RetrogeneDB ID: retro_itri_1252

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393414.1:3293529..3293862(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000019914
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TRAPPC4
• Ensembl ID: ENSSTOG00000014340
• Aliases: None
• Description: trafficking protein particle complex 4 [Source:HGNC Symbol;Acc:19943]

Sequence

>retro_itri_1252
CTTCGGACAGCGCGATGGCATCCGGGGCTTTTTGCCATTGGCTCCCAGCTGTCTCCCGAACAGGGAAGCTCAGACATTGA
GATGCTGGAGACAGACACTTTCAAACTGCACTGCTTCCAGACACTAACAGGGATCAAGTTTGTGGTGCTGGCAGATCCTA
GGCAAGCTGGAATAGATTTTCTTCTTCGAAAAATTTATGAAATTTACTCAGATTTTGCACTCAAGAATCCATTCTACTCC
CTGGAAATGCCCATCAGGTGTGAGCTGTTTGACCACAACCTGAAGCTAGCTTTGGAAGTGGCAGAGAAAGCTGGGACTTT
TGGACCTGAGTCA

Alignment

ORF - retro_itri_1252 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.09 %
• Parental protein coverage: 50.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LMLASMFHSLFAIGSQLSPEQGSSGIEMLETDTFKLHCFQTLTGIKFVVLADPRQAGIDSLLRKIYEIYS
          L..A.....LFAIGSQLSPEQGSS.IEMLETDTFKLHCFQTLTGIKFVVLADPRQAGID.LLRKIYEIYS
Retrocopy LRTARWHPGLFAIGSQLSPEQGSSDIEMLETDTFKLHCFQTLTGIKFVVLADPRQAGIDFLLRKIYEIYS

Parental  DFALKNPFYSLEMPIRCELFDQNLKLALEVAEKAGTFGPGS
          DFALKNPFYSLEMPIRCELFD.NLKLALEVAEKAGTFGP.S
Retrocopy DFALKNPFYSLEMPIRCELFDHNLKLALEVAEKAGTFGPES

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_1252 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1252 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012383	1 retrocopy	retro_cfam_760,
Callithrix jacchus	ENSCJAG00000013703	1 retrocopy	retro_cjac_450,
Dasypus novemcinctus	ENSDNOG00000007885	1 retrocopy	retro_dnov_46,
Myotis lucifugus	ENSMLUG00000004759	1 retrocopy	retro_mluc_1438,
Ictidomys tridecemlineatus	ENSSTOG00000014340	1 retrocopy	retro_itri_1252 ,