RetrogeneDB ID:

retro_itri_121

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393551.1:126287..126728(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSTOG00000020032
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSSTOG00000020231
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_itri_121
AGTTCAACTATTTACGACTGTGTTTCTTTTTTAACCTCAGTTTTGGAGGAATTAGATCAGATAAAAACTAGAAGAGAGGA
AGAAAAGAAACAAAAAGAAAGAGAAGCAGAAGAAGCACAAAAGCAACTATCCCATGGCACTCCTGTTACAATAGAGAATT
TTTCAAGTTGGAAGGCCAAGTTTGATGCAGAACTTTTGGAAATTAAAAAGAAATGGATGAAAGAAGAAGAGCAAGCAGGA
AAAAATAAATTAAGTGGGAAACAGCTATTTGAAACAGATCATAATCTTGACACATCTGATATCCAGTTCTTGGAGGATGC
TGGAAACAATGTGGAGGTAGATGAGTCTTTGTTCCAGGAAATGAACGACTTGGAGCTGGAGGATGATGAAGATGATCCAG
ACTACAATCCCGCTGACCCAGGGAGTGACTCAGCAGACTAA

ORF - retro_itri_121 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.19 %
Parental protein coverage: 68.9 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalIFTLVTAVQEKLNEIVDQIKTRREEEKKQKEREAEEAEKQLFHGTPVTIENFLSWKAKFDAELLEIKKKR
I...V......L.E..DQIKTRREEEKKQKEREAEEA.KQL.HGTPVTIENF.SWKAKFDAELLEIKKK.
RetrocopyIYDCVSFLTSVLEEL-DQIKTRREEEKKQKEREAEEAQKQLSHGTPVTIENFSSWKAKFDAELLEIKKKW
ParentalMKEEEQAGKNKLSGKQLFETDHNLDTSDIQFLEDAGNNVEVDESLFQEMDDLELEDDEDDPDYNPADPGS
MKEEEQAGKNKLSGKQLFETDHNLDTSDIQFLEDAGNNVEVDESLFQEM.DLELEDDEDDPDYNPADPGS
RetrocopyMKEEEQAGKNKLSGKQLFETDHNLDTSDIQFLEDAGNNVEVDESLFQEMNDLELEDDEDDPDYNPADPGS
ParentalDSAD
DSAD
RetrocopyDSAD

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.
Ictidomys tridecemlineatus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_itri_121 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_121 was not experimentally validated.

Retrocopy orthology:
Ictidomys tridecemlineatus 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 13 parental genes, and 18 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000056921 retrocopy
Bos taurus ENSBTAG000000096891 retrocopy
Callithrix jacchus ENSCJAG000000044741 retrocopy
Dasypus novemcinctus ENSDNOG000000075161 retrocopy
Equus caballus ENSECAG000000065872 retrocopies
Echinops telfairi ENSETEG000000190853 retrocopies
Loxodonta africana ENSLAFG000000081701 retrocopy
Monodelphis domestica ENSMODG000000178371 retrocopy
Oryctolagus cuniculus ENSOCUG000000135921 retrocopy
Procavia capensis ENSPCAG000000050161 retrocopy
Ictidomys tridecemlineatus ENSSTOG00000020231 2 retrocopies
retro_itri_121 , retro_itri_365,
Ictidomys tridecemlineatus ENSSTOG000000221241 retrocopy
Tupaia belangeri ENSTBEG000000025432 retrocopies



Copyright © RetrogeneDB 2014-2017