RetrogeneDB ID:

retro_cjac_3359

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:ACFV01174550.1:39556..40207(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000005122
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000006953
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_3359
ATGGTGAAGTATTTCCTGGGCCAGAGCTTGCTCCGGAGTTCCTGGGACCAAGTGTTCGCCGCCTTCTGGCAGCGGTACCC
AAATCCCTATAGCAAACATGTCTTGACGGAAGACATAGTACACCGGGAGGTGACCCCTGACCAGAAACTGCTGTCCCGGC
GACTCCTGACCAAGACCAACAGGATGCCTCGCTGGGCCGAGCGACTGTTTCCTGCCAATGTTGCTCACTCGGTGTACATC
CTGGAGGACTCTACTGTGGACCCACAGAATCAGACCATGACCACCTTCACCTGGAACATCAACCACGCCAGGCTGATGGT
GGTGGAGGAACGATGTGTTTACTGTGTGAACTCTGACGACAGTGGCTGGACCGAAATCCGCCTTGAAGCCTGGGTCTCCT
CTAGCTTATTTGGCGTCTCCAGAGCTGTCCAGGAATTTGGTCTTGCCCGGTTCAAAAGCAACGTGACCAAGACTATGAAG
GGTTTTGAATATATCTTGGCGAAGCTGCAAAGTGAGGCCCCTTCCAAAACACTTGTTGAGACAGCCAAGGAAGCCAAGGA
GAAGGCAAAGGAGACGGCACTGGCAGCTACAGAGAAGGCCAAGGACCTCGCCAGCAAGGCGGCCACCAAGAAGCAGCAGC
AGCAGCAGCAG

ORF - retro_cjac_3359 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.16 %
Parental protein coverage: 99.09 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMVKYFLGQSLLRSSWDQVFAAFWQRYPNPYSKHVLTEDIVHREVTPDQKLLSRRLLTKTNRMPRWAERLF
MVKYFLGQSLLRSSWDQVFAAFWQRYPNPYSKHVLTEDIVHREVTPDQKLLSRRLLTKTNRMPRWAERLF
RetrocopyMVKYFLGQSLLRSSWDQVFAAFWQRYPNPYSKHVLTEDIVHREVTPDQKLLSRRLLTKTNRMPRWAERLF
ParentalPANVAHSVYILEDSIVDPQNQTMTTFTWNINHARLMVVEERCVYCVNSDNSGWTEIRREAWVSSSLFGVS
PANVAHSVYILEDS.VDPQNQTMTTFTWNINHARLMVVEERCVYCVNSD.SGWTEIR.EAWVSSSLFGVS
RetrocopyPANVAHSVYILEDSTVDPQNQTMTTFTWNINHARLMVVEERCVYCVNSDDSGWTEIRLEAWVSSSLFGVS
ParentalRAVQEFGLARFKSNVTKTMKGFEYILAKLQGEAPSKTLVETAKEAKEKAKETALAATEKAKDLASKAATK
RAVQEFGLARFKSNVTKTMKGFEYILAKLQ.EAPSKTLVETAKEAKEKAKETALAATEKAKDLASKAATK
RetrocopyRAVQEFGLARFKSNVTKTMKGFEYILAKLQSEAPSKTLVETAKEAKEKAKETALAATEKAKDLASKAATK
ParentalKQQQQQQ
KQQQQQQ
RetrocopyKQQQQQQ

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






(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
SRP051959_colon 0 .07 RPM 19 .17 RPM
SRP051959_heart 0 .00 RPM 6 .37 RPM
SRP051959_kidney 0 .07 RPM 18 .99 RPM
SRP051959_liver 0 .13 RPM 19 .49 RPM
SRP051959_lung 0 .07 RPM 10 .28 RPM
SRP051959_lymph_node 0 .02 RPM 11 .94 RPM
SRP051959_skeletal_muscle 0 .00 RPM 4 .85 RPM
SRP051959_spleen 0 .08 RPM 12 .18 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3359 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3359 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3359 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 23 parental genes, and 81 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000050092 retrocopies
Canis familiaris ENSCAFG000000164432 retrocopies
Choloepus hoffmanni ENSCHOG000000022511 retrocopy
Callithrix jacchus ENSCJAG00000006953 5 retrocopies
Cavia porcellus ENSCPOG000000257881 retrocopy
Dasypus novemcinctus ENSDNOG000000175501 retrocopy
Equus caballus ENSECAG000000234601 retrocopy
Homo sapiens ENSG000001692307 retrocopies
Gorilla gorilla ENSGGOG000000117623 retrocopies
Loxodonta africana ENSLAFG000000054591 retrocopy
Macropus eugenii ENSMEUG0000000173812 retrocopies
Myotis lucifugus ENSMLUG000000070082 retrocopies
Macaca mulatta ENSMMUG000000090462 retrocopies
Monodelphis domestica ENSMODG000000048043 retrocopies
Mustela putorius furoENSMPUG000000122261 retrocopy
Mus musculus ENSMUSG000000214867 retrocopies
Nomascus leucogenys ENSNLEG000000127145 retrocopies
Otolemur garnettii ENSOGAG000000114554 retrocopies
Pongo abelii ENSPPYG000000160867 retrocopies
Rattus norvegicus ENSRNOG000000164108 retrocopies
Sus scrofa ENSSSCG000000140424 retrocopies
Tupaia belangeri ENSTBEG000000064451 retrocopy
Tursiops truncatus ENSTTRG000000095711 retrocopy



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