RetrogeneDB ID: retro_itri_1072

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393369.1:391556..391772(+)
• Located in intron of: ENSSTOG00000000560

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPP14
• Ensembl ID: ENSSTOG00000015394
• Aliases: None
• Description: ribonuclease P/MRP 14kDa subunit [Source:HGNC Symbol;Acc:30327]

Sequence

>retro_itri_1072
ACCACATATGAAAGAATAGTTTACAAAAATCCCTCTGTGTACCACTACATGAAAGTCTGCCTGGAATTTCAAGATCATGG
AGTTGGTCTGAATGCTGCACAGTTCAAAGAGCTGCTTATTTCTACCCTAAAGGATCTGTTTGGAGTGGTTGGTGCTGCCT
TATCTCTGGATGTCCTGACCTATGAAGAGAAGACCTTGTTAGCCATCTTGAATATG

Alignment

ORF - retro_itri_1072 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.5 %
• Parental protein coverage: 60.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TTYERIVYKNPSEYHYMKVCLEFQDHGVGLNAAQFKQLLISALKDLFGEVGAALPVDVLTYEEKTLSAIL
          TTYERIVYKNPS.YHYMKVCLEFQDHGVGLNAAQFK.LLIS.LKDLFG.VGAAL..DVLTYEEKTL.AIL
Retrocopy TTYERIVYKNPSVYHYMKVCLEFQDHGVGLNAAQFKELLISTLKDLFGVVGAALSLDVLTYEEKTLLAIL

Parental  RI
          ..
Retrocopy NM

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_1072 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1072 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019987	1 retrocopy	retro_btau_1621,
Cavia porcellus	ENSCPOG00000004281	2 retrocopies	retro_cpor_476, retro_cpor_566,
Dasypus novemcinctus	ENSDNOG00000013439	1 retrocopy	retro_dnov_762,
Macropus eugenii	ENSMEUG00000010883	1 retrocopy	retro_meug_838,
Microcebus murinus	ENSMICG00000014541	1 retrocopy	retro_mmur_142,
Myotis lucifugus	ENSMLUG00000007998	1 retrocopy	retro_mluc_2291,
Ornithorhynchus anatinus	ENSOANG00000022513	1 retrocopy	retro_oana_119,
Oryctolagus cuniculus	ENSOCUG00000027202	3 retrocopies	retro_ocun_1160, retro_ocun_1359, retro_ocun_1425,
Rattus norvegicus	ENSRNOG00000039829	1 retrocopy	retro_rnor_1530,
Ictidomys tridecemlineatus	ENSSTOG00000015394	1 retrocopy	retro_itri_1072 ,
Tarsius syrichta	ENSTSYG00000013343	1 retrocopy	retro_tsyr_218,
Vicugna pacos	ENSVPAG00000000935	1 retrocopy	retro_vpac_202,