RetrogeneDB ID: retro_itri_210

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393279.1:37687303..37687671(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GUK1
• Ensembl ID: ENSSTOG00000026156
• Aliases: None
• Description: guanylate kinase 1 [Source:HGNC Symbol;Acc:4693]

Sequence

>retro_itri_210
GAGTTCTCAGGGAACCTGTATGGGACAAGCAAGGCGGCCGTGCCGGGTGTGCAGGCCATGAATCGCATCTGTGTGCTGGA
GGTGGACCTACAGGGCGTGCGCAACACCAAGCAGACAGACCTCCGCCCCATCTACTTTTCTATGCAGCCATCTTCACTGG
ACTTGCTGGAGCAGTGACTGCGCCAGCGCAATGTAGAATCAAAGGAAAGCCTGAGGAAGCTGGCTGCCGCTGGGCAAACA
TGGGCAGCAGCAGAGAGCCGGGCCTGTTCAACCTGGTGATCATCAATGACAAAATGGATGAGGCCTATGTCGCACTGAAG
CAGGCACTGTCTGAGGAAACCAAGAAAGCTCAGGGGACAAGCCATGCC

Alignment

ORF - retro_itri_210 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.4 %
• Parental protein coverage: 57.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EFSGNLYGTSKAAVRAVQAMNRICVLDVDLQGVRNIKKTDLHPIYISVQPPSLDVLEQRLRQRNTETEES
          EFSGNLYGTSKAAV..VQAMNRICVL.VDLQGVRN.K.TDL.PIY.S.QP.SLD.LEQ.LRQRN.E..ES
Retrocopy EFSGNLYGTSKAAVPGVQAMNRICVLEVDLQGVRNTKQTDLRPIYFSMQPSSLDLLEQ*LRQRNVESKES

Parental  LEKRLAAAR-ADMDSSKEPGLFDLVIINDNLDEAYAALKQALSEEIKKAQGTSHS
          L.K.LAAA..A.M.SS.EPGLF.LVIIND..DEAY.ALKQALSEE.KKAQGTSH.
Retrocopy LRK-LAAAG<ANMGSSREPGLFNLVIINDKMDEAYVALKQALSEETKKAQGTSHA

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_210 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_210 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	ENSMODG00000013790	1 retrocopy	retro_mdom_121,
Ictidomys tridecemlineatus	ENSSTOG00000026156	1 retrocopy	retro_itri_210 ,