RetrogeneDB ID: retro_itri_1279

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393424.1:3289426..3289672(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LYRM2
• Ensembl ID: ENSSTOG00000016198
• Aliases: None
• Description: LYR motif containing 2 [Source:HGNC Symbol;Acc:25229]

Sequence

>retro_itri_1279
ATGGCCACTTCCTGCTTACCTCCAATGATGCTAAAGCTAATGCAGTTCATGAGAAGACAACAAGTTCTTAGGCTGAGCAG
AAGGATCTTACAGGAAATTTGGCAAGTTTCAAATGTTTCTGATCACAAATACCTGAAGAACTGGGCAAAAAGAATTCAAA
AGAAATGAAAGTGCCACCAAAGAGGAACAACTCAGATCATAATTGCTCAAGGCACTCTGCAGCTAAAAGAGTTAGAAAAA
ACACTA

Alignment

ORF - retro_itri_1279 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.24 %
• Parental protein coverage: 94.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAASRLPPATLTLKQFMRRQQVLMLYRRILRAIQQVSNNSDRKYLKDWAREEFKRNKSATEEDAIRMMIT
          MA.S.LPP..L.L.QFMRRQQVL.L.RRIL..I.QVSN.SD.KYLK.WA....K..K...........I.
Retrocopy MATSCLPPMMLKLMQFMRRQQVLRLSRRILQEIWQVSNVSDHKYLKNWAKRIQKK*K-CHQRGTTQIIIA

Parental  QGTMQLKELEKTL
          QGT.QLKELEKTL
Retrocopy QGTLQLKELEKTL

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_1279 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1279 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000009916	1 retrocopy	retro_meug_2134,
Microcebus murinus	ENSMICG00000012230	2 retrocopies	retro_mmur_631, retro_mmur_650,
Mus musculus	ENSMUSG00000045854	2 retrocopies	retro_mmus_474, retro_mmus_790,
Otolemur garnettii	ENSOGAG00000034900	1 retrocopy	retro_ogar_508,
Sus scrofa	ENSSSCG00000004324	1 retrocopy	retro_sscr_686,
Ictidomys tridecemlineatus	ENSSTOG00000016198	1 retrocopy	retro_itri_1279 ,
Tursiops truncatus	ENSTTRG00000007420	1 retrocopy	retro_ttru_1516,