RetrogeneDB ID: retro_dord_6

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_7323:23961..24375(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDORG00000006135
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDORG00000015213
• Aliases: None
• Description: None

Sequence

>retro_dord_6
ATGAGGGCGCACCTGGCCCGGCGCTACCTCAGCGATGGCTCGGGGGAGCCCGACCCCCTGAATATGCCCGTGTTTCCGCC
CGACTACGGCCTCCCGGACCGCAAGGAGCGCGTGATGGTGGCCACGCAGCAGGAGATGAACAATGCGCAGCTGAGCCTGG
AGCAGCGCGACTACTGCGCCCACTACCTCATCCGCCTGCTCAAGTGCAAGCGCGACAACTTCCCCAACTTCCTGGCCTGC
AAACATGCCCAACACGACTGGGACTACTGCGAGCACCAAGACTACGTGATGCGCATGAAGGAGTTCGAACGCGAGCGGCG
GCTGCTGCAGCGCAAGCATGGGAGGGAACAGAGGGCAGCCAGAGTGGCCAAGGGTGAGGTGATCGGCGAGGTGGGCTTCG
AGGTGGCCTTGTAG

Alignment

ORF - retro_dord_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.08 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGAHLARRYLSDGSGEPDPLNMPVFPPDYGLPDRKERVMVATQQEMNDAQLSLEQRDYCAHYLIRLLKCK
          M.AHLARRYLSDGSGEPDPLNMPVFPPDYGLPDRKERVMVATQQEMN.AQLSLEQRDYCAHYLIRLLKCK
Retrocopy MRAHLARRYLSDGSGEPDPLNMPVFPPDYGLPDRKERVMVATQQEMNNAQLSLEQRDYCAHYLIRLLKCK

Parental  RDNFPNFLACKHAQHDWDYCEHQDYVMRMKEFERERRLLQRKHRREQRAARVAKGEVIGEVGPEVAL
          RDNFPNFLACKHAQHDWDYCEHQDYVMRMKEFERERRLLQRKH.REQRAARVAKGEVIGEVG.EVAL
Retrocopy RDNFPNFLACKHAQHDWDYCEHQDYVMRMKEFERERRLLQRKHGREQRAARVAKGEVIGEVGFEVAL

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_6 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011470	1 retrocopy	retro_amel_1288,
Canis familiaris	ENSCAFG00000016258	1 retrocopy	retro_cfam_1718,
Dipodomys ordii	ENSDORG00000015213	1 retrocopy	retro_dord_6 ,
Mus musculus	ENSMUSG00000033938	1 retrocopy	retro_mmus_2539,
Otolemur garnettii	ENSOGAG00000009615	1 retrocopy	retro_ogar_2154,