RetrogeneDB ID:

retro_cjac_1283

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:14:53043716..53044142(-)
Located in intron of:ENSCJAG00000010149
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:C9orf85
Ensembl ID:ENSCJAG00000001441
Aliases:None
Description:chromosome 9 open reading frame 85 [Source:HGNC Symbol;Acc:28784]


Retrocopy-Parental alignment summary:






>retro_cjac_1283
AGGCACCAGAATACATTTAGCTTCAAAAATGACAAGTTCAATAAGAGTGTTAAGACCAAGAAAATTAATGCAAAACTTCC
TGATGGAGTGTGTCAGCACTATGAAGAAGTTCTTGAGTGGCGTGTTAACATACAAAAAATATAAATCATTATCAAAACCT
TATAAATGTGTTAAATGTTTATAAAAGACAGTGAGGGATTCTTATCACTTGTGTAGGCCATGCACCTATGAACTTGAAGT
TTGCACAAAATGTGGAAAGAAAGAAGACATTGTTATTCTGTTCAATAAAGAACCAGAAAAAACAGAGGGTATTAAAATAA
TCTAAGTTATAATCATAGAAGAAGCTGCAGAAGAAATGAAGGAAGGGATGATAATTTAGATTACAATATCGATTTAGAAG
ATACAGGAGGAGACCATCAAGTGAAT

ORF - retro_cjac_1283 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.55 %
Parental protein coverage: 91.08 %
Number of stop codons detected: 1
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalKHQNTFSFKNDKFDKSVQTKKINAKLHDGVCQHCKEVLEWRVK-YSKYKPLSKPKKCVKCLQKTVKDSYH
.HQNTFSFKNDKF.KSV.TKKINAKL.DGVCQH..EVLEWRV..Y.KYK.LSKP.KCVKCL.KTV.DSYH
RetrocopyRHQNTFSFKNDKFNKSVKTKKINAKLPDGVCQHYEEVLEWRVN>YKKYKSLSKPYKCVKCL*KTVRDSYH
ParentalIICRPCAYELEVCAKCGKKEDIVIPFNNKSEKTEHIE-NNPSSNHRRSCRRNEESDDDLDFDIDLEDTEG
..CRPC.YELEVC.KCGKKEDIVI.FN...EKTE.I..NN.S.NHRRSCRRNE..DD.LD..IDLEDT.G
Retrocopy-LCRPCTYELEVCTKCGKKEDIVILFNKEPEKTEGIK<NNLSYNHRRSCRRNEGRDDNLDYNIDLEDTGG
ParentalNHQMN
.HQ.N
RetrocopyDHQVN

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
SRP051959_colon 0 .82 RPM 6 .32 RPM
SRP051959_heart 6 .02 RPM 5 .91 RPM
SRP051959_kidney 2 .48 RPM 6 .37 RPM
SRP051959_liver 0 .50 RPM 4 .29 RPM
SRP051959_lung 4 .26 RPM 5 .53 RPM
SRP051959_lymph_node 0 .64 RPM 7 .67 RPM
SRP051959_skeletal_muscle 2 .73 RPM 3 .82 RPM
SRP051959_spleen 2 .18 RPM 7 .12 RPM

ChIP-Seq - click to see more details

Callithrix jacchus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cjac_1283 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_1283 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1283 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2104
Pan troglodytes retro_ptro_1543
Pongo abelii retro_pabe_1996
Macaca mulatta retro_mmul_988
Parental genes homology:
Parental genes homology involve 19 parental genes, and 41 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000072541 retrocopy
retro_amel_730,
Bos taurus ENSBTAG000000068311 retrocopy
retro_btau_39,
Canis familiaris ENSCAFG000000018201 retrocopy
retro_cfam_2126,
Callithrix jacchus ENSCJAG00000001441 2 retrocopies
retro_cjac_1283 , retro_cjac_1374,
Cavia porcellus ENSCPOG000000258482 retrocopies
retro_cpor_1538, retro_cpor_316,
Felis catus ENSFCAG000000319421 retrocopy
retro_fcat_1955,
Homo sapiens ENSG000001556212 retrocopies
retro_hsap_2104, retro_hsap_2895,
Myotis lucifugus ENSMLUG000000243092 retrocopies
retro_mluc_2449, retro_mluc_2526,
Macaca mulatta ENSMMUG000000188812 retrocopies
retro_mmul_670, retro_mmul_988,
Mustela putorius furoENSMPUG000000089711 retrocopy
retro_mputfur_1413,
Mus musculus ENSMUSG000000351716 retrocopies
retro_mmus_1049, retro_mmus_2254, retro_mmus_2286, retro_mmus_2781, retro_mmus_2941, retro_mmus_3698,
Nomascus leucogenys ENSNLEG000000010231 retrocopy
retro_nleu_1272,
Oryctolagus cuniculus ENSOCUG000000245782 retrocopies
retro_ocun_703, retro_ocun_766,
Otolemur garnettii ENSOGAG000000113021 retrocopy
retro_ogar_979,
Pongo abelii ENSPPYG000000297452 retrocopies
retro_pabe_1996, retro_pabe_2397,
Pan troglodytes ENSPTRG000000210182 retrocopies
retro_ptro_1543, retro_ptro_1958,
Rattus norvegicus ENSRNOG000000271615 retrocopies
retro_rnor_1898, retro_rnor_2010, retro_rnor_2242, retro_rnor_2859, retro_rnor_2960,
Sorex araneus ENSSARG000000045231 retrocopy
retro_sara_260,
Tupaia belangeri ENSTBEG000000155566 retrocopies
retro_tbel_1998, retro_tbel_200, retro_tbel_2406, retro_tbel_2410, retro_tbel_3539, retro_tbel_940,


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