RetrogeneDB ID: retro_itri_521

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393298.1:11793497..11793756(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LYPD2
• Ensembl ID: ENSSTOG00000007179
• Aliases: None
• Description: LY6/PLAUR domain containing 2 [Source:HGNC Symbol;Acc:25215]

Sequence

>retro_itri_521
ATGAGGCTGTCACTGCTGGTGTTGGCTCTGGTCACCTGCAGAGAGTTCACAAAGGCCTTAAAATACTACACCTGTCAAGT
ACCCACAGGCGTGTCCAGCTGCATCACCATCATCAATTGAAATGCCAAAGAAACCAAGTGCAAGATCACCCCTCTACTCG
GGAGAGATCATGAACCCCTTGCTGGGAGACTCCATGTTGACCAAATCCTGCACCAGCAGGTATGAGCCACTAGACATATC
ATCAGCCAGATCCACCCAG

Alignment

ORF - retro_itri_521 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.07 %
• Parental protein coverage: 67.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRLALLALALATCGELAMALKCYTCLEPTGVSSCITITNCDANETMCKTT-LYSREIVYPFLGDSTVTKS
          MRL.LL.LAL.TC.E...ALK.YTC..PTGVSSCITI.N..A.ET.CK.T.LYS.EI..P.LGDS..TKS
Retrocopy MRLSLLVLALVTCREFTKALKYYTCQVPTGVSSCITIIN*NAKETKCKIT>LYSGEIMNPLLGDSMLTKS

Parental  CASRCEPSDVDGIGQTR
          C.SR.EP.D......T.
Retrocopy CTSRYEPLDISSARSTQ

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_521 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_521 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	ENSSTOG00000007179	1 retrocopy	retro_itri_521 ,