RetrogeneDB ID: retro_itri_404

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393289.1:4316537..4316912(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C1orf146
• Ensembl ID: ENSSTOG00000012506
• Aliases: None
• Description: chromosome 1 open reading frame 146 [Source:HGNC Symbol;Acc:24032]

Sequence

>retro_itri_404
GTTGAATTTTTATTAATTGATGCTAAAGAATGCATTATGTCAGCTGAAGAAATATTTCTAAACAAAATTGATAAGTTTAT
TAACATTCACCCAAATAGTTTTTTGGTTTTGTTTGCTGTCCTCCATGGGCCTGAAGAAAGGAAATTGATGTTCAGGATTC
AGCAGAGATTCCTGGGAAGTAAAATAAAGGATACTTCCAGGATACAACACCCAGTAAATGCTATTAATCTTATGTGCACT
ATTGCCAAGACTACCTCCAAACCATACAAACGTAGCATCTGCTATAGAATGATAACAACTGAAGCTTACATCTTAGAGCA
AAGTCCTGTTTGGAAAACATTTCAAAACATAAAACTGGGTAGAGATGCAATTAAC

Alignment

ORF - retro_itri_404 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.6 %
• Parental protein coverage: 69.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VAFLLMDAKECIMSAEEIFINKIEKFINIHKNSFLVLFAALHGPEEWKLMFRIQQRFLGSNLRILP-VHN
          V.FLL.DAKECIMSAEEIF.NKI.KFINIH.NSFLVLFA.LHGPEE.KLMFRIQQRFLGS..........
Retrocopy VEFLLIDAKECIMSAEEIFLNKIDKFINIHPNSFLVLFAVLHGPEERKLMFRIQQRFLGSKIKDTSRIQH

Parental  TANAITLMCTIAKTTSKPYIDSICYRMITTKAYIIEQSPVWKMLQKIKLGGDAIN
          ..NAI.LMCTIAKTTSKPY..SICYRMITT.AYI.EQSPVWK..Q.IKLG.DAIN
Retrocopy PVNAINLMCTIAKTTSKPYKRSICYRMITTEAYILEQSPVWKTFQNIKLGRDAIN

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_404 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_404 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 14 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027936	1 retrocopy	retro_btau_490,
Choloepus hoffmanni	ENSCHOG00000004012	1 retrocopy	retro_chof_2167,
Callithrix jacchus	ENSCJAG00000017547	1 retrocopy	retro_cjac_1817,
Erinaceus europaeus	ENSEEUG00000003083	1 retrocopy	retro_eeur_601,
Homo sapiens	ENSG00000203910	1 retrocopy	retro_hsap_3381,
Gorilla gorilla	ENSGGOG00000006653	1 retrocopy	retro_ggor_2289,
Macropus eugenii	ENSMEUG00000013311	1 retrocopy	retro_meug_143,
Myotis lucifugus	ENSMLUG00000016984	1 retrocopy	retro_mluc_1260,
Macaca mulatta	ENSMMUG00000010094	1 retrocopy	retro_mmul_2107,
Nomascus leucogenys	ENSNLEG00000010426	1 retrocopy	retro_nleu_970,
Pongo abelii	ENSPPYG00000001156	1 retrocopy	retro_pabe_2780,
Pan troglodytes	ENSPTRG00000030530	1 retrocopy	retro_ptro_2298,
Ictidomys tridecemlineatus	ENSSTOG00000012506	1 retrocopy	retro_itri_404 ,
Tursiops truncatus	ENSTTRG00000014426	1 retrocopy	retro_ttru_1727,