RetrogeneDB ID: retro_itri_1777

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393763.1:159790..160615(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KPNA3
• Ensembl ID: ENSSTOG00000003006
• Aliases: None
• Description: karyopherin alpha 3 (importin alpha 4) [Source:HGNC Symbol;Acc:6396]

Sequence

>retro_itri_1777
TCACTGGGACTTATCCAACCTCTTCTGTCCTTCATCAATCCCTCCATTCCCATTACCTTCTCAGAATGTCTTATGGATCA
TTGCCAATCTCTACAGGAATAAGGACCCCCTACCACGTATGGAGACAGTTCAGGAGATTTTGCCAGCTTTATGTGTCCTC
ATATACTCTATGGACATAAATATTCTTGTAGGCACTGTTTGGGCTCTGTCATACTTGACAGATGGAGCTAATGAACAGAT
ACAGATGGTTATTGATTCAGGGGTTGTGCCATTTCTTGTGTCCTTTCTGCACCACCAGGAAGTGAACGTTCAAACTGCAG
CCCTCAGAGCAATTGGCAACATAGTGACAGGCACTGATGAGCAGACTCAGGTTCTCTATTGTGATGTCTGATCACACTCC
CCAAATCTCTTATCACTTCCAAAAGAGAAGATAAATAAGGAATCACTATGGTTCCTTTCCAACATTACAGCAGGCAACAA
GCAACAAATTCAAGCTGTAATAGATGCTGAATTAATCCCTATGATTATTCATCAACTTGCTAAGGAAGACTTTGGAACAC
AAAAAGAAGCTGCTTGGACATTGGGAACTTAACAATTAGTGGCAGAAAAGATAAGGTTGAGTACCATGTACAATAGAATG
TAATATCACTATTCTGAAATTTATTGTCAGTAAAAGATTCTCAAGTGGTTCAGGTCATTCTGGATGGTCTAAAAAACATT
CTGATAGTGGCTGGTGATGAAGCAAGCACAATAGCTGAAATAATTGAAGAATGTGGAGGTTTGGAGAAAATTGAAGTCTT
GCAACAATAAGAAAATAAAGACATA

Alignment

ORF - retro_itri_1777 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.43 %
• Parental protein coverage: 55.82 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SLGVVKPLLSFIN-PSIPITFLRNVTWVIVNLCRNKDPPPPMETVQEILPALCVLIYHTDINILVDTVWA
          SLG...PLLSFIN.P..P.....NV.W.I.NL.RNKDP.P.METVQEILPALCVLIY..DINILV.TVWA
Retrocopy SLGLIQPLLSFIN>PPFPLPS-QNVLWIIANLYRNKDPLPRMETVQEILPALCVLIYSMDINILVGTVWA

Parental  LSYLTDGGNEQIQMVIDSGVVPFLVPLLSHQEVKTQHTAALRAVGNIVTGTDEQTQVVLNCDVLSHFPNL
          LSYLTDG.NEQIQMVIDSGVVPFLV..L.HQEV..Q.TAALRA.GNIVTGTDEQTQ.VL.CDV.SH.PNL
Retrocopy LSYLTDGANEQIQMVIDSGVVPFLVSFLHHQEVNVQ-TAALRAIGNIVTGTDEQTQ-VLYCDV*SHSPNL

Parental  LSHPKEKINKEAVWFLSNITAGNQQQVQAVIDAGLIPMIIHQLAKGDFGTQKEAAWA-ISNLTISGRKDQ
          LS.PKEKINKE..WFLSNITAGN.QQ.QAVIDA.LIPMIIHQLAK.DFGTQKEAAW..I.NLTISGRKD.
Retrocopy LSLPKEKINKESLWFLSNITAGNKQQIQAVIDAELIPMIIHQLAKEDFGTQKEAAWT<IGNLTISGRKDK

Parental  VEYLVQQNVIPPFCNLLSVKDSQVVQVVLDGLKNILIMAGDEASTIAEIIEECGGLEKIEVLQQHENEDI
          VEY.VQ.NVI..F.NLLSVKDSQVVQV.LDGLKNILI.AGDEASTIAEIIEECGGLEKIEVLQQ.EN.DI
Retrocopy VEYHVQ*NVISLF*NLLSVKDSQVVQVILDGLKNILIVAGDEASTIAEIIEECGGLEKIEVLQQ*ENKDI

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_1777 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1777 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004850	1 retrocopy	retro_btau_1842,
Rattus norvegicus	ENSRNOG00000014945	1 retrocopy	retro_rnor_987,
Ictidomys tridecemlineatus	ENSSTOG00000003006	1 retrocopy	retro_itri_1777 ,
Tarsius syrichta	ENSTSYG00000008134	1 retrocopy	retro_tsyr_1547,