RetrogeneDB ID: retro_itri_1697

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393641.1:990659..990927(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EGLN1
• Ensembl ID: ENSSTOG00000023570
• Aliases: None
• Description: egl nine homolog 1 (C. elegans) [Source:HGNC Symbol;Acc:1232]

Sequence

>retro_itri_1697
ATGAATGACCTGATACTCCACTGCAACAGCAAGCTGGTCAACTACAAGATCAAGGGTCAGAGGAAAGCCATGGGTTTCTG
GTAACCCAAGCAGTGGGACAGATTTTCCAGTTGGTAATCCAAATGGAAATAAAAGATGTGTGTGGTATATATATTATTTA
AATAAAGACTGGGGTGCTAAGGTAAGTGGAAGTATACTTCAACTTTTCCAAGAAGGAAAAGCCCAGTTTGCTAACATTGA
ACCCAAATTTGATAGACTACTATTTTTC

Alignment

ORF - retro_itri_1697 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.96 %
• Parental protein coverage: 60.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDDLIRHCNGKLGNYKINGRTKAM-VACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILR
          M.DLI.HCN.KL.NYKI.G..KAM.V...P..GT.....V.NPNG..RCV........DW.AKVSG.IL.
Retrocopy MNDLILHCNSKLVNYKIKGQRKAM>VSGNPSSGTDFP--VGNPNGNKRCVWXXXXXXXDWGAKVSGSILQ

Parental  IFPEGKAQFADIEPKFDRLLFF
          .F.EGKAQFA.IEPKFDRLLFF
Retrocopy LFQEGKAQFANIEPKFDRLLFF

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_1697 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1697 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 3 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000007202	1 retrocopy	retro_etel_1722,
Rattus norvegicus	ENSRNOG00000019773	11 retrocopies	retro_rnor_1086, retro_rnor_1783, retro_rnor_2109, retro_rnor_2110, retro_rnor_2411, retro_rnor_2885, retro_rnor_2938, retro_rnor_2939, retro_rnor_2955, retro_rnor_507, retro_rnor_948,
Ictidomys tridecemlineatus	ENSSTOG00000023570	1 retrocopy	retro_itri_1697 ,