RetrogeneDB ID: retro_itri_18

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393319.1:390985..391657(-)
• Located in intron of: ENSSTOG00000025289

Retrocopy information

• Ensembl ID: ENSSTOG00000019433
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000008664
• Aliases: None
• Description: None

Sequence

>retro_itri_18
ATGGCTGGGAATAAAGGAAGAGGTCGCGCTGCCTATACCTTTAATATTGAGGCTGTTGGATTTAGCAGAGGTGAAAAGTT
ACCTGATGTAGTGTTGAAACCACCTCCACTATTTCCTGATACAGATTATAAACCAGTGCCACCGAAAACAGGAGAAGGGG
AAGATTATATGCTGGCCTTGAAACAGGAATTGAGAGAAACAATGAAAAGAATGCTTTATTTTATTGAAACACCTGAAGAA
AAACAAGATATTGAAAGGTATAGTAAAAGGTATATGAAGGTATACAAAGAAGAGTGGAAAGCAGATTGGAGAAGACTCCC
AAGAGAGATGATGCCCAGGAAAAAAAGCAAAAAAGCAGACCCAAAATCCAAAAAGGCAAAAGATACTGACAAAGGTACTT
TACTCGCTAATACTGCAGATGTTTTGAAAAAAATTGAGGAATTGGAAAAGAGAGGTAATGGTGAAAAATCAGATGAGGAA
AATGAAGAAAAAGAAGGAAGCAAAGAGAAAAGTAAAGAAGGTGATGATGATGACAATGACAATGAGGATGCTGCAGAGGA
GGAGTATGCTAAAGAAGAGCAAGAGGAGGAAAATGGCTACATTAATTCATATTTTGAAGATGGAGATGATTTTGGTGCAG
AAAGTGACGACAACATGGATGAAGCAACCTAT

Alignment

ORF - retro_itri_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.54 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGNKGRGRAAYTFNIEAVGFSRGEKLPDVVLKPPPLFPDTDYKPVPLKTGEGEDYMLALKQELRETMKR
          MAGNKGRGRAAYTFNIEAVGFSRGEKLPDVVLKPPPLFPDTDYKPVP.KTGEGEDYMLALKQELRETMKR
Retrocopy MAGNKGRGRAAYTFNIEAVGFSRGEKLPDVVLKPPPLFPDTDYKPVPPKTGEGEDYMLALKQELRETMKR

Parental  MPYFIETPEEKQDIERYSKRYMKVYKEEWKPDWRRLPREMMPRKKCKKADPKSKKAKDTDKGTSLANTAD
          M.YFIETPEEKQDIERYSKRYMKVYKEEWK.DWRRLPREMMPRKK.KKADPKSKKAKDTDKGT.LANTAD
Retrocopy MLYFIETPEEKQDIERYSKRYMKVYKEEWKADWRRLPREMMPRKKSKKADPKSKKAKDTDKGTLLANTAD

Parental  VLKKIEELEKRGDGEKSDEENEEKEGSKEKSKEGDDDDDDNEDAAEEEYDEEEQEEENDYINSYFEDGDD
          VLKKIEELEKRG.GEKSDEENEEKEGSKEKSKEGDDDD.DNEDAAEEEY..EEQEEEN.YINSYFEDGDD
Retrocopy VLKKIEELEKRGNGEKSDEENEEKEGSKEKSKEGDDDDNDNEDAAEEEYAKEEQEEENGYINSYFEDGDD

Parental  FGAESDDNMDEATY
          FGAESDDNMDEATY
Retrocopy FGAESDDNMDEATY

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_18 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_18 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006306	1 retrocopy	retro_chof_125,
Callithrix jacchus	ENSCJAG00000010747	1 retrocopy	retro_cjac_2691,
Echinops telfairi	ENSETEG00000008379	1 retrocopy	retro_etel_1040,
Homo sapiens	ENSG00000113356	2 retrocopies	retro_hsap_1454, retro_hsap_1885,
Gorilla gorilla	ENSGGOG00000000266	2 retrocopies	retro_ggor_1119, retro_ggor_1382,
Myotis lucifugus	ENSMLUG00000014954	1 retrocopy	retro_mluc_2233,
Macaca mulatta	ENSMMUG00000018972	1 retrocopy	retro_mmul_1332,
Nomascus leucogenys	ENSNLEG00000013749	1 retrocopy	retro_nleu_1807,
Otolemur garnettii	ENSOGAG00000005560	1 retrocopy	retro_ogar_3512,
Pongo abelii	ENSPPYG00000015624	1 retrocopy	retro_pabe_1564,
Pan troglodytes	ENSPTRG00000017068	2 retrocopies	retro_ptro_1266, retro_ptro_989,
Rattus norvegicus	ENSRNOG00000016260	2 retrocopies	retro_rnor_458, retro_rnor_503,
Ictidomys tridecemlineatus	ENSSTOG00000008664	1 retrocopy	retro_itri_18 ,
Tupaia belangeri	ENSTBEG00000002278	2 retrocopies	retro_tbel_2495, retro_tbel_3069,