RetrogeneDB ID:

retro_cjac_30

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:3:85158618..85159086(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000023320
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL23A
Ensembl ID:ENSCJAG00000013126
Aliases:None
Description:ribosomal protein L23a [Source:HGNC Symbol;Acc:10317]


Retrocopy-Parental alignment summary:






>retro_cjac_30
GGCGCCAAAGCGAAGAAGGAAGCTCCTGCCCCTCCTAAAGCCGAAGCCAAAGCGAAGGCTTTAAAGGCCAAGAAGGCAGT
GTTGAAAGGTGTCCACAGCCACAAAAAAAAGAAGATCCGCACGTCACCCACCTTCCGGCGGCCCAAGACACTGCGACTCC
GGAGGCAGCCCAAATATCCTCGGAAGAGCGCCCCCAGGAGAAACAAACTTGACCACTATGCGATCATCAAGTTTCCACTG
ACCACTGAGTCTGCCAGGAAGAAGATAGAAGACAACAACACACTTGTGTTCATTGTGGATGTTAAAGCCAACAAGCACCA
GATCAAACAGGCTGTGAAGAAGCTCTATGACATTGATGTGGCCAAGGTCAACACCCTGATTCGGCCTGATGGAGAGAAGA
AGGCATATGTTCCACTGGCTCCTGATTACAATGCTTTGGATGTTGCAAACAAAATTGGGATCATCTAA

ORF - retro_cjac_30 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.04 %
Parental protein coverage: 98.08 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKAKKEAPAPPKAEAKAKALKAKKAVLKGVHSHKKKKIRTSPTFRRPKTLRLRRQPKYPRKSAPRRNKLDH
KAKKEAPAPPKAEAKAKALKAKKAVLKGVHSHKKKKIRTSPTFRRPKTLRLRRQPKYPRKSAPRRNKLDH
RetrocopyKAKKEAPAPPKAEAKAKALKAKKAVLKGVHSHKKKKIRTSPTFRRPKTLRLRRQPKYPRKSAPRRNKLDH
ParentalYAIIKFPLTTESAMKKIEDNNTLVFIVDVKANKHQIKQAVKKLYDIDVAKVNTLIRPDGEKKAYVRLAPD
YAIIKFPLTTESA.KKIEDNNTLVFIVDVKANKHQIKQAVKKLYDIDVAKVNTLIRPDGEKKAYV.LAPD
RetrocopyYAIIKFPLTTESARKKIEDNNTLVFIVDVKANKHQIKQAVKKLYDIDVAKVNTLIRPDGEKKAYVPLAPD
ParentalYDALDVANKIGII
Y.ALDVANKIGII
RetrocopyYNALDVANKIGII

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 .09 RPM 102 .31 RPM
SRP051959_heart 0 .04 RPM 111 .13 RPM
SRP051959_kidney 0 .22 RPM 140 .33 RPM
SRP051959_liver 0 .19 RPM 159 .53 RPM
SRP051959_lung 0 .23 RPM 140 .32 RPM
SRP051959_lymph_node 0 .34 RPM 242 .34 RPM
SRP051959_skeletal_muscle 0 .09 RPM 108 .73 RPM
SRP051959_spleen 0 .13 RPM 184 .29 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_30 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_30 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_30 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 20 parental genes, and 463 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000053112 retrocopies
Bos taurus ENSBTAG000000463946 retrocopies
Callithrix jacchus ENSCJAG00000013126 7 retrocopies
Dasypus novemcinctus ENSDNOG0000001948765 retrocopies
Felis catus ENSFCAG0000000402135 retrocopies
Homo sapiens ENSG0000019824257 retrocopies
Gorilla gorilla ENSGGOG0000001673626 retrocopies
Loxodonta africana ENSLAFG0000001338716 retrocopies
Myotis lucifugus ENSMLUG000000124484 retrocopies
Monodelphis domestica ENSMODG000000192973 retrocopies
Mustela putorius furoENSMPUG0000001417912 retrocopies
Mus musculus ENSMUSG000000585468 retrocopies
Nomascus leucogenys ENSNLEG0000000287260 retrocopies
Procavia capensis ENSPCAG0000001700230 retrocopies
Pongo abelii ENSPPYG0000000810849 retrocopies
Pteropus vampyrus ENSPVAG0000000292232 retrocopies
Rattus norvegicus ENSRNOG000000233446 retrocopies
Sarcophilus harrisii ENSSHAG0000001454913 retrocopies
Sus scrofa ENSSSCG000000177689 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000001132823 retrocopies



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