RetrogeneDB ID: retro_itri_277

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393281.1:33492754..33493175(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000014607
• Aliases: None
• Description: None

Sequence

>retro_itri_277
GAGTCCGAGACTTGGGATGATGTGGACTTCCTAACAAGGCAGAAAAAATTGCAGGCTGAAGCCAAGATGGCCCTCATCTT
GGCCAAGCCCATGGACAAAATGCAAGTGGAGGTGGAGAAACAGAACAGGAAGAAGTTTCCCATGGCTAATCTCCTGCCTC
ACCTGCCTCATAGCAGGGAGTGCTTGATAAAGAGGAACCTGAAGATCACTTGACCTTCATGGCATAACCCTGGTCAGCTG
CAGGTGATAAGTCAATGATCTCCATTCCCAGATCAAAAGCTCTAATGAAGAGTTGGTGCAGTTGCTCCTTAACCAAGACA
AGCTGAATACAGAGCAAGATACCATGCTGGTGGACATCAAAGTCTTGACCAGACATGCTGAAAGTCAGCAGAAGCACATG
GCAGAGAAGATGTCTGCAAAG

Alignment

ORF - retro_itri_277 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.02 %
• Parental protein coverage: 52.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ESESLDDMDFLTRQKKLQAEAKMALAMAKPMAKMQVEVEKQNRKKSPVADLLPHLPHISECLMKRSLK-P
          ESE..DD.DFLTRQKKLQAEAKMAL..AKPM.KMQVEVEKQNRKK.P.A.LLPHLPH..ECL.KR.LK..
Retrocopy ESETWDDVDFLTRQKKLQAEAKMALILAKPMDKMQVEVEKQNRKKFPMANLLPHLPHSRECLIKRNLK>S

Parental  ADLRGMTL-GQLQVI-VNDLHSQIESLNEELVQLLLIRDELHTEQDAMLVDIEDLTRHAESQQKHMAEKM
          .DL.G.TL.GQLQVI.VNDLHSQI.S.NEELVQLLL..D.L.TEQD.MLVDI..LTRHAESQQKHMAEKM
Retrocopy LDLHGITL<GQLQVI>VNDLHSQIKSSNEELVQLLLNQDKLNTEQDTMLVDIKVLTRHAESQQKHMAEKM

Parental  PAK
          .AK
Retrocopy SAK

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_277 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_277 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
Monodelphis domestica	ENSMODG00000011375	1 retrocopy	retro_mdom_1389,
Ictidomys tridecemlineatus	ENSSTOG00000014607	1 retrocopy	retro_itri_277 ,