RetrogeneDB ID:

retro_cfam_682

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:15:28506356..28507058(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCAFG00000005989
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCAFG00000010127
Aliases:SNRPN, SNURF
Description:Small nuclear ribonucleoprotein-associated protein [Source:UniProtKB/TrEMBL;Acc:E2RPQ0]


Retrocopy-Parental alignment summary:






>retro_cfam_682
ATGACTGTGGGAAACAGCAGCCAGACGCTGCAGCACATTGACTATAGAATGAGATGTATCTTGCAAGATGGCCAAATCTT
CATTGGCACCTTTAAGGCTTTTGACAAGCGTATGAACTTGATTCTCTGTGATTGTGATGAATTCAGGAAGATCAAGCCAA
GGAATGTGAAGCAGCCAGAGCGTGAAGAAAAGCGTGTTTTGGGTCTCGTGTTACTACGTGGAGAGAACTTGGCTTCCATG
ACTGTGGAAGGACCACCCCCCAAAGATACTGGCATTGCTCGAGTACCATTTGCTGGAGCTGCAGGACGTCCTGGGGTTGG
CAGGGCAGCTGGCAGAGAAGTTCCAGCTGGTGTTCCAATTCCCCAGGCTCCTGTTGGATTAGCAGGCCCTGTCTGAGGGG
TTGGGGGCCATCCCAACAGGTAATGACTCCACAGGGAAGAGGAACTGTAGCAGCTGCTGCAGTTGCTGCTACTGCCAGCA
TTCCTGGGGCCCCAACTCAATACCCACCAGGACAGGGGACCCCACCTGGGGCGAGCAACACCACCTCCAGGAATTATGGC
TCCTCCACGTGGTATAATGGGCCCACCAATTGGGCTTCCCCCTGCTCGAGGGATGCCTAAAGGCATGCACCCTCCAGGAA
TGAGACCCCCTTCACCAGGAATTAGAGGCCCACCTCCCTCAGGAATACATCCACCAAGACCC

ORF - retro_cfam_682 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.36 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 1
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalMTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNAKQPEREEKRVLGLV
MTVG.SS..LQHIDYRMRCILQDG.IFIGTFKAFDK.MNLILCDCDEFRKIKP.N.KQPEREEKRVLGLV
RetrocopyMTVGNSSQTLQHIDYRMRCILQDGQIFIGTFKAFDKRMNLILCDCDEFRKIKPRNVKQPEREEKRVLGLV
ParentalLLRGENLVSMTVEGPPPKDTGIARVPLAGAAGGPGVGRAAGRGVPAGVPIPQAPAGLAGPVRGVGG-PSQ
LLRGENL.SMTVEGPPPKDTGIARVP.AGAAG.PGVGRAAGR.VPAGVPIPQAP.GLAGPV.GVGG.PSQ
RetrocopyLLRGENLASMTVEGPPPKDTGIARVPFAGAAGRPGVGRAAGREVPAGVPIPQAPVGLAGPV*GVGG<PSQ
ParentalQVMTPQGRGTVAAAAVAATASIAGAPTQYPPGRGTPPTP-VGRATPPPGIMAPPPGMRPPMGPPIGLPPA
QVMTPQGRGTVAAAAVAATASI.GAPTQYPPG.G...TP..GRATPPPGIMAPP.G....MGPPIGLPPA
RetrocopyQVMTPQGRGTVAAAAVAATASIPGAPTQYPPGQG---TP>LGRATPPPGIMAPPRGI---MGPPIGLPPA
ParentalRGTPIGMPPPGMRPPPPGIRGPPPPGMRPPRP
RG.P.GM.PPGMRPP.PGIRGPPP.G..PPRP
RetrocopyRGMPKGMHPPGMRPPSPGIRGPPPSGIHPPRP

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
SRP012049_cerebellum 0 .00 RPM 274 .63 RPM
SRP017611_brain 0 .08 RPM 300 .58 RPM
SRP017611_kidney 0 .00 RPM 99 .58 RPM
SRP017611_liver 0 .00 RPM 11 .67 RPM

ChIP-Seq - click to see more details

Canis familiaris was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cfam_682 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_682 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_682 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 22 parental genes, and 54 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000070343 retrocopies
retro_amel_1048, retro_amel_714, retro_amel_839,
Bos taurus ENSBTAG000000082511 retrocopy
retro_btau_620,
Canis familiaris ENSCAFG000000066933 retrocopies
retro_cfam_1268, retro_cfam_1773, retro_cfam_461,
Canis familiaris ENSCAFG00000010127 6 retrocopies
retro_cfam_1753, retro_cfam_1874, retro_cfam_2039, retro_cfam_627, retro_cfam_682 , retro_cfam_752,
Choloepus hoffmanni ENSCHOG000000018462 retrocopies
retro_chof_2275, retro_chof_385,
Cavia porcellus ENSCPOG000000202701 retrocopy
retro_cpor_878,
Felis catus ENSFCAG000000222982 retrocopies
retro_fcat_1390, retro_fcat_1895,
Homo sapiens ENSG000001287391 retrocopy
retro_hsap_2580,
Gorilla gorilla ENSGGOG000000039881 retrocopy
retro_ggor_1615,
Loxodonta africana ENSLAFG000000094581 retrocopy
retro_lafr_1012,
Myotis lucifugus ENSMLUG000000233613 retrocopies
retro_mluc_1192, retro_mluc_1816, retro_mluc_2156,
Macaca mulatta ENSMMUG000000231391 retrocopy
retro_mmul_644,
Mustela putorius furoENSMPUG000000146381 retrocopy
retro_mputfur_1080,
Mus musculus ENSMUSG000000009483 retrocopies
retro_mmus_1285, retro_mmus_1733, retro_mmus_665,
Oryctolagus cuniculus ENSOCUG000000035324 retrocopies
retro_ocun_1291, retro_ocun_488, retro_ocun_689, retro_ocun_846,
Otolemur garnettii ENSOGAG000000073925 retrocopies
retro_ogar_1179, retro_ogar_3042, retro_ogar_3060, retro_ogar_475, retro_ogar_722,
Pongo abelii ENSPPYG000000062691 retrocopy
retro_pabe_1900,
Pan troglodytes ENSPTRG000000068261 retrocopy
retro_ptro_1507,
Rattus norvegicus ENSRNOG000000159766 retrocopies
retro_rnor_1122, retro_rnor_1314, retro_rnor_1485, retro_rnor_2161, retro_rnor_2462, retro_rnor_2517,
Sus scrofa ENSSSCG000000281242 retrocopies
retro_sscr_350, retro_sscr_405,
Ictidomys tridecemlineatus ENSSTOG000000013391 retrocopy
retro_itri_44,
Tursiops truncatus ENSTTRG000000109665 retrocopies
retro_ttru_1005, retro_ttru_1051, retro_ttru_1473, retro_ttru_580, retro_ttru_600,


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