RetrogeneDB ID: retro_itri_362

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393286.1:22705078..22705670(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMED10
• Ensembl ID: ENSSTOG00000007392
• Aliases: None
• Description: transmembrane emp24-like trafficking protein 10 (yeast) [Source:HGNC Symbol;Acc:16998]

Sequence

>retro_itri_362
TTCCTACTCGGACCCAGCTGGGTCCTCGCCATCTCTTTCCATCTGCCCGTTAACTCCTGCAAGTGTCTCCACGAGGAGAT
CCACAAGAACCTGTCATGACGGGCGCCTACGAGACTGCGGACCAGTCTGGGGGGTGCTGGCGGCCTGCGCACCCACCTCA
AGATCACAGATTCTGCTGGACATATTTTATACTCCAAGAAAGATGCATCCAAGGGGAAGTTGGCTTTCACCACTGAAGAT
CATGACATGTTTGAAGTATGTTTTGAGAGCAACAGGACAGGGCGGATCCCTGACCAACTCCTGATCCTAGACATGAAGCA
TGGAGTGGAGGCTAAAAATTATAAAGAGATGGCAAAAGTCGAGAAGCTCAGACCATTAGAGGTGGAGCTAAGACGCCTAG
AAGAACTTTCGGGATCTATTGTTAATGATTCTGCCTACATGAAGAAGCCAGAGGAGGAAATGTGTGATACCAATGAGTCA
CCAAACACTGAGTCCTGTACTTTAGCATCTTTTCACTGTCCTGCCTTATTGGACTAGCACCTGGCAGGTCTTCTGCCTTC
ATTGCTTCTTCAAGGCCAAGAAGTTAACTGAG

Alignment

ORF - retro_itri_362 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.66 %
• Parental protein coverage: 90.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FLLGPSSVLAISFHLPVNSRKCLREEIHKDL-LVTGAYEIADQS-GGAGGLRTHLKITDSAGHILYSKED
          FLLGPS.VLAISFHLPVNS.KCL.EEIHK.L...TGAYE.ADQS.GGAGGLRTHLKITDSAGHILYSK.D
Retrocopy FLLGPSWVLAISFHLPVNSCKCLHEEIHKNL<VMTGAYETADQS>GGAGGLRTHLKITDSAGHILYSKKD

Parental  ASKGKFAFTTEDYDMFEVCFESKGTGRIPDQLVILDMKHGVEAKNYEEIAKVEKLKPLEVELRRLEDLSE
          ASKGK.AFTTED.DMFEVCFES..TGRIPDQL.ILDMKHGVEAKNY.E.AKVEKL.PLEVELRRLE.LS.
Retrocopy ASKGKLAFTTEDHDMFEVCFESNRTGRIPDQLLILDMKHGVEAKNYKEMAKVEKLRPLEVELRRLEELSG

Parental  SIVNDFAYMKKREEEMRDTNESTNTR-VLYFSIFSMFCLIGLA-TWQVFYLRRFFKAKKLIE
          SIVND.AYMKK.EEEM.DTNES.NT..VLYFSIFS..CLIGLA.TWQVF.L..FFKAKKL.E
Retrocopy SIVNDSAYMKKPEEEMCDTNESPNTE<VLYFSIFSLSCLIGLA<TWQVFCLHCFFKAKKLTE

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_362 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_362 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 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016899	1 retrocopy	retro_acar_187,
Callithrix jacchus	ENSCJAG00000020627	2 retrocopies	retro_cjac_1409, retro_cjac_4223,
Dasypus novemcinctus	ENSDNOG00000019851	1 retrocopy	retro_dnov_1225,
Echinops telfairi	ENSETEG00000010607	1 retrocopy	retro_etel_1798,
Homo sapiens	ENSG00000170348	2 retrocopies	retro_hsap_2701, retro_hsap_4014,
Gorilla gorilla	ENSGGOG00000007453	1 retrocopy	retro_ggor_2696,
Myotis lucifugus	ENSMLUG00000017125	2 retrocopies	retro_mluc_2079, retro_mluc_2093,
Macaca mulatta	ENSMMUG00000015168	2 retrocopies	retro_mmul_2316, retro_mmul_885,
Mus musculus	ENSMUSG00000021248	2 retrocopies	retro_mmus_1093, retro_mmus_649,
Nomascus leucogenys	ENSNLEG00000016453	2 retrocopies	retro_nleu_2897, retro_nleu_2963,
Oryctolagus cuniculus	ENSOCUG00000004669	1 retrocopy	retro_ocun_875,
Pongo abelii	ENSPPYG00000029389	1 retrocopy	retro_pabe_3296,
Pan troglodytes	ENSPTRG00000006552	2 retrocopies	retro_ptro_1823, retro_ptro_2724,
Rattus norvegicus	ENSRNOG00000007901	2 retrocopies	retro_rnor_1729, retro_rnor_2031,
Ictidomys tridecemlineatus	ENSSTOG00000007392	1 retrocopy	retro_itri_362 ,
Vicugna pacos	ENSVPAG00000003089	1 retrocopy	retro_vpac_573,