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 symbol: TTC14
• Ensembl ID: ENSSTOG00000003827
• Aliases: None
• Description: tetratricopeptide repeat domain 14 [Source:HGNC Symbol;Acc:24697]

Sequence

>retro_itri_1061
ATGGATGGGGACCTTCTGGGGCAGTTGCTAAATTACCACCTGTGGTCATTGCTGTCCTTGCTATGCCAGAATGAATAACA
GGACAATCAGTACTTCTAGAGCCTTCTATGTTGGGTATCAGAGCCTGCTGGAGGCTGCTGTCCAAGTAGCATTTACATGG
CAGAAAAGAGAATAGAGTTAATTAACAATATTGAGATACAAAAATTCATCTCCAAAAAAGCAGATTAACTTTTTGCACTT
TCCTAGAAATCAGATGTACCTACAACTTCTAAAGTTAATGAAGACAATGTAGATCATTATGCAGTCATCCCACTTTTAAA
GCAAGTCATGGGAATATTTAATGTGGAGGGGAATGAGCTGTTTTTCCAAGATATTGAAAATGGTGATGTAGTGATTGAAA
GAATTAATTCTACTTTGGGAATTTTGTTTTTTCATTGTATTAATCTGTTTAGGAAGTGGCATCACCAGAGACATATACCA
CTTAGAAATCACAGTTCTTTGTCCATTAAGAGATATGCCTTTTCACAGTCACCATGGGGATCCTTTATCATATTACCAAA
CTGTGACATTATTCAAAATGGAATCAAGGATTTTGGCAGATTTCATGAAAAACTAGCAGTGTCTCTTTATAGCTCATCTC
TTTCGTCACACCTATTTGGTTATTAAACTAGGTGTAATTACTTCTGAAGAGCTTCCTTTGTAATATAGGAGGAGTGTTGA
ACTAAATAGCAATTCTCTAGATTCCTATGAAAATATTATACAGAGATCTCTGGGATTTGTTAATCCAGAATTAGTTGAAT
TCCTTCTGGGAAAACCAGGATTAGATGAATCTAATACATCATCTTTAATGAGAAGTCTATAAAGCAAAAATTTCTCTGAA
GATGATTTTGCTCCTGCATTAAGAAAAAATTTGTCTGCAGTTAGGCTTTAATATGTGTGAATACTGGAGTTAACTATTTT
AAGGTTTAATGCCATGTGGATGGTATGAATGGATACAGTAAAACTCCGGAAATAGATAAGCAAAATGTGGAAGGTTTGGT
AGCTCAAGGAACATTATACATGACAAAGGGAAATCTAAAAAAGTCCAGAAGATTTTAAGCTTGCATTAGAAAACTGTCCA
ACTCACAGGAATGCAAGAAAATACCTCTGCCAACTACTTGTAGAAGGAGGAGGGCAGTTAGAAGAAGAAAACTTTTTAAA
TTCTGAAAGTTACTATAAGAAAGTTTTGGTTTTGGATGAGATTTTAAAGATACAGAGGACGATTTGCAGAAACTTTATAA
ATATATGCAGAGA

Alignment

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

Expression

RNA-Seq

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

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1061 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1061 was not experimentally validated.

Homology

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.

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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 ,