RetrogeneDB ID:

retro_itri_430

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393291.1:3739903..3740238(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL36A
Ensembl ID:ENSSTOG00000027251
Aliases:None
Description:ribosomal protein L36a [Source:HGNC Symbol;Acc:10359]


Retrocopy-Parental alignment summary:






>retro_itri_430
GCAGATAACGCTGCCGCAAACATGGTGAACGTTCCTAAGACCCGCCCCGACGTTCTGTAAGAAATGTGACAAACACCAAC
CCCATAAAGTGACAGTACAAGAAGGGCAAGGATTCTCTGTATGCACAGGGAAAGTGGCGGTATGACAGGAAACAGAGTGG
CTATGGTGGGCAGACCAAGCCAATTTTCAGGAAAAAGGCTGAAACTACAAAGAAGATTGTGCTGAGGGTTGAGTGTGTAG
AGCCTAGCTGAAGATCTAAAAGAATGCTGGCTATGAAGAGATGCAAGCATTTTGAACTGGGAGGAGATAAGAGAAAGGGC
CAAGTGACCCAGTTC

ORF - retro_itri_430 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.22 %
Parental protein coverage: 79.58 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalADNAAANMVNVPKTRR-TFCKKCGKHQPHKVTQYKKGK-DSLYAQGKRRYDRKQSGYGGQTKPIFRKKAK
ADNAAANMVNVPKTR..TFCKKC.KHQPHKVT....G..DSLYAQGK.RYDRKQSGYGGQTKPIFRKKA.
RetrocopyADNAAANMVNVPKTRP>TFCKKCDKHQPHKVT-VQEGQ>DSLYAQGKWRYDRKQSGYGGQTKPIFRKKAE
ParentalTTKKIVLRLECVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVIQF
TTKKIVLR.ECVEP..RSKRMLA.KRCKHFELGGD.KRKGQV.QF
RetrocopyTTKKIVLRVECVEPS*RSKRMLAMKRCKHFELGGD-KRKGQVTQF

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_430 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_430 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 10 parental genes, and 82 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000085031 retrocopy
Callithrix jacchus ENSCJAG000000048644 retrocopies
Homo sapiens ENSG0000024134314 retrocopies
Monodelphis domestica ENSMODG000000255782 retrocopies
Mus musculus ENSMUSG000000794351 retrocopy
Pongo abelii ENSPPYG0000002583737 retrocopies
Pteropus vampyrus ENSPVAG000000015691 retrocopy
Rattus norvegicus ENSRNOG000000114941 retrocopy
Sarcophilus harrisii ENSSHAG000000134791 retrocopy
Ictidomys tridecemlineatus ENSSTOG00000027251 20 retrocopies



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