RetrogeneDB ID: retro_itri_21

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393647.1:33134..33476(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000012265
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000012922
• Aliases: None
• Description: None

Sequence

>retro_itri_21
ATGTATTACAAATTTAGTGGATTCACACAGAAGTTAACTGGAGCATGGGCTTCGGAAGCCTATAGCCCACAGGGTTTAAG
GCCAGTGGTTTCCACAGAAGCACCACCTATCATATTTGCCACACCAACTAAACTGACCTCTAGTCCCACTGGTTATGATT
ATGTGAGGAAGAACAAGGTTCCAGAGCTACAGAAGTTTTTCCAGAAATCTGGTGGTGTGCCCATTCACCTGAAACAAGGC
CTTCCTGACCAAATGCTTTACCAGACCACCATGGGCCTGACTGTGGGAGGGACCATCTACTGCCTGATTGCCCTCTATAT
GGCTTCACAGCCCAAAAAACAA

Alignment

ORF - retro_itri_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.98 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MYYKFSGFTQKLTGAWASEAYSPQGLRPVVSTEAPPIIFATPTKLTSSPTGYDYARKNKVPELQKFFQKS
          MYYKFSGFTQKLTGAWASEAYSPQGLRPVVSTEAPPIIFATPTKLTSSPTGYDY.RKNKVPELQKFFQKS
Retrocopy MYYKFSGFTQKLTGAWASEAYSPQGLRPVVSTEAPPIIFATPTKLTSSPTGYDYVRKNKVPELQKFFQKS

Parental  DGVPVHLKRGLPDQMLYRTTMALTVGGTIYCLIALYMASQPKNK
          .GVP.HLK.GLPDQMLY.TTM.LTVGGTIYCLIALYMASQPK..
Retrocopy GGVPIHLKQGLPDQMLYQTTMGLTVGGTIYCLIALYMASQPKKQ

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_21 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_21 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.

---

Parental genes homology:

Parental genes homology involve 16 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032040	1 retrocopy	retro_cfam_1847,
Callithrix jacchus	ENSCJAG00000014705	1 retrocopy	retro_cjac_1492,
Echinops telfairi	ENSETEG00000011940	1 retrocopy	retro_etel_650,
Homo sapiens	ENSG00000115944	1 retrocopy	retro_hsap_825,
Gorilla gorilla	ENSGGOG00000010739	1 retrocopy	retro_ggor_674,
Macaca mulatta	ENSMMUG00000016278	1 retrocopy	retro_mmul_110,
Mustela putorius furo	ENSMPUG00000008875	1 retrocopy	retro_mputfur_97,
Mus musculus	ENSMUSG00000024248	2 retrocopies	retro_mmus_32, retro_mmus_926,
Nomascus leucogenys	ENSNLEG00000016666	1 retrocopy	retro_nleu_258,
Oryctolagus cuniculus	ENSOCUG00000027189	3 retrocopies	retro_ocun_1617, retro_ocun_1781, retro_ocun_28,
Otolemur garnettii	ENSOGAG00000016029	1 retrocopy	retro_ogar_114,
Pan troglodytes	ENSPTRG00000011865	1 retrocopy	retro_ptro_575,
Sarcophilus harrisii	ENSSHAG00000012014	1 retrocopy	retro_shar_479,
Ictidomys tridecemlineatus	ENSSTOG00000002536	5 retrocopies	retro_itri_435, retro_itri_464, retro_itri_608, retro_itri_890, retro_itri_892,
Ictidomys tridecemlineatus	ENSSTOG00000012922	1 retrocopy	retro_itri_21 ,
Tupaia belangeri	ENSTBEG00000014124	3 retrocopies	retro_tbel_2384, retro_tbel_4472, retro_tbel_4545,