RetrogeneDB ID: retro_itri_973

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393353.1:7492871..7493227(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLTP
• Ensembl ID: ENSSTOG00000004484
• Aliases: None
• Description: glycolipid transfer protein [Source:HGNC Symbol;Acc:24867]

Sequence

>retro_itri_973
ATGGCGCTGCTGGCGGAGCACCTGCTGAAGCCGCTGCCCAAGGACAAGCAGATAGAGACCGGGCCCTTCCTGGAGGCGGT
GTCCACCTGCTGCCCTTCTTCGATTGCCTTGGGTCCCCCGTGTTTACACCCATCAAGGCAGACATAAGTGGCAACATCAC
GAAAATCAAAGCTGTGTATGACACCAACCCATCCAAGTTCCGGACCCTGCAGAACATCCTGGAGGTGGAGAAGGAAATGT
ATGGAGCAGAATGGCCCAAAGTGGGGGCCACGCTGGCACTGATGTGGCTGAAAAGAGGCCTTCGCTTCATCCAGGTCTTC
CTCCAGAGCATCTGTGATGGCGAGCGACCTCACAAC

Alignment

ORF - retro_itri_973 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.17 %
• Parental protein coverage: 56.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALLAEHLLKPLPADKQIETGPFLEAVS-HLPPFFDCLGSPVFTPIKADISGNITKIKAVYDTDPAKFRT
          MALLAEHLLKPLP.DKQIETGPFLEAVS.HL.PFFDCLGSPVFTPIKADISGNITKIKAVYDT.P.KFRT
Retrocopy MALLAEHLLKPLPKDKQIETGPFLEAVS<HLLPFFDCLGSPVFTPIKADISGNITKIKAVYDTNPSKFRT

Parental  LQNILEVEKEMYGAEWPKVGATLALMWLKRGLRFIQVFLQSICDGERDEN
          LQNILEVEKEMYGAEWPKVGATLALMWLKRGLRFIQVFLQSICDGER..N
Retrocopy LQNILEVEKEMYGAEWPKVGATLALMWLKRGLRFIQVFLQSICDGERPHN

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_973 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_973 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 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000016033	1 retrocopy	retro_etel_1197,
Myotis lucifugus	ENSMLUG00000012545	5 retrocopies	retro_mluc_1056, retro_mluc_1902, retro_mluc_2135, retro_mluc_2397, retro_mluc_658,
Pongo abelii	ENSPPYG00000004939	1 retrocopy	retro_pabe_28,
Pan troglodytes	ENSPTRG00000005431	1 retrocopy	retro_ptro_41,
Ictidomys tridecemlineatus	ENSSTOG00000004484	1 retrocopy	retro_itri_973 ,