RetrogeneDB ID: retro_dord_590

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_37112:4791..5120(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDORG00000007859
• Aliases: None
• Description: None

Sequence

>retro_dord_590
ATGGGTGCCAGCAGCTCCAAAGCTCAGGGCCTTTGGCCCTTCACCTTGGCAGTGGGGGTCGGCGGCTCAGAGGCGGCGGG
CACTTAGCAAGTTTTGGTGCGGCCTCGATCCGTGCGGTGCCACCCTTCGTATTCACGTGCGTCGGTTCCATGTTCTATGA
TGAAGATGGAGATCTGGCTCATGAATTCTATGAGGAGACAATCATCACCAAGAATGGGCAGAAGCGGGCCAAGCTGAGGT
GGGTACATAAGAATCTGATTCCTCAGGGCATCGTGAAACTGGATCCTCCCCGCATCTATGTGGATTTCCCTGTGATCCTC
TATGAGGTG

Alignment

ORF - retro_dord_590 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.29 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGASGSKARGLWPFTSAAGGGGPEAAGTEQALVRPRS-RAVPPFVFTRRGSMFYDEDGDLAHEFYEETII
          MGAS.SKA.GLWPFT.A.G.GG.EAAGT.Q.LVRPRS.RAVPPFVFT..GSMFYDEDGDLAHEFYEETII
Retrocopy MGASSSKAQGLWPFTLAVGVGGSEAAGT*QVLVRPRS<RAVPPFVFTCVGSMFYDEDGDLAHEFYEETII

Parental  TKNGQKRAKLRRVHKNLIPQGIVKLDPPRIHVDFPVILYEV
          TKNGQKRAKLR.VHKNLIPQGIVKLDPPRI.VDFPVILYEV
Retrocopy TKNGQKRAKLRWVHKNLIPQGIVKLDPPRIYVDFPVILYEV

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_590 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 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000007859	2 retrocopies	retro_dord_20, retro_dord_590 ,
Felis catus	ENSFCAG00000031595	1 retrocopy	retro_fcat_1831,
Myotis lucifugus	ENSMLUG00000002499	1 retrocopy	retro_mluc_874,
Mus musculus	ENSMUSG00000010054	2 retrocopies	retro_mmus_2347, retro_mmus_2349,
Oryctolagus cuniculus	ENSOCUG00000005259	1 retrocopy	retro_ocun_1687,
Otolemur garnettii	ENSOGAG00000008080	3 retrocopies	retro_ogar_2293, retro_ogar_2714, retro_ogar_3421,
Rattus norvegicus	ENSRNOG00000021528	1 retrocopy	retro_rnor_2952,
Tarsius syrichta	ENSTSYG00000010483	2 retrocopies	retro_tsyr_1922, retro_tsyr_2132,
Vicugna pacos	ENSVPAG00000007903	1 retrocopy	retro_vpac_221,