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:
| Parental | QNEFLSTPPRSLRK-RLIVPRSHSDSESEYSASNSEDDEGVAQEYEESTNAVTFRQKIEAQNTVVSASVC |
| ..E.LST...SLRK.R...P...SDS.SEYSASNS.D.EGVA.E.....NAVT..QKI.A.N.VVSA.VC | |
| Retrocopy | KSESLSTLVHSLRK<R*TFPSTRSDSQSEYSASNSKDEEGVAKEH----NAVTSSQKIQAHNRVVSAPVC |
| Parental | KGTPSKKMKRDKRNDLVEEYFEAHSSSKVLTSDRTLQKLKKAKLDQQTLRNLLSKVSPSFSAELKQLNQQ |
| K.T.S...KR.K.NDLV.EYFEAHS....L..DRTL.KLK..K..Q..........S...SAE..QLNQ. | |
| Retrocopy | KETTSRE*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 |
| Parental | HMGTFRSVLDQLDWIINKFKEDSSLKLFLLIHNLDSQMLRGEKSQQIIGQLSSL----HNIY |
| .MG...SV.DQL.WIINKFKEDSSLK.FLL.HNL.SQM..G..SQ.I.....S.....H.IY | |
| Retrocopy | CMGDLWSVPDQLEWIINKFKEDSSLKFFLLVHNLYSQMMGGDNSQHISRVATSM*HTPHSIY |
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_1042 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
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 ,
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