RetrogeneDB ID: | retro_itri_1061 | ||
Retrocopy location | Organism: | Squirrel (Ictidomys tridecemlineatus) | |
| Coordinates: | JH393366.1:838781..840074(+) | ||
| Located in intron of: | ENSSTOG00000001080 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TTC14 | ||
| Ensembl ID: | ENSSTOG00000003827 | ||
| Aliases: | None | ||
| Description: | tetratricopeptide repeat domain 14 [Source:HGNC Symbol;Acc:24697] |
Retrocopy-Parental alignment summary:
>retro_itri_1061
ATGGATGGGGACCTTCTGGGGCAGTTGCTAAATTACCACCTGTGGTCATTGCTGTCCTTGCTATGCCAGAATGAATAACA
GGACAATCAGTACTTCTAGAGCCTTCTATGTTGGGTATCAGAGCCTGCTGGAGGCTGCTGTCCAAGTAGCATTTACATGG
CAGAAAAGAGAATAGAGTTAATTAACAATATTGAGATACAAAAATTCATCTCCAAAAAAGCAGATTAACTTTTTGCACTT
TCCTAGAAATCAGATGTACCTACAACTTCTAAAGTTAATGAAGACAATGTAGATCATTATGCAGTCATCCCACTTTTAAA
GCAAGTCATGGGAATATTTAATGTGGAGGGGAATGAGCTGTTTTTCCAAGATATTGAAAATGGTGATGTAGTGATTGAAA
GAATTAATTCTACTTTGGGAATTTTGTTTTTTCATTGTATTAATCTGTTTAGGAAGTGGCATCACCAGAGACATATACCA
CTTAGAAATCACAGTTCTTTGTCCATTAAGAGATATGCCTTTTCACAGTCACCATGGGGATCCTTTATCATATTACCAAA
CTGTGACATTATTCAAAATGGAATCAAGGATTTTGGCAGATTTCATGAAAAACTAGCAGTGTCTCTTTATAGCTCATCTC
TTTCGTCACACCTATTTGGTTATTAAACTAGGTGTAATTACTTCTGAAGAGCTTCCTTTGTAATATAGGAGGAGTGTTGA
ACTAAATAGCAATTCTCTAGATTCCTATGAAAATATTATACAGAGATCTCTGGGATTTGTTAATCCAGAATTAGTTGAAT
TCCTTCTGGGAAAACCAGGATTAGATGAATCTAATACATCATCTTTAATGAGAAGTCTATAAAGCAAAAATTTCTCTGAA
GATGATTTTGCTCCTGCATTAAGAAAAAATTTGTCTGCAGTTAGGCTTTAATATGTGTGAATACTGGAGTTAACTATTTT
AAGGTTTAATGCCATGTGGATGGTATGAATGGATACAGTAAAACTCCGGAAATAGATAAGCAAAATGTGGAAGGTTTGGT
AGCTCAAGGAACATTATACATGACAAAGGGAAATCTAAAAAAGTCCAGAAGATTTTAAGCTTGCATTAGAAAACTGTCCA
ACTCACAGGAATGCAAGAAAATACCTCTGCCAACTACTTGTAGAAGGAGGAGGGCAGTTAGAAGAAGAAAACTTTTTAAA
TTCTGAAAGTTACTATAAGAAAGTTTTGGTTTTGGATGAGATTTTAAAGATACAGAGGACGATTTGCAGAAACTTTATAA
ATATATGCAGAGA
ORF - retro_itri_1061 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 65.6 % |
| Parental protein coverage: | 55.97 % |
| Number of stop codons detected: | 9 |
| Number of frameshifts detected: | 6 |
Retrocopy - Parental Gene Alignment:
| Parental | MDRDLLRQSLNCHGSSLLSLL-RNEQQDNPHFRSLLGSASEPARGPPPQQ-HLQGRKEKRVDIIEIQKFI |
| MD.DLL.Q.LN.H..SLLSLL..NE.QDN..F.SLL...SEPA.G..P...............IEIQKFI | |
| Retrocopy | MDGDLLGQLLNYHLWSLLSLLCQNE*QDNQYF*SLLCWVSEPAGGCCPSSIYMAEKRIELINNIEIQKFI |
| Parental | SKKADLLFALSWKSDAPATSEVNEDNEDHYAVMPPLEQFMEIPSMDRRELFFRDIERGDIVIGRISS-IR |
| SKKAD.LFALS.KSD.P.TS.VNEDN.DHYAV.P.L.Q.M.I......ELFF.DIE.GD.VI.RI.S... | |
| Retrocopy | SKKAD*LFALS*KSDVPTTSKVNEDNVDHYAVIPLLKQVMGIFNVEGNELFFQDIENGDVVIERINS>LW |
| Parental | EFGFFMVLICLGSGIMRDISHLEITALCPLRDVPSHSNHGDPLSYYQT-GDIIRAGIKDIDRYHEKLAVS |
| EF.FF.VLICLGSGI.RDI.HLEIT.LCPLRD.P.HS.HGDPLSYYQT..DII..GIKD..R.HEKLAVS | |
| Retrocopy | EFCFFIVLICLGSGITRDIYHLEITVLCPLRDMPFHSHHGDPLSYYQT<CDIIQNGIKDFGRFHEKLAVS |
| Parental | LYSSALPPHLSG-IKLGVITSEELPLYYRRSVELNSNSLESYENIMQSSLGFVNPGVVEFLLEKLGIDES |
| LYSS.L..HL.G.IKLGVITSEELPL.YRRSVELNSNSL.SYENI.Q.SLGFVNP..VEFLL.K.G.DES | |
| Retrocopy | LYSSSLSSHLFG>IKLGVITSEELPL*YRRSVELNSNSLDSYENIIQRSLGFVNPELVEFLLGKPGLDES |
| Parental | NPPSLMRGLQSKNFSEDDYASALRKKQSA-SWALKCVKIGVDYFKVGRHVDAMNEYNKALEIDKQNVEAL |
| N..SLMR.L.SKNFSEDD.A.ALRK..SA.S.AL.CV..GV.YFKV..HVD.MN.Y.K..EIDKQNVE.L | |
| Retrocopy | NTSSLMRSL*SKNFSEDDFAPALRKNLSA<S*ALICVNTGVNYFKV*CHVDGMNGYSKTPEIDKQNVEGL |
| Parental | VARGALYATKGSLNKAIEDFELALENCPTHRNARKYLCQTLVER-GGQLEEEEKFLNAESYYKKALALDE |
| VA.G.LY.TKG.L.K....F..............K....T...R.GGQL.EEE.FLN.ESYYKK.L.LDE | |
| Retrocopy | VAQGTLYMTKGNLKKS-RRF*ACIRKLSNSQECKKIPLPTTCRR>GGQL-EEENFLNSESYYKKVLVLDE |
| Parental | -TFKDAEDALQKLHKYMQK |
| ..FKD.ED.LQKL.KYMQ. | |
| Retrocopy | <DFKDTEDDLQKLYKYMQR |
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_1061 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_1061 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 | ENSSTOG00000003827 | 1 retrocopy |
retro_itri_1061 ,
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