RetrogeneDB ID: retro_dord_627

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_42275:1544..1889(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Uxt
• Ensembl ID: ENSDORG00000001025
• Aliases: None
• Description: ubiquitously expressed transcript [Source:MGI Symbol;Acc:MGI:1277988]

Sequence

>retro_dord_627
AAAGTATTGGACCATCAAGACAAGATATATGAGCAGCTGGCCACATACCTTCAGCTGAAAAATGTCATTGAGTAACTCCA
GGAAGCTAATCACTCAGAGTTATATATGGAGGTGGATTTGGGCTGTAACTTCTTCATTGACACAGTGGTTTCAGATACTT
CACGCATCTACGTAGCCCTGGGATATAGGTTTTTCCTGGAGTTGACACTGGCAGAAGCACTCAATTTCATTGATCTTAAG
AGCTCTCTCCTCACAAAGCTCAGCAACAGCCTAACCAAGGACTCCATGAATAGCAAGGCTCATGTCCATATGTTGTTAGA
GGGGCTGAAAGAACTACAGGGCATG

Alignment

ORF - retro_dord_627 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.83 %
• Parental protein coverage: 92.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KVLDHRDKVYEQLATYLQLKNVIERL-EANHSELYMQVDLGCNFFVDTVVSDTSRIYVALGYGFFLELTL
          KVLDH.DK.YEQLATYLQLKNVIE.L.EANHSELYM.VDLGCNFF.DTVVSDTSRIYVALGY.FFLELTL
Retrocopy KVLDHQDKIYEQLATYLQLKNVIE*LQEANHSELYMEVDLGCNFFIDTVVSDTSRIYVALGYRFFLELTL

Parental  AEALKFIDRKSSLLTELSNSLTKDSMNIKAHIHMLLEGLRELQGL
          AEAL.FID.KSSLLT.LSNSLTKDSMN.KAH.HMLLEGL.ELQG.
Retrocopy AEALNFIDLKSSLLTKLSNSLTKDSMNSKAHVHMLLEGLKELQGM

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_627 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000009154	1 retrocopy	retro_cpor_1302,
Dipodomys ordii	ENSDORG00000001025	1 retrocopy	retro_dord_627 ,
Erinaceus europaeus	ENSEEUG00000006151	1 retrocopy	retro_eeur_543,
Macropus eugenii	ENSMEUG00000003352	1 retrocopy	retro_meug_59,
Microcebus murinus	ENSMICG00000016263	1 retrocopy	retro_mmur_1156,
Mustela putorius furo	ENSMPUG00000013405	1 retrocopy	retro_mputfur_999,
Mus musculus	ENSMUSG00000001134	3 retrocopies	retro_mmus_1424, retro_mmus_1766, retro_mmus_715,
Rattus norvegicus	ENSRNOG00000009893	5 retrocopies	retro_rnor_521, retro_rnor_522, retro_rnor_683, retro_rnor_692, retro_rnor_882,
Tarsius syrichta	ENSTSYG00000012719	2 retrocopies	retro_tsyr_237, retro_tsyr_778,