RetrogeneDB ID:

retro_cjac_1108

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:13:79543390..79543762(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:C15orf40
Ensembl ID:ENSCJAG00000015877
Aliases:None
Description:chromosome 15 open reading frame 40 [Source:HGNC Symbol;Acc:28443]


Retrocopy-Parental alignment summary:






>retro_cjac_1108
CTGGGGCTTGGCCGTGGGCTGCGGCAGCTCAAGGCAGCACTGAGTACCCGCGGCTCCACTCAGCTCCCTCTTGGCACCCA
GATGCCTAAGAAGACTGGTGCGATGAACAAGGGTAAAAGTCTGATCACGAAACCAGAGAGACTACTTCCTCCCTTAGATC
CTATGGCAGTTAATCCTAAAGGTTGTGTCACCATAGCCATCCATTCCAAACCTGGCTCCAAACAACAAAATACTGTCACA
GATTTGACAGCAGAGTGGAAAATGTGGCTATTGCAGCACCTCGAACAGAGGGGAGGCTAATGCTGAACATTAGAGGTATT
TTTCTAAGTCTTAGAACTCAGAGATAATGTGGTTTTGGATAAGGTGGTACAT

ORF - retro_cjac_1108 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.34 %
Parental protein coverage: 83.33 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalLRLYRALGQVGAEPSTWGSARRPLAAEMPKKAGATTKGKSQSKEPERSLPPSGPVAVDPKGCVTIAIHAK
L.L.R.L.Q..A..ST.GS...PL...MPKK.GA..KGKS....PER.LPP..P.AV.PKGCVTIAIH.K
RetrocopyLGLGRGLRQLKAALSTRGSTQLPLGTQMPKKTGAMNKGKSLITKPERLLPPLDPMAVNPKGCVTIAIHSK
ParentalPGSK-QNAVTDLTAE-AINVAIAAPPSE-GEANAELCRYLSK-VLELRKSDVVLDKLCY
PGSK.QN.VTDLTAE...NVAIAAP..E.GEANAE..RY.SK.VLELR...VVLDK...
RetrocopyPGSKQQNTVTDLTAE<VENVAIAAPRTE<GEANAEH*RYFSK<VLELR-DNVVLDKVVH

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 .00 RPM 3 .13 RPM
SRP051959_heart 0 .00 RPM 4 .81 RPM
SRP051959_kidney 0 .00 RPM 5 .06 RPM
SRP051959_liver 0 .00 RPM 4 .05 RPM
SRP051959_lung 0 .00 RPM 3 .94 RPM
SRP051959_lymph_node 0 .00 RPM 4 .41 RPM
SRP051959_skeletal_muscle 0 .00 RPM 8 .52 RPM
SRP051959_spleen 0 .00 RPM 3 .93 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_1108 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_1108 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1108 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1881
Gorilla gorilla retro_ggor_1378
Pongo abelii retro_pabe_1561
Parental genes homology:
Parental genes homology involve 19 parental genes, and 30 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000165222 retrocopies
retro_btau_1724, retro_btau_485,
Canis familiaris ENSCAFG000000131852 retrocopies
retro_cfam_39, retro_cfam_420,
Callithrix jacchus ENSCJAG00000015877 2 retrocopies
retro_cjac_1108 , retro_cjac_4086,
Equus caballus ENSECAG000000224591 retrocopy
retro_ecab_374,
Homo sapiens ENSG000001696091 retrocopy
retro_hsap_1881,
Gorilla gorilla ENSGGOG000000230621 retrocopy
retro_ggor_1378,
Microcebus murinus ENSMICG000000095642 retrocopies
retro_mmur_1387, retro_mmur_1601,
Myotis lucifugus ENSMLUG000000075151 retrocopy
retro_mluc_2487,
Macaca mulatta ENSMMUG000000158901 retrocopy
retro_mmul_664,
Monodelphis domestica ENSMODG000000193741 retrocopy
retro_mdom_145,
Nomascus leucogenys ENSNLEG000000109301 retrocopy
retro_nleu_1803,
Oryctolagus cuniculus ENSOCUG000000050721 retrocopy
retro_ocun_211,
Procavia capensis ENSPCAG000000164461 retrocopy
retro_pcap_51,
Pongo abelii ENSPPYG000000067371 retrocopy
retro_pabe_1561,
Rattus norvegicus ENSRNOG000000195142 retrocopies
retro_rnor_1547, retro_rnor_2334,
Sorex araneus ENSSARG000000063141 retrocopy
retro_sara_147,
Sarcophilus harrisii ENSSHAG000000179472 retrocopies
retro_shar_233, retro_shar_442,
Sus scrofa ENSSSCG000000301311 retrocopy
retro_sscr_221,
Tupaia belangeri ENSTBEG000000143876 retrocopies
retro_tbel_1151, retro_tbel_2000, retro_tbel_3071, retro_tbel_3546, retro_tbel_4182, retro_tbel_4371,


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