RetrogeneDB ID: retro_itri_150

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393578.1:150962..152048(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000020114
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000009019
• Aliases: None
• Description: None

Sequence

>retro_itri_150
ATGGGGAACGTGTTGGCCGCTAGCTCGCCGCCCGCAGGGCCGCCGCCTCCACCTGCGCCGGCCCTCGTGGGGCTGCCGCC
ACCTCCGCCCTCGCCGCCGGGCTTCACGCTGCCGCCGCTCGGAGGCGGCCTTGGTGCTGGGGCCAGCGCGGGTCGAGGTT
CGGACCGAACCGCGGGGGCTGCCACCGTCAGTGCCGCAGGGGTCGCTGACAACGGGGCCTGCGACTGCCTGCCCAACCCC
GGCACGTTCGAGGAGTGCCACCGGAAGTGCAAGGAGCTGTTTCCCATTCAGATGGAGGGTGTCAAGCTTACAGTCAACAA
AGGGTTGAGTAACCATTTCCAGGTGAACCACACAGTAGCCCTCAGCACAATCGGGGAGTCCAACTACCACTTCGGGGTCA
CGTATGTGGGGACAAAGCAGCTGAGTCCCACAGAGGCGTTCCCAGTGCTGGTGGGTGACATGGATAACAGTGGCAGCCTC
AACGCTCAGGTCATTCACCAGCTGGGCCCTGGCCTCAGGTCCAAGATGGCCATCCAGACCCAGCAGTCGAAGTTTGTGAA
CTGGCAGGTGGATGGGGAGTACCGAGGTTCCGACTTCACGGCAGCCGTCACCCTAGGAAACCCAGACGTTCTCGTGGGTT
CAGGAATCCTCGTGGCCCACTACCTCCAGAGCATCACGCCATGCCTGACCCTGGGTGGCGAGCTGGTCTACCACCGGCGG
CCCGGAGAGGAAGGCACCGTCATGTCGCTGGCTGGGAAATACACACTTAACAACTGGTTGGCCACAGTGACACTGGGCCA
AGCTGGCATGCACGCGACGTACTACCACAAAGCCAGTGACCAGTTGCAGGTAGGCGTGGAGTTCGAGGCCAGCACGAGGA
TGCAGGACACTAGCGTCTCCTTTGGGTACCAGCTGGACCTGCTGAAGGCCAACCTCCTCTTCAAAGCCTCCGTGGACAGT
AACTGGATCGTGGGCGCCACCCTGGAGAAGAAGCTGCCGCCCCTGCCTCTGACGCTGGCCCTCGGGGCCTTCCTGAACCA
CCGCAAGAACAAGTTCCAGTGCGGCTTCGGCCTCACCGTCGGCTGA

Alignment

ORF - retro_itri_150 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGNVLAASSPPAGPPPPPAPALVGLPPPPPSPPGFTLPPLGGGLGAGASAGRGSDRTAGAATVSAAGVAD
          MGNVLAASSPPAGPPPPPAPALVGLPPPPPSPPGFTLPPLGGGLGAGASAGRGSDRTAGAATVSAAGVAD
Retrocopy MGNVLAASSPPAGPPPPPAPALVGLPPPPPSPPGFTLPPLGGGLGAGASAGRGSDRTAGAATVSAAGVAD

Parental  NGACDCLPNPGTFEECHRKCKELFPIQMEGVKLTVNKGLSNHFQVNHTVALSTIGESNYHFGVTYVGTKQ
          NGACDCLPNPGTFEECHRKCKELFPIQMEGVKLTVNKGLSNHFQVNHTVALSTIGESNYHFGVTYVGTKQ
Retrocopy NGACDCLPNPGTFEECHRKCKELFPIQMEGVKLTVNKGLSNHFQVNHTVALSTIGESNYHFGVTYVGTKQ

Parental  LSPTEAFPVLVGDMDNSGSLNAQVIHQLGPGLRSKMAIQTQQSKFVNWQVDGEYRGSDFTAAVTLGNPDV
          LSPTEAFPVLVGDMDNSGSLNAQVIHQLGPGLRSKMAIQTQQSKFVNWQVDGEYRGSDFTAAVTLGNPDV
Retrocopy LSPTEAFPVLVGDMDNSGSLNAQVIHQLGPGLRSKMAIQTQQSKFVNWQVDGEYRGSDFTAAVTLGNPDV

Parental  LVGSGILVAHYLQSITPCLALGGELVYHRRPGEEGTVMSLAGKYTLNNWLATVTLGQAGMHATYYHKASD
          LVGSGILVAHYLQSITPCL.LGGELVYHRRPGEEGTVMSLAGKYTLNNWLATVTLGQAGMHATYYHKASD
Retrocopy LVGSGILVAHYLQSITPCLTLGGELVYHRRPGEEGTVMSLAGKYTLNNWLATVTLGQAGMHATYYHKASD

Parental  QLQVGVEFEASTRMQDTSVSFGYQLDLPKANLLFKGSVDSNWIVGATLEKKLPPLPLTLALGAFLNHRKN
          QLQVGVEFEASTRMQDTSVSFGYQLDL.KANLLFK.SVDSNWIVGATLEKKLPPLPLTLALGAFLNHRKN
Retrocopy QLQVGVEFEASTRMQDTSVSFGYQLDLLKANLLFKASVDSNWIVGATLEKKLPPLPLTLALGAFLNHRKN

Parental  KFQCGFGLTIG
          KFQCGFGLT.G
Retrocopy KFQCGFGLTVG

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_150 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_150 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 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000130204	5 retrocopies	retro_hsap_1300, retro_hsap_1386, retro_hsap_2321, retro_hsap_2537, retro_hsap_3159,
Gorilla gorilla	ENSGGOG00000023033	1 retrocopy	retro_ggor_1356,
Microcebus murinus	ENSMICG00000014041	1 retrocopy	retro_mmur_420,
Myotis lucifugus	ENSMLUG00000028928	1 retrocopy	retro_mluc_697,
Macaca mulatta	ENSMMUG00000014303	1 retrocopy	retro_mmul_1998,
Nomascus leucogenys	ENSNLEG00000001726	2 retrocopies	retro_nleu_2368, retro_nleu_2542,
Oryctolagus cuniculus	ENSOCUG00000023582	1 retrocopy	retro_ocun_1143,
Pongo abelii	ENSPPYG00000025858	1 retrocopy	retro_pabe_174,
Pan troglodytes	ENSPTRG00000011126	1 retrocopy	retro_ptro_39,
Ictidomys tridecemlineatus	ENSSTOG00000003800	2 retrocopies	retro_itri_301, retro_itri_724,
Ictidomys tridecemlineatus	ENSSTOG00000009019	1 retrocopy	retro_itri_150 ,
Drosophila melanogaster	FBgn0016041	1 retrocopy	retro_dmel_74,