RetrogeneDB ID:

retro_eeur_447

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_307043:7490..7794(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:BTF3L4
Ensembl ID:ENSEEUG00000004502
Aliases:None
Description:basic transcription factor 3-like 4 [Source:HGNC Symbol;Acc:30547]


Retrocopy-Parental alignment summary:






>retro_eeur_447
GTGAATATGATTAAAGATGATGGGACAGTTATTCATTTCAACAAGCCCTGAAGCCCAAGCTTCCCTTTCTGCTAATACCT
TCATAATAACTGGTCATGCAGAAGCCAAACCAATCACAGAAATGCTTCCTGGAATATTAAGTCAGTTTGGTGCTGACAGT
TTAACAAGCCTTAGGAAGTGAGCTGAACAGTTCCCTAGGCAAGTGTCAGATAGCAAAGCACCACAACCTGTAGACATTGA
TGAGGACGACGTTTTTCCAGATCTTATAGAAAATTTTGATGAGGCATCAACGAATGAAGCCAAC

ORF - retro_eeur_447 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.44 %
Parental protein coverage: 64.56 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalVNMIKDDGTVIHFN-NPKVQASLSANTFAITGHAEAKPITEMLPGILSQLGADSLTSLRKLAEQFPRQVL
VNMIKDDGTVIHFN..P..QASLSANTF.ITGHAEAKPITEMLPGILSQ.GADSLTSLRK.AEQFPRQV.
RetrocopyVNMIKDDGTVIHFN>SPEAQASLSANTFIITGHAEAKPITEMLPGILSQFGADSLTSLRK*AEQFPRQVS
ParentalDSKAPKPEDIDEEDDDVPDLVENFDEASKNEAN
DSKAP.P.DID.EDD..PDL.ENFDEAS.NEAN
RetrocopyDSKAPQPVDID-EDDVFPDLIENFDEASTNEAN

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
SRP017611_brain 1 .29 RPM 22 .08 RPM
SRP017611_kidney 0 .38 RPM 24 .94 RPM
SRP017611_liver 0 .80 RPM 12 .54 RPM
Erinaceus europaeus was not studied using ChIP-Seq data.
Erinaceus europaeus was not studied using EST data.
Erinaceus europaeus was not studied using FANTOM5 data.
retro_eeur_447 was not experimentally validated.

Retrocopy orthology:
Erinaceus europaeus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

Parental genes homology:
Parental genes homology involve 21 parental genes, and 98 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000215824 retrocopies
Cavia porcellus ENSCPOG000000040061 retrocopy
Ciona savignyi ENSCSAVG000000096531 retrocopy
Dasypus novemcinctus ENSDNOG000000031814 retrocopies
Erinaceus europaeus ENSEEUG00000004502 3 retrocopies
retro_eeur_215, retro_eeur_447 , retro_eeur_456,
Echinops telfairi ENSETEG0000001192311 retrocopies
Homo sapiens ENSG000001347173 retrocopies
Loxodonta africana ENSLAFG000000161243 retrocopies
Macropus eugenii ENSMEUG0000000613510 retrocopies
Microcebus murinus ENSMICG000000028071 retrocopy
Myotis lucifugus ENSMLUG000000168841 retrocopy
Macaca mulatta ENSMMUG000000036361 retrocopy
Monodelphis domestica ENSMODG000000007702 retrocopies
Mus musculus ENSMUSG000000285682 retrocopies
Nomascus leucogenys ENSNLEG000000160412 retrocopies
Oryctolagus cuniculus ENSOCUG000000015173 retrocopies
Procavia capensis ENSPCAG000000064283 retrocopies
Pongo abelii ENSPPYG000000013532 retrocopies
Pan troglodytes ENSPTRG000000007353 retrocopies
Rattus norvegicus ENSRNOG000000085128 retrocopies
Tupaia belangeri ENSTBEG0000001330730 retrocopies



Copyright © RetrogeneDB 2014-2017