RetrogeneDB ID: retro_itri_1560

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393541.1:202591..203134(+)
• Located in intron of: ENSSTOG00000025446

Retrocopy information

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

Parental gene information

• Parental gene symbol: APEX1
• Ensembl ID: ENSSTOG00000010096
• Aliases: None
• Description: APEX nuclease (multifunctional DNA repair enzyme) 1 [Source:HGNC Symbol;Acc:587]

Sequence

>retro_itri_1560
ATGCCAAAACATGGGGAAAAGGGAGCACTGGCAGAAGATGGGGAGGAGCCCAAGACAGAGCCAGAGGTCAAGAAGAGTAA
GGTGGAAGCAAAAAAAAAATGAAAAAGAGGCAGCAGAAGATGGCCCAGTTCTATAGGAAGACCCTCCATATCCAAAAACT
TCACCCACTGGCAAATCGGCCGCACTCAAGATCTGCTCCTGAAATGTGAATCAGCCTCGAGCCTGGATTAAGAAGAAAGG
TTTAGACACAGTAAAGGAGGAAGTCTCAAACACCATGTGCCTTCCAGAGACTAAATTTTGCAAGAACAGACTATGCCTGA
ACTTCAAGAGCAGCCTAGACTATTCCATCAGTCATGATCAGCTCCTTTGGACAAGGATAGATGGTGCAGCATGGGTCTAC
TTTCCAGCCAGTGCTAGCTCAAAGTCTGTTACGGCATTGGTGAGGAGGAAGGCCTTGTGATTGTGGTGGAATCTGACACA
GTTGTACTGGCGGCTTATGTACCTAATGCAGGCAGCTGTCTGTTAAGACTGGAGTACTGGCAG

Alignment

ORF - retro_itri_1560 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.17 %
• Parental protein coverage: 58.49 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPKRGKKGAAAEDGEEPKTEPE-SKKSKVGAKKKEKETAGEGPVLYEDPPDKKTSPSGKSATLKICSWNV
          MPK.G.KGA.AEDGEEPKTEPE.S............E.A..GPVL.EDPP..KTSP.GKSA.LKICS.NV
Retrocopy MPKHGEKGALAEDGEEPKTEPE>SRRVRWKXXXXXXEAAEDGPVL*EDPPYPKTSPTGKSAALKICS*NV

Parental  DGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKL-PPELQELPGLSHQYWAAPSDKEGYSGVGLLSRQC
          ...RAWIKKKGLD.VKEE.....CL.ETK...N.L..PELQE.P.L.HQ...AP.DK......GLLS.QC
Retrocopy NQPRAWIKKKGLDTVKEEVSNTMCLPETKFCKNRL<MPELQEQPRLFHQS*SAPLDKDRWCSMGLLSSQC

Parental  PIKVSYGIGEEEHDQEGRVIVAEFDKFVLVTAYVPNAGRGLVRLEYRQ
          ..KV.YGIGEEE....G.VIV.E.D..VL..AYVPNAG..L.RLEY.Q
Retrocopy *LKVCYGIGEEE----GLVIVVESDTVVL-AAYVPNAGSCLLRLEYWQ

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_1560 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1560 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002745	1 retrocopy	retro_btau_1729,
Echinops telfairi	ENSETEG00000004855	1 retrocopy	retro_etel_1392,
Loxodonta africana	ENSLAFG00000021872	1 retrocopy	retro_lafr_948,
Mus musculus	ENSMUSG00000035960	2 retrocopies	retro_mmus_2027, retro_mmus_433,
Otolemur garnettii	ENSOGAG00000013335	3 retrocopies	retro_ogar_1284, retro_ogar_2145, retro_ogar_3243,
Rattus norvegicus	ENSRNOG00000009663	1 retrocopy	retro_rnor_2971,
Ictidomys tridecemlineatus	ENSSTOG00000010096	1 retrocopy	retro_itri_1560 ,
Tupaia belangeri	ENSTBEG00000006405	1 retrocopy	retro_tbel_3409,