RetrogeneDB ID: retro_dord_249

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_6686:168592..168944(-)
• Located in intron of: ENSDORG00000003865

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDORG00000009236
• Aliases: None
• Description: None

Sequence

>retro_dord_249
CACCGCATGGGAGCCTGGTGGACCTGGCCTGAAAACTTCGATGCTCCATTGGTTTTTTTACCTGACAGAAGAACAGGAGA
AATACATATTCAGCCATGGGGACACATTCCTCCCCTGCATTGAGAAACACAGCCACACCCTCATTCAGCTGGAGCCCTGG
TTCACAGCCACAGGCAACACTCAAGTCACTGTGGTGGGTCCACCAAAGGCCAGGCAGTGGCTCAGGAACATGGCTCAGTA
TTTGGGGCACCAGGATGCTCATTGTCAAGCCCAAGGTTTGGAAATGCTGCAGCATGTCTGGAGCCAGCCCCTCACCAAGG
AGGACTTGGCCTTTTCTTTCATTGCTTCCCTG

Alignment

ORF - retro_dord_249 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.2 %
• Parental protein coverage: 74.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HSMGAWWTWPENFDAPLVF-YLTEEQEKVIFGQGDAFLPCIEKHSHTLIQLEPWFTATSHTQVTVVGPPK
          H.MGAWWTWPENFDAPLVF.YLTEEQEK.IF..GD.FLPCIEKHSHTLIQLEPWFTAT..TQVTVVGPPK
Retrocopy HRMGAWWTWPENFDAPLVF>YLTEEQEKYIFSHGDTFLPCIEKHSHTLIQLEPWFTATGNTQVTVVGPPK

Parental  AKQWLRNMVQYLGHQDARCQAQGYQMLQSVRSQPLTNKDLAASLSALL
          A.QWLRNM.QYLGHQDA.CQAQG..MLQ.V.SQPLT..DLA.S..A.L
Retrocopy ARQWLRNMAQYLGHQDAHCQAQGLEMLQHVWSQPLTKEDLAFSFIASL

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_249 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000009236	4 retrocopies	retro_dord_249 , retro_dord_47, retro_dord_607, retro_dord_82,
Microcebus murinus	ENSMICG00000006451	1 retrocopy	retro_mmur_647,
Macaca mulatta	ENSMMUG00000018573	1 retrocopy	retro_mmul_84,
Mus musculus	ENSMUSG00000067750	1 retrocopy	retro_mmus_464,
Oryctolagus cuniculus	ENSOCUG00000028154	1 retrocopy	retro_ocun_735,
Otolemur garnettii	ENSOGAG00000006102	1 retrocopy	retro_ogar_2275,