RetrogeneDB ID:

retro_btau_485

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:12:3436364..3436635(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:C21H15ORF40
Ensembl ID:ENSBTAG00000016522
Aliases:C21H15orf40, C15orf40
Description:UPF0235 protein C15orf40 homolog [Source:RefSeq peptide;Acc:NP_001068854]


Retrocopy-Parental alignment summary:






>retro_btau_485
ACCATAGCCATCCATGCCAAAGCTGGTTCCAAACAAAATGCCGGTGACAGACGTGACAACCGAGGCTGTGAGTGTAGACA
TCACAGCGCCTCCGACCGAGGGAGAGGCCAACGCAGAGCTGTACCTCTGTCTTTCCAAGGTCTTAGAACTCGGGAAGAGT
GATGTGGTTTTGGATAAGGGCGGTAAATCTCCTGAAAAAGTGGTCAGGCTTTTGGCCTCCACACCTCCAGAAGAGATCTT
GGAGAAACTGAAAAAGCAAGTTGAAAATAAA

ORF - retro_btau_485 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.81 %
Parental protein coverage: 68.18 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalSIAIHAKPGSKQNA-VTDVTTEAVSVAIAAPPTEGEANAELCRYLSKVLELRKSDVVLDKGGKSREKVVK
.IAIHAK.GSKQNA.VTDVTTEAVSV.I.APPTEGEANAEL...LSKVLEL.KSDVVLDKGGKS.EKVV.
RetrocopyTIAIHAKAGSKQNA>VTDVTTEAVSVDITAPPTEGEANAELYLCLSKVLELGKSDVVLDKGGKSPEKVVR
ParentalLLASTPPEEILEKLKKQVEKK
LLASTPPEEILEKLKKQVE.K
RetrocopyLLASTPPEEILEKLKKQVENK

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
ERP005899_liver 0 .00 RPM 12 .47 RPM
ERP005899_muscle 0 .00 RPM 8 .97 RPM
SRP017611_brain 0 .00 RPM 12 .56 RPM
SRP017611_kidney 0 .00 RPM 19 .38 RPM
SRP017611_liver 0 .00 RPM 7 .78 RPM
SRP030211_testis 0 .00 RPM 15 .66 RPM

ChIP-Seq - click to see more details

Bos taurus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_btau_485 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_485 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_485 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 19 parental genes, and 30 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG00000016522 2 retrocopies
retro_btau_1724, retro_btau_485 ,
Canis familiaris ENSCAFG000000131852 retrocopies
retro_cfam_39, retro_cfam_420,
Callithrix jacchus ENSCJAG000000158772 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,


Copyright © RetrogeneDB 2014-2017