RetrogeneDB ID: retro_itri_544

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393300.1:16220691..16221072(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRTAP4-1
• Ensembl ID: ENSSTOG00000004308
• Aliases: None
• Description: keratin associated protein 4-1 [Source:HGNC Symbol;Acc:18907]

Sequence

>retro_itri_544
TGCTGCAAACCTACCTGTTGCAGAACCACCTGCTGCAGGACCAGCTGCTGGAAACCAGCCTGTGTCACCAGCTGCTGCCA
GCCCTGCTGTCCCTCAACTTGCTGTGAAACCACCTGCTGCAGGACCACCTGCTGCAAACCAGCCTGTGATATCAGCTGCT
GCAGCACACCCTGCTGTGAGCCCAGATGCTGTGAGCCTTGCTACTGCCCCAGCTACTGCCTCACTCCCTGCTGCCAACCC
TGCTGCTACCAGCCTTGCTGTCCCCCAGCTTGCTGTGAAACCACCTGCCACAGGACCACCTGCTGCAAATCAACCTGTGA
GCCCAACTGCTGTGAGCCTTGCTGCTGCCCCAGTTGCTACATCATTCCCCGCTGCCAGCCC

Alignment

ORF - retro_itri_544 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.79 %
• Parental protein coverage: 72.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CCQPTCCRTTCCRPSC----CGCGCCQPRCCQTTCCRTTCCRPSCCLLSCCCHPTCCRTTCCSTTCCRPC
          CC.PTCCRTTCCR.SC....C...CCQP.CC..TCC.TTCCR..CC.....C...CC.T.CC...CC.PC
Retrocopy CCKPTCCRTTCCRTSCWKPACVTSCCQP-CCPSTCCETTCCRTTCC--KPACDISCCSTPCCEPRCCEPC

Parental  CCMASCCRPSC--CCGSCCCRPCCLQTTCCRTTCCRPCCCVASCCRPSCCCYDCCCSPCCQP
          .C...C..P.C..CC...CC.P.C..TTC.RTTCC....C...CC.P.CCC..C...P.CQP
Retrocopy YCPSYCLTPCCQPCCYQPCCPPACCETTCHRTTCCK-STCEPNCCEP-CCCPSCYIIPRCQP

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_544 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_544 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
Felis catus	ENSFCAG00000005246	1 retrocopy	retro_fcat_1673,
Otolemur garnettii	ENSOGAG00000003102	1 retrocopy	retro_ogar_94,
Ictidomys tridecemlineatus	ENSSTOG00000004308	1 retrocopy	retro_itri_544 ,
Tupaia belangeri	ENSTBEG00000008312	1 retrocopy	retro_tbel_13,