RetrogeneDB ID: retro_itri_1014

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393358.1:7625312..7625653(-)
• Located in intron of: ENSSTOG00000016124

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000025097
• Aliases: None
• Description: None

Sequence

>retro_itri_1014
AAAGCAGAATCCAAAGATGGTCATCCTTGTCTGAAGGAATTCATAGCTCACGCTGCTCTTGACCTTGCCGGTGAAAACAT
GTGGCTTTCGAACAACATGTATTTGAAAACTATGGACAAATTCAATAAGTGGTTTGTGTCAGCATTTGTCACTGTAGAGC
ATATGAGATTTATTATGCTTCATGATACAGGGCAAGAAGATGGAATCAGGAACTTATGTACTGATGTTGATGATTTATAT
ATAAAATTTGCAATGAATCCATTTTATAAACTCAATTGTCTTGTTCAGTCAGGGCATTTGACAGAAAATTTCAATCCTTT
GGGAAGAAACACCTTTTAAGC

Alignment

ORF - retro_itri_1014 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.65 %
• Parental protein coverage: 81.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KAESKDDHRHLNQFIAHAALDLVDENMWLSNNMYLKTVDKFNEWFVSAFVTAGHMRFIMLHDIRQEDGIK
          KAESKD.H..L..FIAHAALDL..ENMWLSNNMYLKT.DKFN.WFVSAFVT..HMRFIMLHD..QEDGI.
Retrocopy KAESKDGHPCLKEFIAHAALDLAGENMWLSNNMYLKTMDKFNKWFVSAFVTVEHMRFIMLHDTGQEDGIR

Parental  NFFTDVYDLYIKFAMNPFYEPNSPIRSS-AFDRKVQFLGKKHLLS
          N..TDV.DLYIKFAMNPFY..N....S..AFDRK.Q..GKKHLLS
Retrocopy NLCTDVDDLYIKFAMNPFYKLNCLVQSG<AFDRKFQSFGKKHLLS

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_1014 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1014 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001719	1 retrocopy	retro_acar_53,
Canis familiaris	ENSCAFG00000011754	2 retrocopies	retro_cfam_1608, retro_cfam_368,
Homo sapiens	ENSG00000196459	1 retrocopy	retro_hsap_73,
Microcebus murinus	ENSMICG00000004690	1 retrocopy	retro_mmur_1022,
Macaca mulatta	ENSMMUG00000022619	1 retrocopy	retro_mmul_326,
Monodelphis domestica	ENSMODG00000017312	2 retrocopies	retro_mdom_1737, retro_mdom_1901,
Mus musculus	ENSMUSG00000079317	2 retrocopies	retro_mmus_198, retro_mmus_2522,
Otolemur garnettii	ENSOGAG00000002870	2 retrocopies	retro_ogar_369, retro_ogar_60,
Pan troglodytes	ENSPTRG00000021674	1 retrocopy	retro_ptro_72,
Sorex araneus	ENSSARG00000006353	1 retrocopy	retro_sara_244,
Ictidomys tridecemlineatus	ENSSTOG00000025097	1 retrocopy	retro_itri_1014 ,