RetrogeneDB ID:

retro_btau_550

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:14:67172755..67173300(+)
Located in intron of:ENSBTAG00000012357
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:BT.62437
Ensembl ID:ENSBTAG00000002949
Aliases:None
Description:chromobox protein homolog 1 [Source:RefSeq peptide;Acc:NP_001193344]


Retrocopy-Parental alignment summary:






>retro_btau_550
ATGGGGAAAAAGAAAACCAGATGAAAGTGGAGGGAGGTGCTAGAATAAGAGAAAGAAAATCTGTGGTGGAAAAAGTTCCA
GACTGCCCAGTGGTACACGGCAAAGTGGTATACCTCCGAAGTGGAAGGGGTTCTCAGAGGACAATGCATGGAGCAGAAGA
GAACCTGGAATGCCCTGGCCTCATTGCCAAGTTTCTGCATTTACAGAAGAAAGCACACAGGACAAATAAATCAGAGAGAG
GTAAGCACAAACCTGATTCTGATTCTGATTTGGAAAATAAGGTGGAAGACAGCAAACCAAACAAGAAGAAAGAAGAGTCA
GAAAACCCATGAGGCTTTGCCCAGGGTTTGGAACTGGAACAGGCTACTGGAGCGACAGACTCCAGTGGAGAACTCATGCT
TCAGGTGAATTGGAAATACTCTGATGCCACCGACTTGGTCCCTGCCAAGGTCAAGCACCCATAGATAGTCATATACCTCT
ATAAGGAAAGGCTGACTTGGCATTCCTACCCCTCAGAGGATGATGACAAAAACAATGACAGGAAT

ORF - retro_btau_550 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 61.17 %
Parental protein coverage: 100. %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMGKKQNKKKVEEVLEEEEEEY-VVEKVLDRRVVKGKVEYLLKWKGFSDEDNTWEPEENLDCPDLIAEFLQ
MGKK....K..EVLE.E.E...VVEKV.D..VV.GKV.YL....G..........EENL.CP.LIA.FL.
RetrocopyMGKKKTR*KWREVLE*EKENL<VVEKVPDCPVVHGKVVYLRS--GRGSQRTMHGAEENLECPGLIAKFLH
ParentalSQKTAHETDKSEGGKRKADSDS--EDKGEESKPKKKKEESEKPRGFARGLEPERIIGATDSSGELMFLMK
.QK.AH.T.KSE.GK.K.DSDS..E.K.E.SKP.KKKEESE.P.GFA.GLE.E...GATDSSGELM....
RetrocopyLQKKAHRTNKSERGKHKPDSDSDLENKVEDSKPNKKKEESENP*GFAQGLELEQATGATDSSGELMLQVN
ParentalWKNSDEADLVPAKEANVKCPQVVISFYEERLTWHSYPSEDDDKKDDKN
WK.SD..DLVPAK...VK.P..VI..Y.ERLTWHSYPSEDDDK..D.N
RetrocopyWKYSDATDLVPAK---VKHP*IVIYLYKERLTWHSYPSEDDDKNNDRN

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 0 .72 RPM
ERP005899_muscle 0 .16 RPM 6 .18 RPM
SRP017611_brain 0 .09 RPM 8 .72 RPM
SRP017611_kidney 0 .06 RPM 9 .01 RPM
SRP017611_liver 0 .00 RPM 2 .87 RPM
SRP030211_testis 0 .01 RPM 20 .91 RPM
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_550 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_550 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_550 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 17 parental genes, and 51 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000048902 retrocopies
Bos taurus ENSBTAG00000002949 9 retrocopies
Callithrix jacchus ENSCJAG000000075322 retrocopies
Dipodomys ordii ENSDORG000000007162 retrocopies
Erinaceus europaeus ENSEEUG000000048743 retrocopies
Echinops telfairi ENSETEG000000002037 retrocopies
Felis catus ENSFCAG000000060561 retrocopy
Myotis lucifugus ENSMLUG000000050302 retrocopies
Mus musculus ENSMUSG000000186661 retrocopy
Oryctolagus cuniculus ENSOCUG000000080213 retrocopies
Otolemur garnettii ENSOGAG000000056589 retrocopies
Ochotona princeps ENSOPRG000000036991 retrocopy
Pongo abelii ENSPPYG000000088911 retrocopy
Rattus norvegicus ENSRNOG000000086892 retrocopies
Sarcophilus harrisii ENSSHAG000000081921 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000239863 retrocopies
Tarsius syrichta ENSTSYG000000047692 retrocopies



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