RetrogeneDB ID: retro_itri_653

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393309.1:11696411..11697707(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: SEC23A
• Ensembl ID: ENSSTOG00000013426
• Aliases: None
• Description: Sec23 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:10701]

Sequence

>retro_itri_653
AAAATAATTTTGAATCTTTTGTGTCAAGTGGATTATTGAGCAAAGCTCTGGTCTTGCAACTTTTCTTATCAAAATATCAG
TTTCTAACTACTTATGCTGGGATATCTAAACTGAATCAGTATGCTGAACATTTGCCTCAGTTCTCTCGCATTGAATATGT
AGTTCTGTGTGGTCCTCAGAAACCTTTGATATTCCTCTATGTGGTTGATACTTGCATGGAACATGAAGATTTACAAGCCT
TAATAGAATCCATGCAGATATCACTAAGTCTCCTATCACCTAGAGCTTTGATTTGCCTTTGGGGAGGAATGTGCAGGTTC
ATAAACTTGGATGTGAACGTATTTCAAAAAGCTATGTCTTCAAGGGAACAAAAGATGGTTTTCCAAACAACTGTAGGAGA
TGCTGGGACCCTCTAGAGTACCACTTACTCAAGCAACACATGGTCCTCAGGTACAGCAGCCACATGCATCCAATAAATTT
TTTATAGCCACTACAGAATATAGACATGAATCTCCCATATCTTCTGGGAGAACAGCAGTGAGACCCTTGGCCTATATTAC
AGGGAAAGGGACCTTTGTGTACCTCAGAAATGGCACTTTGCATAGCTGTAGGACTAATCAAGTGTATTTTCCCCAACGCT
GGTGCTCATATTATGATGTCCATGGGTGGTCTTGCTATTCAAGCAGCTAGAATGGTGGTTGGAGATGAATTGATGATGCC
TAGAAGATCATGGCATGATATTGAAAAAGACAATGTCAAGTATGTTTAAAAAGGACCCAAGCATTTTGAAGAACTGGCTA
ATCAAGCTGCTACAACTCGTCATGTTATTGACATCTATGCATGTGCATTAGATCAGACAGGTCTCTTGCAGATAAAATGC
TGTTCCAACCTTACTGGTGAAAACATGGTAATGGGAGATTCTTTTAACACTTCCTTATCAAACAAACTTTTCAAACAGTC
TTTCCCAAAGATATTCATGAACAGTTTAAAATGAGCTTTGGTGGTGCATTAGAAATAAACACTTTAAGGGAAATAAAAAT
TTCAGGAGCAATTGGACCCTGTGTGTCTCTCAATTCAAAAGGACCCTGTATGCCTGCAAAATGTGATAGGAATGTGTGGC
ATTTGTCAAGGTAAGTTATGCAGATTCTATCTCACTACAACCTTAGCTATGTATTTTGGTGTTGTTAATCAGCATAATGC
TCCAATTCTTCATGGTGGACATTGTGCAATCCAGTTTGTGACATGGTATCATCATGCAATGGGCAGAGATGCATCAGAGT
GACCACCATTACTAGG

Alignment

ORF - retro_itri_653 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.95 %
• Parental protein coverage: 86.83 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  RAVLNPLCQVDYRAKLWACNFCYQ-RNQFPPTYAGISELNQPAELLPQFSSIEYVVLRGPQMPLIFLYVV
          ...LN.LCQVDY.AKLW.CNF.YQ...QF..TYAGIS.LNQ.AE.LPQFS.IEYVVL.GPQ.PLIFLYVV
Retrocopy KIILNLLCQVDY*AKLWSCNFSYQ<KYQFLTTYAGISKLNQYAEHLPQFSRIEYVVLCGPQKPLIFLYVV

Parental  DTCMEDEDLQALKESMQMSLSLLPPTALVGLITFGRM-VQVHELGCEGISKSYVFRGTKD-LSAKQLQEM
          DTCME.EDLQAL.ESMQ.SLSLL.P.AL..L...G.M.VQVH.LGCE.ISKSYVF.GTKD....KQL.EM
Retrocopy DTCMEHEDLQALIESMQISLSLLSPRALICL--WGGM<VQVHKLGCERISKSYVFKGTKD<WFSKQL*EM

Parental  LGLSKVPVTQATRGPQVQQPPPSNR-FLQPVQKIDMNLTDLLGELQRDPWPVPQGKRPLRSSGVALSIAV
          LG.S.VP.TQAT.GPQVQQP..SN..FL.P.Q.IDMNL..LLGE.Q.DPWP..QGK.PL..S..AL.IAV
Retrocopy LGPSRVPLTQATHGPQVQQPHASNK>FL*PLQNIDMNLPYLLGEQQ*DPWPILQGKGPLCTSEMALCIAV

Parental  GLLECTFPNTGARIMMFIGGPATQGPGMVVGDELKTPIRSWHDIEKDNAKYVKKGTKHFEALANRAATTG
          GL..C.FPN.GA.IMM..GG.A.Q...MVVGDEL..P.RSWHDIEKDN.KYV.KG.KHFE.LAN.AATT.
Retrocopy GLIKCIFPNAGAHIMMSMGGLAIQAARMVVGDELMMPRRSWHDIEKDNVKYV*KGPKHFEELANQAATTR

Parental  HVIDIYACALDQTGLLEMKCCPNLTGGYMVMGDSFNTS-LFKQTFQRVFTKDMHGQFKMGFGGTLEIKTS
          HVIDIYACALDQTGLL..KCC.NLTG..MVMGDSFNTS.L.KQTFQ.VF.KD.H.QFKM.FGG.LEI.T.
Retrocopy HVIDIYACALDQTGLLQIKCCSNLTGENMVMGDSFNTS<LIKQTFQTVFPKDIHEQFKMSFGGALEINTL

Parental  REIKISGAIGPCVSLNSKGPCVS-ENEIGTGGTCQWKICGLSPTTTLAIYFEVVNQHNAPIPQGGRGAIQ
          REIKISGAIGPCVSLNSKGPC....N.IG..G.CQ.K.C....TTTLA.YF.VVNQHNAPI..GG..AIQ
Retrocopy REIKISGAIGPCVSLNSKGPCMP>QNVIGMCGICQGKLCRFYLTTTLAMYFGVVNQHNAPILHGGHCAIQ

Parental  FVTQYQHS-SGQRRIRVTTIAR
          FVT.Y.H...GQR.IRVTTI.R
Retrocopy FVTWYHHA<NGQRCIRVTTITR

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_653 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_653 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	ENSSTOG00000013426	1 retrocopy	retro_itri_653 ,