RetrogeneDB ID: retro_dord_382

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_151451:871..1243(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Chmp3
• Ensembl ID: ENSDORG00000002851
• Aliases: None
• Description: charged multivesicular body protein 3 [Source:MGI Symbol;Acc:MGI:1913950]

Sequence

>retro_dord_382
ATGGCGGTCCTGTGAGTGGCTGGCTCCTTGCAGAAGAGCACCGAAGTGATGAAGGCCATGCAAAGTCTTGTGAAGATTCC
TGAGATACAGGCCACCATGAGGGAGCTGTCCAAAGTGATGGTGAAGGCTGGCATCATAGAAGAGCTGTTAGAGGACACCT
TTGAAAGCATGGAAGATCAGGAAGAAATGGAAGAAGAAGCAGAAATGGAAATTGACAAAATCTTGTTTGAAATTGCTGCA
GGGTCCTTGGGCAAAGTGCCCAGTAAAGTGACAGGTGCTCTTCCTGAGCCTGAACCTGCAGGAGCAACAGCTGCCGAAGA
GGAGGAAGAGGCCCTGGAGGCCATGCAGTCCCGGCTGGCCACACTGCGAAGC

Alignment

ORF - retro_dord_382 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.53 %
• Parental protein coverage: 57.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LAVLRVAGSLQKSTEVMKAMQSLVKIPEIQATMRELSKEMMKAGIIEEMLEDTFESMDDQEEMEEEAEME
          .AVL.VAGSLQKSTEVMKAMQSLVKIPEIQATMRELSK.M.KAGIIEE.LEDTFES..............
Retrocopy MAVL*VAGSLQKSTEVMKAMQSLVKIPEIQATMRELSKVMVKAGIIEELLEDTFESXXXXXXXXXXXXXX

Parental  IDKILFEITAGALGKAPSKVTDALPEPEPAGATAASEEEEEEEALEAMQSRLATLRS
          IDKILFEI.AG.LGK.PSKVT.ALPEPEPAGATAA...EEEEEALEAMQSRLATLRS
Retrocopy IDKILFEIAAGSLGKVPSKVTGALPEPEPAGATAA---EEEEEALEAMQSRLATLRS

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_382 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.

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000002851	1 retrocopy	retro_dord_382 ,
Macropus eugenii	ENSMEUG00000009111	1 retrocopy	retro_meug_178,
Microcebus murinus	ENSMICG00000005492	3 retrocopies	retro_mmur_1110, retro_mmur_1396, retro_mmur_47,
Mustela putorius furo	ENSMPUG00000009273	1 retrocopy	retro_mputfur_1508,
Mus musculus	ENSMUSG00000053119	1 retrocopy	retro_mmus_1683,
Ochotona princeps	ENSOPRG00000002191	2 retrocopies	retro_opri_18, retro_opri_436,
Sorex araneus	ENSSARG00000008917	1 retrocopy	retro_sara_13,