RetrogeneDB ID:

retro_itri_1042

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393361.1:5133076..5133869(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ORC2
Ensembl ID:ENSSTOG00000009599
Aliases:None
Description:origin recognition complex, subunit 2 [Source:HGNC Symbol;Acc:8488]


Retrocopy-Parental alignment summary:






>retro_itri_1042
AAATCTGAATCTCTGTCAACACTTGTCCATAGTCTAAGGAAAGATGAACATTTCCAAGCACTCGTTCTGACAGCCAAAGT
GAATATTCTGCTTCCAACTCCAAGGATGAGGAAGGGGTTGCTAAGGAACATAATGCAGTCACGTCTAGTCAAAAGATTCA
AGCTCACAACAGAGTAGTTTCAGCTCCTGTTTGCAAAGAAACAACTTCAAGAGAATAAAAAAGAGAGAAAACAAATGATT
TAGTTCAAGAATATTTTGAAGCTCATAGCTGTTTAGAAATTTTAGCCTTCGATAGAACATTGAAGAAGCTAAAGAGAGAC
AAAACCGGTCAGAAGTTTGTGCAATTTATTGAGCAAGATTCTCTTTTGTTGTCTGCTGAATGTGAACAACTAAATCAACA
CATGAAAAATCATTTCATAAAAGGATGCTGCAGTTCCGTCTTGGGTTCTACATGGTACTTTATGATTTGGGTCCTAGGAG
AAATTTACTAGAAAGGTTTTGAAACACCAGGCTGCAAGATATTACTACTCGTGCTGTCATCAATGTCTTCCTTCCTGGAG
TCAGTGTGAGATCAGTCCTGAATTATATAACAGAAGAAATGTTTGACTGTATGGGTGATCTCTGGAGTGTACCAGATCAG
TTAGAGTGGATAATCAACAAATTTAAAGAAGATTCCTCTTTGAAATTCTTTCTTCTCGTCCACAATTTGTATAGCCAAAT
GATGGGAGGGGATAACAGCCAGCATATTAGTAGAGTTGCCACCTCTATGTAACATACACCTCATAGCATCTAC

ORF - retro_itri_1042 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 57.35 %
Parental protein coverage: 62.06 %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalQNEFLSTPPRSLRK-RLIVPRSHSDSESEYSASNSEDDEGVAQEYEESTNAVTFRQKIEAQNTVVSASVC
..E.LST...SLRK.R...P...SDS.SEYSASNS.D.EGVA.E.....NAVT..QKI.A.N.VVSA.VC
RetrocopyKSESLSTLVHSLRK<R*TFPSTRSDSQSEYSASNSKDEEGVAKEH----NAVTSSQKIQAHNRVVSAPVC
ParentalKGTPSKKMKRDKRNDLVEEYFEAHSSSKVLTSDRTLQKLKKAKLDQQTLRNLLSKVSPSFSAELKQLNQQ
K.T.S...KR.K.NDLV.EYFEAHS....L..DRTL.KLK..K..Q..........S...SAE..QLNQ.
RetrocopyKETTSRE*KREKTNDLVQEYFEAHSCLEILAFDRTLKKLKRDKTGQKFVQ-FIEQDSLLLSAECEQLNQH
Parental-YEKLFHKWMLQLHLGFNIVLYGLGSKRDLLERFRTTMLQD-SIHVVINGFFPGISVKSILNSITEEVLD
..EK.FHK.MLQ..LGF..VLY.LG..R.LLERF..T.LQD.....VIN.F.PG.SV.S.LN.ITEE..D
Retrocopy<HEKSFHKRMLQFRLGFYMVLYDLGPRRNLLERF*NTRLQDITTRAVINVFLPGVSVRSVLNYITEEMFD
ParentalHMGTFRSVLDQLDWIINKFKEDSSLKLFLLIHNLDSQMLRGEKSQQIIGQLSSL----HNIY
.MG...SV.DQL.WIINKFKEDSSLK.FLL.HNL.SQM..G..SQ.I.....S.....H.IY
RetrocopyCMGDLWSVPDQLEWIINKFKEDSSLKFFLLVHNLYSQMMGGDNSQHISRVATSM*HTPHSIY

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






RNA-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_itri_1042 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_1042 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 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Ictidomys tridecemlineatus ENSSTOG00000009599 1 retrocopy
retro_itri_1042 ,




Copyright © RetrogeneDB 2014-2017