RetrogeneDB ID:

retro_cpor_1131

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_5:13399964..13400702(+)
Located in intron of:ENSCPOG00000002265
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CAPNS1
Ensembl ID:ENSCPOG00000000115
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_1131
ATGTTTCTAGCAAAGGCTTTTTTGGAAGGGGCGGATCGGGGTCTTGGAGAAGCTCTGGGAGGCCTTCTAGGAGGAGGTGG
TCAGAGAAGAGGAGGAGGAAGTCTTGGAGGGATAGTAGGAGGAATTGTGAATTTCATCAGCGAGGCTGCTGCAGCTCAGT
ACACTCCAGAGCCACCTCCCACCCCTCAGCATTTCACCAATGTGGAGGCTTCTGAAAGTGAGGAAGTTAGACGGTTTCGG
CAACAGTTCACACAGCTGGCTGGACCGGACATGGAGGTGGGTGCCACCGACTTGATGAATATCCTCAACAAAGTGCTTTC
TAAGCACAAGGAACTGAAGACTGATGGCTTTACTCTCGACACCTGCCGGAGTATTGTGTCTGTCATGGACAATGACACCA
CTGGGAAGCTGGGCTTTGAAGAGTTTAAGTATCTGTGGAACAACATCAAGAAGTGGCAGTGTGTCTTTAAGCAATGTGAT
AGAGACCACTCGGGGTTTCTGAATAACTCTCAGCTGCGCGAAGCTCTGCAGGCAGCTGGCTTCCAGCTGAATGAACAGCT
TTACCAAATGATCGTTCGACGGTATGCTGAGGATGATGAAGGTATGGATTTTAACAATTTCATCAGCTGCCTGGTCCGTC
TGGATGCCATGTTTCGTTCCTTCAAGGCTCTGGATAGAGATGCAGATGGCCTGATTCAAGTGTCGATCAGAGAGTGGCTA
CAGCTGACCATGTATTCC

ORF - retro_cpor_1131 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.45 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMFLVNSFLKGGSGGGGG--GGLAGGLGDVLGGFTAMRILGGVISAISEAAA-QYNPEPPPPRTHYSNIEA
MFL...FL.G...G.G...GGL.GG.G...GG.....I.GG....ISEAAA.QY.PEPPP...H..N.EA
RetrocopyMFLAKAFLEGADRGLGEALGGLLGGGGQRRGGGSLGGIVGGIVNFISEAAAAQYTPEPPPTPQHFTNVEA
ParentalNESEEVRQFRRLFAQLAGDDMEVSATELMNILNKVVTRHPDLKTDGFGLDTCRSMVAVMDSDTTGKLGFE
.ESEEVR.FR..F.QLAG.DMEV.AT.LMNILNKV...H..LKTDGF.LDTCRS.V.VMD.DTTGKLGFE
RetrocopySESEEVRRFRQQFTQLAGPDMEVGATDLMNILNKVLSKHKELKTDGFTLDTCRSIVSVMDNDTTGKLGFE
ParentalEFKYLWNNIKKWQAIYKQFDIDRSGTIGSRELPGAFQAAGFHLNEHLYNMIIRRYSDEGGSMDFDNFISC
EFKYLWNNIKKWQ...KQ.D.D.SG......L..A.QAAGF.LNE.LY.MI.RRY......MDF.NFISC
RetrocopyEFKYLWNNIKKWQCVFKQCDRDHSGFLNNSQLREALQAAGFQLNEQLYQMIVRRYAEDDEGMDFNNFISC
ParentalLVRLDAMFRAFKSLDKDGSGQIQVNIQEWLQLTMYS
LVRLDAMFR.FK.LD.D..G.IQV.I.EWLQLTMYS
RetrocopyLVRLDAMFRSFKALDRDADGLIQVSIREWLQLTMYS

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 .17 RPM 48 .37 RPM
SRP017611_kidney 0 .00 RPM 115 .99 RPM
SRP017611_liver 0 .00 RPM 13 .84 RPM
SRP040447_lung 0 .20 RPM 129 .58 RPM
SRP040447_skeletal_muscle 0 .00 RPM 107 .22 RPM

ChIP-Seq - click to see more details

Cavia porcellus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cpor_1131 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_1131 was not experimentally validated.

Retrocopy orthology:
Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
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 ENSCPOG00000000115 1 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 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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