGIVNFISEAAAAQYTPEPPPTQQHFTSVEASESE
ParentalEVRQFRRLFAQLAGDDMEVSATELMNILNKVVTRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKY
EVR.FR..F.QLAG.DMEV.AT.LMNILNKV...H.DLKTDGF..DTCRS.V.VMDSDTTGKLGFEEFKY
RetrocopyEVRRFRQQFTQLAGPDMEVGATDLMNILNKVLSKHKDLKTDGFSLDTCRSIVSVMDSDTTGKLGFEEFKY
ParentalLWNNIKRWQAIYKQFDTDRSGTICSSELPGAFEAAGFHLNEHLYNMIIRRYSDESGNMDFDNFISCLVRL
LWNNIK.WQ..YKQ.D.D.SG...SS.L.GA..AAGF.LNE.LY.MI.RRY..E.G.MDF.NFISCLVRL
RetrocopyLWNNIKKWQCVYKQYDRDHSGSLGSSQLRGALQAAGFQLNEQLYQMIVRRYANEDGDMDFNNFISCLVRL
ParentalDAMFRAFKSLDKDGTGQIQVNIQEWLQLTMYS
DAMFRAFKSLD.D..G.IQV.I.EWLQLTMYS
RetrocopyDAMFRAFKSLDRDRDGLIQVSIKEWLQLTMYS

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
SRP007412_brain_prefrontal_cortex 0 .02 RPM 226 .68 RPM
SRP007412_cerebellum 0 .04 RPM 157 .66 RPM
SRP007412_heart 0 .03 RPM 160 .92 RPM
SRP007412_kidney 0 .03 RPM 274 .72 RPM
SRP007412_liver 0 .10 RPM 153 .95 RPM
SRP007412_testis 0 .11 RPM 301 .82 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_1112 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_1112 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1112 has 10 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_98
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
Equus caballus retro_ecab_707
Parental genes homology:
Parental genes homology involve 25 parental genes, and 35 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,
Felis catus ENSFCAG000000141491 retrocopy
retro_fcat_1691,
Homo sapiens ENSG000001262471 retrocopy
retro_hsap_98,
Gorilla gorilla ENSGGOG000000036992 retrocopies
retro_ggor_1241, retro_ggor_263,
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,
Pongo abelii ENSPPYG000000098982 retrocopies
retro_pabe_1359, retro_pabe_448,
Pelodiscus sinensis ENSPSIG000000127931 retrocopy
retro_psin_45,
Pan troglodytes ENSPTRG00000010887 2 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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