RetrogeneDB ID:

retro_btau_237

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:X:85898911..85899382(+)
Located in intron of:ENSBTAG00000012543
Retrocopy
information
Ensembl ID:ENSBTAG00000022278
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL23A
Ensembl ID:ENSBTAG00000046394
Aliases:RPL23A, RPL23AY
Description:60S ribosomal protein L23a [Source:UniProtKB/Swiss-Prot;Acc:Q24JY1]


Retrocopy-Parental alignment summary:






>retro_btau_237
ATGGCGCCGAAGGCGAAGAAGGAAGCCCCTGCTCCTCCTAAAGCTGAAGCCAAAGCAAAGGCTTTGAAGGCCAAGAAAGC
AGTGTTGAAAGGTGTCCACAGCCACAAAAAAAAGAAGATCCGGACGTCGCCCACCTTCCGGCGGCCCAAAACACTGCGGC
TCAGGAGGCAGCCCAAATACCCTCGGAAGAGCGCGCCTAGGAGAAACAAACTTGACCACTATGCCATCATCAAATTCCCC
CTCACCACCGAGTCAGCCATGAAGAAAATAGAAGACAACAACACACTGGTATTCATTGTGGACGTCAAGGCCAACAAGCA
CCAAATTAAACAGGCTGTGAAGAAGCTCTATGACATTGACGTGGCTAAGGTCAATACTCTGATCAGGCCTGATGGAGAGA
AGAAGGCATATGTTCGACTGGCTCCTGACTATGATGCTTTGGATGTTGCCAACAAAATTGGCATCATCTAA

ORF - retro_btau_237 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 100. %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAPKAKKEAPAPPKAEAKAKALKAKKAVLKGVHSHKKKKIRTSPTFRRPKTLRLRRQPKYPRKSAPRRNK
MAPKAKKEAPAPPKAEAKAKALKAKKAVLKGVHSHKKKKIRTSPTFRRPKTLRLRRQPKYPRKSAPRRNK
RetrocopyMAPKAKKEAPAPPKAEAKAKALKAKKAVLKGVHSHKKKKIRTSPTFRRPKTLRLRRQPKYPRKSAPRRNK
ParentalLDHYAIIKFPLTTESAMKKIEDNNTLVFIVDVKANKHQIKQAVKKLYDIDVAKVNTLIRPDGEKKAYVRL
LDHYAIIKFPLTTESAMKKIEDNNTLVFIVDVKANKHQIKQAVKKLYDIDVAKVNTLIRPDGEKKAYVRL
RetrocopyLDHYAIIKFPLTTESAMKKIEDNNTLVFIVDVKANKHQIKQAVKKLYDIDVAKVNTLIRPDGEKKAYVRL
ParentalAPDYDALDVANKIGII
APDYDALDVANKIGII
RetrocopyAPDYDALDVANKIGII

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
ERP005899_liver 0 .00 RPM 140 .95 RPM
ERP005899_muscle 0 .00 RPM 700 .04 RPM
SRP017611_brain 0 .00 RPM 79 .66 RPM
SRP017611_kidney 0 .06 RPM 164 .54 RPM
SRP017611_liver 0 .00 RPM 107 .15 RPM
SRP030211_testis 0 .00 RPM 54 .99 RPM
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_237 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_237 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_237 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 21 parental genes, and 467 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000053112 retrocopies
Bos taurus ENSBTAG00000046394 6 retrocopies
Callithrix jacchus ENSCJAG000000131267 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
Sus scrofa ENSSSCG000000298024 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000001132823 retrocopies



Copyright © RetrogeneDB 2014-2017