RetrogeneDB ID: retro_dord_443

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_18951:7551..7917(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Synj2bp
• Ensembl ID: ENSDORG00000010450
• Aliases: None
• Description: synaptojanin 2 binding protein [Source:MGI Symbol;Acc:MGI:1344347]

Sequence

>retro_dord_443
CTGAGACTCAACATTGTTGGTGGGACAGATCAACAGTATGTCTCCAATGACAGTAGTATCTACATCTTCTGAATCAAAGA
GAATGAGGCTGCAGCCCGGGATGTGCCACTTCAAGAGGGTGATAAGATCCTCTCTGTACATGGCCAAGCCCTAAAGAACC
TGCTGCACCAGGATGCTGTGGACCTCTTAAATAATGCAAACTATGCTGTGTCCCAGAGAGTGCAGCACTAGTGAAAGCTG
CAGAATAGACTTTTAGGATGTCAAGATGAAGGGGAACCAAACAGTATTCCTGTAGCTGTGATGCTTTTGCCACTGTGCTC
TCCCATGGTAGCAGCCTGGGCCTTCATGAAGTGCCAACAACAGCTT

Alignment

ORF - retro_dord_443 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LGFNIVGGTDQQYVSNDSGIYVSRIKENGAAAQDGRLQEGDKILSVNGQDLKNLLHQDAVDLFRNAGYAV
          L..NIVGGTDQQYVSNDS.IY...IKEN.AAA.D..LQEGDKILSV.GQ.LKNLLHQDAVDL..NA.YAV
Retrocopy LRLNIVGGTDQQYVSNDSSIYIF*IKENEAAARDVPLQEGDKILSVHGQALKNLLHQDAVDLLNNANYAV

Parental  SLRVQHRLQVQNGPIGHRGEGEPNSIPVAVMLLPVFALTMLAAWAFMKYRQQL
          S.RVQH....QN...G...EGEPNSIPVAVMLLP.....M.AAWAFMK..QQL
Retrocopy SQRVQH**KLQNRLLGCQDEGEPNSIPVAVMLLPLCS-PMVAAWAFMKCQQQL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq

Dipodomys ordii was not studied using ChIP-Seq data.

EST

Dipodomys ordii was not studied using EST data.

TSS

Dipodomys ordii was not studied using FANTOM5 data.

Lab

retro_dord_443 was not experimentally validated.

Homology

Retrocopy orthology:

Dipodomys ordii 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007586	1 retrocopy	retro_btau_1114,
Dipodomys ordii	ENSDORG00000010450	1 retrocopy	retro_dord_443 ,
Macaca mulatta	ENSMMUG00000011086	1 retrocopy	retro_mmul_2308,
Mus musculus	ENSMUSG00000090935	3 retrocopies	retro_mmus_1428, retro_mmus_1538, retro_mmus_1802,
Otolemur garnettii	ENSOGAG00000013211	1 retrocopy	retro_ogar_1515,