RetrogeneDB ID: retro_itri_1120

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393380.1:24002..24974(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CALCOCO2
• Ensembl ID: ENSSTOG00000013395
• Aliases: None
• Description: calcium binding and coiled-coil domain 2 [Source:HGNC Symbol;Acc:29912]

Sequence

>retro_itri_1120
ATGGAAAAAACAATAGAAGATCCCCCCACATCAGCTGTCTTGCTTGATCGTTGTCATTTCTCTCAGGTCATCTTTAATAG
TGTGGAGAAGTTCTATGTCCCTGGAGGGGACATCACATGCTATTATACCTTCGCCGAGCATTTCATCCCCCGTTGAAAGG
ACTGGATTGGCATCTTTAGAATGGGATGGAAGACAACCCGTGAATATTATACCTTCATATGGGTTGCTTTGCCTAGTGAC
ATAAACAACAAATCAGCCAAACAGCAGGAAGTCCAATTTAAAGCTTATTACTTGCCTAAGGATGATGAGTATTACCAGTT
CTGCTATGTGCATCAGGATGGTGTGGTCCGGGGAGCAAGTATCCCTTTCCAGTTCCGTCCAGAAAGTGAGGAGGACATCC
TGGTTGTTACTACTAAGGGAAAGGTAGAAGAGATTGAGCAGCACAACGAGGAGCTTTGCAAAGAAAACCAGGAACTGAAG
GACAGCTGTGCCAGCCTCCAGAAGCAGAACTCAAGCATGCAGGCTGAGCTCCAAAGGAAGCAGGAGGAGCTGGAGACTCT
ACAGAGTATCAATAAGAAATTGGAACAGAAAGTGAAAGAGCAGAAAACCTGTTGGGAAACTGAGCTGCTTCAACTAAAAG
AACATAACCTGAAGGTGTCCTCAGAAAATGAGAAGATGGGAATCAGAGTGGATCAGCTTCAGGCCCAGCTATCAACTCAA
GAGAAGGAAATGGAAAAGCTTGTTCAGGGAGATCAAGATAAAGCAGAACAGTTGGAACATCTGAAAAATGAAAATGACCA
ACTCTTTCTCAGTTTGACTGAACAGAGGGAGCAGCAGAAGAAGCTCCAGCAGATAGTGGAGGATATGAAGCAGAAAGAAA
CTACTTCAGCGAAGAAACAACAGGAGTTAATGGATGAGAATTTTGACCTGTCAAGAAGACTGAGTGAGAACAAGATTATA
TGTGATGTTCTG

Alignment

ORF - retro_itri_1120 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.15 %
• Parental protein coverage: 73.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEKTIEDPPTSAVLLDRCHFSQVIFNSVEKFYVPGGDITCYYTFAEHFIPRRKDWIGIFRVGWKTTREYY
          MEKTIEDPPTSAVLLDRCHFSQVIFNSVEKFYVPGGDITCYYTFAEHFIPR.KDWIGIFR.GWKTTREYY
Retrocopy MEKTIEDPPTSAVLLDRCHFSQVIFNSVEKFYVPGGDITCYYTFAEHFIPR*KDWIGIFRMGWKTTREYY

Parental  TFMWVALPSDINNKSAKQQEVQFKAYYLPKDDEYYQFCYVDQDGVVRGASIPFQFRPESEEDILVVTTKG
          TF.WVALPSDINNKSAKQQEVQFKAYYLPKDDEYYQFCYV.QDGVVRGASIPFQFRPESEEDILVVTTKG
Retrocopy TFIWVALPSDINNKSAKQQEVQFKAYYLPKDDEYYQFCYVHQDGVVRGASIPFQFRPESEEDILVVTTKG

Parental  KVEEIEQHNEELCKENQELKDSCASLQKQNSSMQAELQRKQEELETLQSINKKLEQKVKEQKTCWETELL
          KVEEIEQHNEELCKENQELKDSCASLQKQNSSMQAELQRKQEELETLQSINKKLEQKVKEQKTCWETELL
Retrocopy KVEEIEQHNEELCKENQELKDSCASLQKQNSSMQAELQRKQEELETLQSINKKLEQKVKEQKTCWETELL

Parental  QLKEHNLKVSSENEKMGIRVDQLQAQLSTQEKEMEKLVQGDQDKAKQLEHLKNENDQLFLSLTEQREQQK
          QLKEHNLKVSSENEKMGIRVDQLQAQLSTQEKEMEKLVQGDQDKA.QLEHLKNENDQLFLSLTEQREQQK
Retrocopy QLKEHNLKVSSENEKMGIRVDQLQAQLSTQEKEMEKLVQGDQDKAEQLEHLKNENDQLFLSLTEQREQQK

Parental  KLQQIVEDMKQKETTAAKKQQELMDENFDLSRRLSENKIICDVL
          KLQQIVEDMKQKETT.AKKQQELMDENFDLSRRLSENKIICDVL
Retrocopy KLQQIVEDMKQKETTSAKKQQELMDENFDLSRRLSENKIICDVL

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_1120 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1120 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000006056	3 retrocopies	retro_mmus_1016, retro_mmus_1108, retro_mmus_2097,
Otolemur garnettii	ENSOGAG00000011709	1 retrocopy	retro_ogar_3090,
Rattus norvegicus	ENSRNOG00000031074	1 retrocopy	retro_rnor_1194,
Ictidomys tridecemlineatus	ENSSTOG00000013395	1 retrocopy	retro_itri_1120 ,