RetrogeneDB ID: retro_itri_1832

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393956.1:135254..136037(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000023598
• Aliases: None
• Description: None

Sequence

>retro_itri_1832
ATTGATCCATTTGGTGGTGATCCTTTCAAAGGTTCAGATCCATTTGCATCTGACTCTTTCTTCAAGCAGTCTTCTACTGA
TCCTTTTGCCACTTTAAGTAATGACGCTTTTAGTGCATCCAGCCAGAGCAATAATACATCAGTAGAAACATTGAAGCACA
ATGATCCTTTTGCTCCTGGTGGGACAATTGTTATTGCAGCAAGTGATTCAGCCCCAGACCCCTTTGCTTCTGTTTTTGGA
AATGAATCATTTGAAGATGGATTTGCTGACTGCAGCACATTGTCAAAGGCGAACAATGAAGATCCTTTTAACTCAGCCAC
ATCAAGCTCTGTCAACAATGTGGTCACTCCAAAAAATGTGTTTGATGAAACATCCATCAAGAGTGAAGATGTACCCCCAG
CACTGCCACCTAAGACGGGAACTCCAACAAGACCCTGCCCACCATCACCTGGGAAAAGACCCATCAACAAATTGGATTCT
TCTGATCCCTTTAAAGTGAATGATCCATTTCAGCCTTTCCCAGGCAATAATAGCCCCAAAGAAAAAGATCCTGATATGTA
TTGGGATCCATTCACTTCTTCTTCTACTTGCACTACCAATAAAGAGGGTGACCTAAGCAATTTTGCTAACTTCAGTGCTT
ATCCCTCTGAAGAAGATATGATTGAATGGGCCAAGAGGGAGAGTGAGAGAGAGGAAGAACAAAGGCTTGCCCGACTGAAT
CAGCAAGAACAAGAAGACCTAGAACTGGCTATTGCACTCAGCAAATCTGAGATATCAGAAGCA

Alignment

ORF - retro_itri_1832 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.17 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LDPFGGDPFKGSDPFASDSFFKQSSTDPFATLSNDPFSASSQSNNTSVETLKHNDPFAPGGTIVIAASDS
          .DPFGGDPFKGSDPFASDSFFKQSSTDPFATLSND.FSASSQSNNTSVETLKHNDPFAPGGTIVIAASDS
Retrocopy IDPFGGDPFKGSDPFASDSFFKQSSTDPFATLSNDAFSASSQSNNTSVETLKHNDPFAPGGTIVIAASDS

Parental  ATDPFASVFGNESFEDGFADFSTLSKANNEDPFNSATSSSVNNVVTPKNVFDETSIKSEDVPPALPPKTG
          A.DPFASVFGNESFEDGFAD.STLSKANNEDPFNSATSSSVNNVVTPKNVFDETSIKSEDVPPALPPKTG
Retrocopy APDPFASVFGNESFEDGFADCSTLSKANNEDPFNSATSSSVNNVVTPKNVFDETSIKSEDVPPALPPKTG

Parental  TPTRPCPPPPGKRPINKLDSSDPFKVNDPFQPFPGNDSPKEKDPDMYCDPFTSSSTSTTNKEADPSNFAN
          TPTRPCPP.PGKRPINKLDSSDPFKVNDPFQPFPGN.SPKEKDPDMY.DPFTSSST.TTNKE.D.SNFAN
Retrocopy TPTRPCPPSPGKRPINKLDSSDPFKVNDPFQPFPGNNSPKEKDPDMYWDPFTSSSTCTTNKEGDLSNFAN

Parental  FSAYPSEEDMIEWAKRESEREEEQRLARLNQQEQEDLELAIALSKSEISEA
          FSAYPSEEDMIEWAKRESEREEEQRLARLNQQEQEDLELAIALSKSEISEA
Retrocopy FSAYPSEEDMIEWAKRESEREEEQRLARLNQQEQEDLELAIALSKSEISEA

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_1832 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1832 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000023598	1 retrocopy	retro_itri_1832 ,