RetrogeneDB ID:

retro_itri_200

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393279.1:14926842..14927424(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL19
Ensembl ID:ENSSTOG00000011120
Aliases:None
Description:ribosomal protein L19 [Source:HGNC Symbol;Acc:10312]


Retrocopy-Parental alignment summary:






>retro_itri_200
ATGCTCAAGCTTCAAAAGAGAATTGCCTCCAGTGTCCTCTGCTGTGGCAAAAAGAAGGTCTGGTTGAGACCCCAAGGAGA
CCAATGAAATCGCGAGTGCCAACTCTTGTTAGCAGATCTGGAAGATCAAAGAAGGACTGATCATCCACAAACCAGTGACT
GTCCATTCACTCACTGATGCCAGGAAAAAAAATACCTTGCCTCCCTGGAAGGGCAGGCATAGAGGCAAAGGTAAGCGAAA
AGATACAGCTAATGTTCAAATGCCAGAGAAGGTAACCTGGATGAGAAGGATGCAGATTCTTCAGAGGCTACTCCAGAGAT
ACCCTGAATCTAAGAAGATTGACCAGACACAAGCATCACAGTCTCTACCTGAAGGTAAAGGGGAATGTGTTCAAAAACAA
GCAGATCCTCCTGGAACACATCCATAAACTGAAAGGAGATAAGGCCCAAGAGAAACCACTAGCTGACCAGGCTGAGGTTC
GGAGATCTAAGACCAGAGGGGCACGAAAACCATGAGGAGTACATCTAGGACAAGAAGGAAGAGACCATCAAGACACTGTC
CAAAGAGGATGAGAATAAGAAA

ORF - retro_itri_200 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.72 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMLRLQKRLASSVLRCGKKKVWL-DPNETNEIANANSRQQIRKLIKDGLIIRKPVTVHSRARCRKN-TLAR
ML.LQKR.ASSVL.CGKKKVWL.DP.ETNEIA.ANS..QI.K.IK.GLII.KPVTVHS....R...TL..
RetrocopyMLKLQKRIASSVLCCGKKKVWL>DPKETNEIASANSC*QIWK-IKEGLIIHKPVTVHSLTDARXXXTLPP
ParentalRKGRHMGIGKRKGTANARMPEKVTWMRRMRILRRLLRRYRESKKID-RHMYHSLYLKVKGNVFKNKRILM
.KGRH.G.GKRK.TAN..MPEKVTWMRRM.IL.RLL.RY.ESKKID.RH..HSLYLKVKGNVFKNK.IL.
RetrocopyWKGRHRGKGKRKDTANVQMPEKVTWMRRMQILQRLLQRYPESKKID>RHKHHSLYLKVKGNVFKNKQILL
ParentalEHIHKLKADKARKKLLADQAEARRSKTKEARK-RREERLQAKKEEIIKTLSKEEETKK
EHIHKLK.DKA..K.LADQAE.RRSKT..ARK...E.....K.E.I.KTLSKE.E.KK
RetrocopyEHIHKLKGDKAQEKPLADQAEVRRSKTRGARK>HEEYI*DKKEETI-KTLSKEDENKK

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_200 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_200 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 8 parental genes, and 104 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000085204 retrocopies
Equus caballus ENSECAG000000250806 retrocopies
Myotis lucifugus ENSMLUG0000001255511 retrocopies
Macaca mulatta ENSMMUG000000042352 retrocopies
Nomascus leucogenys ENSNLEG0000000074819 retrocopies
Pongo abelii ENSPPYG0000000849220 retrocopies
Rattus norvegicus ENSRNOG0000000474137 retrocopies
Ictidomys tridecemlineatus ENSSTOG00000011120 5 retrocopies



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