RetrogeneDB ID: retro_itri_1554

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393538.1:337873..338318(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000019996
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RRP15
• Ensembl ID: ENSSTOG00000001244
• Aliases: None
• Description: ribosomal RNA processing 15 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:24255]

Sequence

>retro_itri_1554
CAGCTTGATAAGAAGTGGGAGTGGGAAATGATGTGCAGAGTAAAGCCAGATGTCATCAGAGACAAAGAAACAGAGAGAAA
TCTTCAGAGAATTGCAACAAGGGGTGTGGTGCAGTTATTTAATGCTGTTCAGAAACATCAAAAGAATGTTGATGAAAAGA
TTAAAGAAGCAGGAGACTCTATTAGAAAGCGCACTAAGTTGATATCATCTGTTTCCAAGAAAGATTTTATTAAGTGTTCT
AAGAGGAATGGATGGGAGTACAAATGAAAAAAGTTCATCTGGGAAGAACTCAAAAGCCAAACATACTGAAATCAAATCAG
AAGATGGCCCAGGTTGGACAATTCTGCGTGATGATTTCATGATGGGTGCGCCTATGAAAGACTGGGACAAGGAAAGCGAT
GGGCCAGATAATAGCAGACCAGGATCTGCAAGTGACTCCGACACA

Alignment

ORF - retro_itri_1554 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.63 %
• Parental protein coverage: 52.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QLDKKREWEMMCRVKPDVVRDKETERNLQRIATRGVVQLFNAVQKHQKNVDEKIKEAGGSIRKRTKLISS
          QLDKK.EWEMMCRVKPDV.RDKETERNLQRIATRGVVQLFNAVQKHQKNVDEKIKEAG.SIRKRTKLISS
Retrocopy QLDKKWEWEMMCRVKPDVIRDKETERNLQRIATRGVVQLFNAVQKHQKNVDEKIKEAGDSIRKRTKLISS

Parental  VCKKDFI-SVLRGMDGSTNEKSSSGKNSKAKQTEIKSEDGPGWTILRDDFMMGASMKDWDKESDGPDNSR
          V.KKDFI.SVLRGMDGSTNEKSSSGKNSKAK.TEIKSEDGPGWTILRDDFMMGA.MKDWDKESDGPDNSR
Retrocopy VSKKDFI>SVLRGMDGSTNEKSSSGKNSKAKHTEIKSEDGPGWTILRDDFMMGAPMKDWDKESDGPDNSR

Parental  PGSTSDSDT
          PGS.SDSDT
Retrocopy PGSASDSDT

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_1554 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1554 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 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000174	1 retrocopy	retro_chof_1961,
Callithrix jacchus	ENSCJAG00000012916	2 retrocopies	retro_cjac_3789, retro_cjac_455,
Mus musculus	ENSMUSG00000001305	1 retrocopy	retro_mmus_3531,
Oryctolagus cuniculus	ENSOCUG00000017863	4 retrocopies	retro_ocun_1738, retro_ocun_820, retro_ocun_962, retro_ocun_992,
Ictidomys tridecemlineatus	ENSSTOG00000001244	1 retrocopy	retro_itri_1554 ,
Tarsius syrichta	ENSTSYG00000012715	1 retrocopy	retro_tsyr_2006,