RetrogeneDB ID: retro_itri_1530

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393530.1:1615586..1616004(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MORN4
• Ensembl ID: ENSSTOG00000026926
• Aliases: None
• Description: MORN repeat containing 4 [Source:HGNC Symbol;Acc:24001]

Sequence

>retro_itri_1530
TTCACCTACTCTAGTGGGGAGGAATACCGTGGTGAGTGGAAGGAGGGCCGCAGGCATGGTTTTGGTCAACTGCTGTTTGC
AGATGGTGGCACCTAACTGGGTCATTTTGGAGAATGGGCTCTTTAATGGCTTTGGGGTACTGACCTTTTCAGATGGTTCA
GGGTATGAGGGGGAGTTTGCCCAGGGCAAGTTTAATGGCATCGGAGTCTTCATTCAGCATGACTACATGACCTTTGAGGG
GGAATTTTAAAATGGCAGAGTGGATGGTTTTGACCTGCTGACTTTCCCTGATGGTTCTCATGGAATACCCAGCAACCAAA
GTCTATTTGAGAACAATAAGCTGCTGCGGAGGGAGAAGTGTTCCGCGGTGGTTCAGCGGGTCCAGAGTGCCTCCAAGTCC
ACCAGAAAACTCACTGCT

Alignment

ORF - retro_itri_1530 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.57 %
• Parental protein coverage: 95.21 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FTYSSGEEYHGEWKEGRRHGYGQLLFADGGTYLGHF-ENGLFNGFGVLTFSDGSRYEGEFAQGKFNGVGV
          FTYSSGEEY.GEWKEGRRHG.GQLLFADGGT.LGHF.ENGLFNGFGVLTFSDGS.YEGEFAQGKFNG.GV
Retrocopy FTYSSGEEYRGEWKEGRRHGFGQLLFADGGT*LGHF>ENGLFNGFGVLTFSDGSGYEGEFAQGKFNGIGV

Parental  FIRHDNMTFEGEFKNGRVDGFGLLTFPDGSHGIPRNEGLFENNKLLRREKCSAVVQRAQSASKSARNLTA
          FI.HD.MTFEGEF.NGRVDGF.LLTFPDGSHGIP.N..LFENNKLLRREKCSAVVQR.QSASKS.R.LTA
Retrocopy FIQHDYMTFEGEF*NGRVDGFDLLTFPDGSHGIPSNQSLFENNKLLRREKCSAVVQRVQSASKSTRKLTA

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_1530 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1530 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000026926	2 retrocopies	retro_itri_1530 , retro_itri_733,