RetrogeneDB ID: retro_itri_20

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393490.1:1578672..1579869(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000028077
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000004938
• Aliases: None
• Description: None

Sequence

>retro_itri_20
ATGGCCAGCCATCGCTGCGCCGCCGCGGCCCTCGCCTCGCAGGACTGCAGTAACGGATGCTCCGCTGAATACCTTGGAGA
AGGAGGATCAAAAGAGGTGGTGGAGACTTTCAGGGCTAAAGATCTAATAATCACACCAGCCACCATCTTGAAGGAAAAAC
CAGATCCCAATACTCTAGTTTTTGGAACTGTGTTTACGGATCACATGTTGACAGTGGAGTGGTCCTCTGAGTTTGGATGG
GAGAAACCTCACATCAAGCCTTTTCAAAACTTGTCACTGCATCCTGGATCATCGACTTTGCATTATGCAGTAGAATTATT
TGAAGGTTTAAAGGCATTTCGAGGAGTAGATAATAAAATTCGACTGTTTCGGCCAGAACTCAACATGGAGAGAATGTGTA
AGTCTGCTATGAGAGCCACTTTGCCGGTGTTTGACAAGGAAGAGCTTCTGGAGTGTATTCAGCAGCTTGTGCAGTTGGAT
CAAGAATGGGTGCCCTATTCCACCTCTGCCAGTCTCTACATTCGTCCCACATTTATTGGAACTGAGCCTTCTCTTGGAGT
CAAGAAGCCTACCAAAGCCCTGCTCTTTGTAATCTTAAGCCCAGTGGGACCTTATTTTTCAAGCGGAACCTTTAATCCAG
TGTCCCTGTGGGCCAACCCGAAGTATGTCAGAGCCTGGAAAGGTGGGACTGGAGACTGCAAGATGGGAGGGAATTATGGG
TCATCTCTTTTTGCCCAAAGTGAAGCAGCAGAGAATGGTTGTCAGCAGGTTCTCTGGCTCTATGGAGAGGATAATCAGAT
AACGGAAGTCGGAACTATGAATCTTTTTCTTTACTGGATAAATGAAGATGGAGAGGAAGAACTGGCAACTCCTCCGCTAG
ATGGCATCATTCTTCCAGGAGTGACGAGGCGGTGCATCCTGGACCTGGCGCACAAGTGGGGTGAATTTAAAGTGTCAGAG
AGGTACCTCACCATGGACGACTTGACAACTGCCCTGGAGGGGAACAGAGTGAGGGAGATGTTTGGCTCTGGCACAGCCTG
CATTGTCTGCCCAGTTTCTGATATACTATACAAGGGCGAGACGATACACATTCCAACTATGGAGAATGGTCCTAAGCTTG
CAACCCGTATCTTGGGCAAATTGACTGATATCCAGTATGGAAGAGAAGAGAGCGACTGGACAATTGTATTATCCTGA

Alignment

ORF - retro_itri_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.75 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASHRCAAAALASQDCSNGCSAEYLGEGGSKEVVETFRAKDLIITPATILKEKPDPNTLVFGTVFTDHML
          MASHRCAAAALASQDCSNGCSAEYLGEGGSKEVVETFRAKDLIITPATILKEKPDPNTLVFGTVFTDHML
Retrocopy MASHRCAAAALASQDCSNGCSAEYLGEGGSKEVVETFRAKDLIITPATILKEKPDPNTLVFGTVFTDHML

Parental  TVEWSSEFGWEKPHIKPFQNLSLHPGSSTLHYAVELFEGLKAFRGVDNKIRLFRPELNMERMCKSAMRAT
          TVEWSSEFGWEKPHIKPFQNLSLHPGSSTLHYAVELFEGLKAFRGVDNKIRLFRPELNMERMCKSAMRAT
Retrocopy TVEWSSEFGWEKPHIKPFQNLSLHPGSSTLHYAVELFEGLKAFRGVDNKIRLFRPELNMERMCKSAMRAT

Parental  LPVFDKEELLECIQQLVQLDQEWVPYSTSASLYIRPTFIGTEPSLGVKKPTKALLFVILSPVGPYFSSGT
          LPVFDKEELLECIQQLVQLDQEWVPYSTSASLYIRPTFIGTEPSLGVKKPTKALLFVILSPVGPYFSSGT
Retrocopy LPVFDKEELLECIQQLVQLDQEWVPYSTSASLYIRPTFIGTEPSLGVKKPTKALLFVILSPVGPYFSSGT

Parental  FNPVSLWANPKYVRAWKGGTGDCKMGGNYGSSLFAQSEAAENGCQQVLWLYGEDNQIISPEVGNIGAFLS
          FNPVSLWANPKYVRAWKGGTGDCKMGGNYGSSLFAQSEAAENGCQQVLWLYGEDNQI...EVG....FL.
Retrocopy FNPVSLWANPKYVRAWKGGTGDCKMGGNYGSSLFAQSEAAENGCQQVLWLYGEDNQI--TEVGTMNLFLY

Parental  WLLKPTEEELATPPLDGIILPGVTRRCILDLAHKWGEFKVSERYLTMDDLTTALEGNRVREMFGSGTACI
          W.....EEELATPPLDGIILPGVTRRCILDLAHKWGEFKVSERYLTMDDLTTALEGNRVREMFGSGTACI
Retrocopy WINEDGEEELATPPLDGIILPGVTRRCILDLAHKWGEFKVSERYLTMDDLTTALEGNRVREMFGSGTACI

Parental  VCPVSDILYKGETIHIPTMENGPKLATRILGKLTDIQYGREESDWTIVLS
          VCPVSDILYKGETIHIPTMENGPKLATRILGKLTDIQYGREESDWTIVLS
Retrocopy VCPVSDILYKGETIHIPTMENGPKLATRILGKLTDIQYGREESDWTIVLS

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_20 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_20 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011431	1 retrocopy	retro_chof_451,
Ictidomys tridecemlineatus	ENSSTOG00000004938	1 retrocopy	retro_itri_20 ,