RetrogeneDB ID:

retro_cjac_1997

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:20:28420253..28420851(+)
Located in intron of:ENSCJAG00000014476
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000000072
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_1997
ATGGCAAAGTTGCAGGTCCTGCTGCTTAATGGTCGAGGCCATCTCCTGGGTCGCCTGGTGGCCACTGTGGCTAAGCAGGT
ACTGCTGGGCTGACGGTGGTGGTCACATGCTGTGAGGGCATCAACATTTCTGGCAATTTCTACAGAAACGAGTTGAAGTA
CCTGGCTTTCCTCCGCAAGCAAATGAACACCAACCCTTCCCGAGGCCCCTATCACTTCCAGGCCACCAGCCTCTAGCAGA
GTGTGCAAGGCATGCTGTCCCACAAGACCAAGTGAAGCCAGGCTGCCCTGGACTGCCTCAAGGTGCTTGACAGCATCCCA
CCATCCCATGACAAGAAAAAGCACATGGTGGTTCCTGCTTCCCTCAAGGTTGTGCGTCTGAAGCATACAAGAAAGTCTAC
ATATCTGGGGCACCTGCTCACGAGGTTAGCTGGAAGTACCAGGCAGTGACAGCCACCCTGGAGAAGAGGAAGGAGAAAGC
CAAGATCCACTACTGGAAGAAGAAACAGCTCATGAGGCTATGGAAACCAGCCGAGAAGAATGTGGAGAAGGAAACTGACA
AATACACAGAAGTCCTCTAGACCCACGGACTCCTGGTT

ORF - retro_cjac_1997 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.56 %
Parental protein coverage: 100. %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMAEVQVLVLDGRGHLLGRLAAIVAKQVLLGRK-VVVVRCEGINISGNFYRNKLKYLAFLRKRMNTNPSRG
MA..QVL.L.GRGHLLGRL.A.VAKQVLLG...VVV..CEGINISGNFYRN.LKYLAFLRK.MNTNPSRG
RetrocopyMAKLQVLLLNGRGHLLGRLVATVAKQVLLG*R<VVVTCCEGINISGNFYRNELKYLAFLRKQMNTNPSRG
ParentalPYHFRAPSRIFWRTVRGMLPHKTKRGQAALDRLKVFDGIPPPYDKKKRMVVPAALKVVRLKPTRKFAYLG
PYHF.A.S......V.GML.HKTK..QAALD.LKV.D.IPP..DKKK.MVVPA.LKVVRLK.TRK..YLG
RetrocopyPYHFQATS--L*QSVQGMLSHKTK*SQAALDCLKVLDSIPPSHDKKKHMVVPASLKVVRLKHTRKSTYLG
ParentalRL-AHEVGWKYQAVTATLEEKRKEKAKIHYRKKKQLMRLRKQAEKNVEKKINKYTEVLKTHGLLV
.L.AHEV.WKYQAVTATL.EKRKEKAKIHY.KKKQLMRL.K.AEKNVEK...KYTEVL.THGLLV
RetrocopyHL<AHEVSWKYQAVTATL-EKRKEKAKIHYWKKKQLMRLWKPAEKNVEKETDKYTEVL*THGLLV

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 1 .38 RPM 232 .26 RPM
SRP051959_heart 0 .68 RPM 251 .83 RPM
SRP051959_kidney 0 .80 RPM 225 .32 RPM
SRP051959_liver 0 .69 RPM 286 .16 RPM
SRP051959_lung 1 .01 RPM 328 .90 RPM
SRP051959_lymph_node 1 .21 RPM 516 .94 RPM
SRP051959_skeletal_muscle 0 .41 RPM 345 .41 RPM
SRP051959_spleen 1 .09 RPM 377 .88 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1997 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1997 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1997 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 30 parental genes, and 192 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000140272 retrocopies
Bos taurus ENSBTAG000000052963 retrocopies
Canis familiaris ENSCAFG000000298923 retrocopies
Callithrix jacchus ENSCJAG00000000072 16 retrocopies
Cavia porcellus ENSCPOG000000124172 retrocopies
Equus caballus ENSECAG000000158323 retrocopies
Erinaceus europaeus ENSEEUG000000140716 retrocopies
Echinops telfairi ENSETEG000000170762 retrocopies
Felis catus ENSFCAG000000091944 retrocopies
Homo sapiens ENSG0000014254122 retrocopies
Gorilla gorilla ENSGGOG0000000293211 retrocopies
Loxodonta africana ENSLAFG000000162133 retrocopies
Microcebus murinus ENSMICG000000093186 retrocopies
Myotis lucifugus ENSMLUG0000000494510 retrocopies
Macaca mulatta ENSMMUG0000000755114 retrocopies
Mustela putorius furoENSMPUG000000026043 retrocopies
Mus musculus ENSMUSG000000741293 retrocopies
Nomascus leucogenys ENSNLEG0000000521123 retrocopies
Oryctolagus cuniculus ENSOCUG000000252589 retrocopies
Otolemur garnettii ENSOGAG000000046257 retrocopies
Ochotona princeps ENSOPRG000000011943 retrocopies
Procavia capensis ENSPCAG000000040864 retrocopies
Pongo abelii ENSPPYG000000102511 retrocopy
Pan troglodytes ENSPTRG000000112981 retrocopy
Pteropus vampyrus ENSPVAG000000109583 retrocopies
Rattus norvegicus ENSRNOG0000002061810 retrocopies
Sus scrofa ENSSSCG000000031664 retrocopies
Tupaia belangeri ENSTBEG000000165793 retrocopies
Tarsius syrichta ENSTSYG000000087914 retrocopies
Tursiops truncatus ENSTTRG000000054857 retrocopies



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