RetrogeneDB ID: retro_itri_1176

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393394.1:1143603..1144329(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000015416
• Aliases: None
• Description: None

Sequence

>retro_itri_1176
CATGTTTTCCTGGAATATGATCAGGATCTAAGTGTTAGGCCAAAAAATACCAAAGAAATGTTTGGTGGCTTCTTTAAAAG
TGTGGTAAAAAGTGCTGATGAAGTTCTTTTCTCTGGAGTTAAGGAGGTAGATGACTTCTTTGAGCAAGAGAAGAACTTCC
TTATTAACAATTACAACAAGATCAAGGATTCCTGTGCTAAAGCTGACAGAATGACCAGATCTCACAAAAATGTTGCTGAT
GACTATATTCACACTGCAGCCTCCTTGCAGAGCCTGGCTTTAGAAGAACCCACAGTCATCAAAAAATACCTATTGAAGGT
TGCTGAACTCTTTGAAAAACTTAGGAAAGTGGAGGGTTGTGTCTCATCAGATGAAGATTTAAAGCTGACAGAACTTCTCT
GATACTACATGCTCAATATAGAGGCTGCAAAGGATCTCTTATACAGACGCACCAAATCCCTTATTGACTATGAGAACTCA
AACAAAGCTCTGGATAAAGCCAGGTTAAAAAGCAAAGATGTCAAGTTGGCTGAGGCACACCAACAGGAATGTTGCCAGAA
ATTTGAACAGCTTTCTGAATCTGCAAAAGAAGAACTTATAAATTTCAAACGGAAGAGAGTGGCAGCGTTTAGAAAAAACC
TAATTGAGATGTCTGAACTGGAAATAAAGCATGCCAGAAACAATGTCTCCCTCTTGCAGAGCTGCATTGACTTATTCAAG
AACAAC

Alignment

ORF - retro_itri_1176 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.04 %
• Parental protein coverage: 61.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HPVLSKDRNLSVRRKNTKEMFGGFFKSVVKSADEVLFSGVKEVDDFFEQEKNFLINYYNRIKDSCAKADR
          H..L..D..LSVR.KNTKEMFGGFFKSVVKSADEVLFSGVKEVDDFFEQEKNFLIN.YN.IKDSCAKADR
Retrocopy HVFLEYDQDLSVRPKNTKEMFGGFFKSVVKSADEVLFSGVKEVDDFFEQEKNFLINNYNKIKDSCAKADR

Parental  MTRSHKNVADDYIHTAASLQSLALEEPTVIKKYLLKVAELFEKLRKVEGRVSSDEDLKLTELLRYYMLNI
          MTRSHKNVADDYIHTAASLQSLALEEPTVIKKYLLKVAELFEKLRKVEG.VSSDEDLKLTELL.YYMLNI
Retrocopy MTRSHKNVADDYIHTAASLQSLALEEPTVIKKYLLKVAELFEKLRKVEGCVSSDEDLKLTELL*YYMLNI

Parental  EAAKDLLYRRTKALIDYENSNKALDKARLKSKDVKLAEAHQQECCQKFEQLSESAKEELINFKRKRVAAF
          EAAKDLLYRRTK.LIDYENSNKALDKARLKSKDVKLAEAHQQECCQKFEQLSESAKEELINFKRKRVAAF
Retrocopy EAAKDLLYRRTKSLIDYENSNKALDKARLKSKDVKLAEAHQQECCQKFEQLSESAKEELINFKRKRVAAF

Parental  RKNLIEMSELEIKHARNNVSLLQSCIDLFKNN
          RKNLIEMSELEIKHARNNVSLLQSCIDLFKNN
Retrocopy RKNLIEMSELEIKHARNNVSLLQSCIDLFKNN

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_1176 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1176 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 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010128	2 retrocopies	retro_chof_1478, retro_chof_2166,
Callithrix jacchus	ENSCJAG00000004947	2 retrocopies	retro_cjac_2192, retro_cjac_3243,
Homo sapiens	ENSG00000089006	2 retrocopies	retro_hsap_1051, retro_hsap_2945,
Gorilla gorilla	ENSGGOG00000008953	1 retrocopy	retro_ggor_829,
Macropus eugenii	ENSMEUG00000009110	1 retrocopy	retro_meug_475,
Macaca mulatta	ENSMMUG00000011476	2 retrocopies	retro_mmul_1746, retro_mmul_832,
Nomascus leucogenys	ENSNLEG00000009714	1 retrocopy	retro_nleu_2071,
Oryctolagus cuniculus	ENSOCUG00000017072	1 retrocopy	retro_ocun_1323,
Otolemur garnettii	ENSOGAG00000006157	1 retrocopy	retro_ogar_1203,
Pongo abelii	ENSPPYG00000010730	2 retrocopies	retro_pabe_2442, retro_pabe_877,
Pan troglodytes	ENSPTRG00000013278	2 retrocopies	retro_ptro_2052, retro_ptro_717,
Sus scrofa	ENSSSCG00000007088	1 retrocopy	retro_sscr_593,
Ictidomys tridecemlineatus	ENSSTOG00000015416	1 retrocopy	retro_itri_1176 ,
Tursiops truncatus	ENSTTRG00000016432	1 retrocopy	retro_ttru_410,