RetrogeneDB ID: retro_itri_904

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393341.1:2883585..2883884(+)
• Located in intron of: ENSSTOG00000008770

Retrocopy information

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

Parental gene information

• Parental gene symbol: CUTA
• Ensembl ID: ENSSTOG00000002474
• Aliases: None
• Description: cutA divalent cation tolerance homolog (E. coli) [Source:HGNC Symbol;Acc:21101]

Sequence

>retro_itri_904
GGCGGTCAAGCGTCCGCAGCTCTACTCGGCGGAGGGGCCGCTCTGTTCCTGTCTTGTCTTTGGATGCCTGCATTGCTGCC
TGTGGCCTCCCGCCTTCTGTTGCTACCCCGAGCACTGCTGACCATGGCCTCTGGAAGCCCCCCATCCCAGCCCACTATGG
CATCTGGCTCTAGCTATGTTCCAGGATCGGTTCTGCAGCCTTTGTCACTTGCCCCAACGAAAAGGTCGCCAAGGAAATTG
CCAGATCTTTGGTGTAGAAGCGCCTAACAGTCAACCTCATCCCTCAGATTACATCCATG

Alignment

ORF - retro_itri_904 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.26 %
• Parental protein coverage: 57.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GGPASAALLGGGAALFLSCLWMPALLPVASRLLLLPRALLTMASGSPPSQPTTASGSSYVPGSV-SAAFV
          GG.ASAALLGGGAALFLSCLWMPALLPVASRLLLLPRALLTMASGSPPSQPT.ASGSSYVPGSV.SAAFV
Retrocopy GGQASAALLGGGAALFLSCLWMPALLPVASRLLLLPRALLTMASGSPPSQPTMASGSSYVPGSV<SAAFV

Parental  TCPNEKVAKEIARALVEKRLAACVNLIPQITSI
          TCPNEKVAKEIAR.LV.KRL...VNLIPQITS.
Retrocopy TCPNEKVAKEIARSLV*KRLT--VNLIPQITSM

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_904 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_904 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009616	1 retrocopy	retro_dnov_2395,
Otolemur garnettii	ENSOGAG00000015556	1 retrocopy	retro_ogar_2719,
Ictidomys tridecemlineatus	ENSSTOG00000002474	1 retrocopy	retro_itri_904 ,