RetrogeneDB ID: retro_dord_491

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_23117:770..1146(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ccdc25
• Ensembl ID: ENSDORG00000006595
• Aliases: None
• Description: coiled-coil domain containing 25 [Source:MGI Symbol;Acc:MGI:1914429]

Sequence

>retro_dord_491
TGCAAGATGAACAACATTAATGTGGTATACACGCCATAATCTAACCTGAAGAAACAGCTGACATGGATTTGGGGCAGATA
GCTCTTCTCAGGGAGAAGGATGTAAAAATTGTGACAATCGAGAATAAAGTGAATTAGATCCTGAATCAATTAGAAAAGAC
TAAATCAGAGTGGTTCCCAGACGTGGCAGCACAGAGAGAGATAGACCATGAAGAGAGAAATGAGAAAAAAAAGCCCAGAT
TCAGGAAATCAAAAGGAGAGAGAAAGAAGAGATGATGAAGAAGAAGGAAACAGAGAAACTAAAGAGGTATTCATTCCTAA
TGAAAGTTGAGAACACATCTTCAAATCAGGATGGGCAAGATTCCAATGAATTCATG

Alignment

ORF - retro_dord_491 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.94 %
• Parental protein coverage: 63.64 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CKMNNVNVVYTPWSNLKK-TADMDVGQIGFHRQKDVKIVTVEKKVNEILNRLEKTKSERFPDLAAEKE-G
          CKMNN.NVVYTP.SNLKK.TADMD.GQI...R.KDVKIVT.E.KVN.ILN.LEKTKSE.FPD.AA..E..
Retrocopy CKMNNINVVYTP*SNLKK<TADMDLGQIALLREKDVKIVTIENKVN*ILNQLEKTKSEWFPDVAAQRE<D

Parental  RDREERNEKKAQIQEMKRREKEEMKKKREMDELRSYSSLMKVENMSSNQDGNDSDEFM
          R...E.....AQIQE....................YS.LMKVEN.SSNQDG.DS.EFM
Retrocopy RP*REK*XXXAQIQEIXXXXXXXXXXXXXXXXXXXYSFLMKVENTSSNQDGQDSNEFM

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_491 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012971	2 retrocopies	retro_chof_2254, retro_chof_847,
Dipodomys ordii	ENSDORG00000006595	1 retrocopy	retro_dord_491 ,
Echinops telfairi	ENSETEG00000006478	1 retrocopy	retro_etel_434,
Homo sapiens	ENSG00000147419	1 retrocopy	retro_hsap_1701,
Gorilla gorilla	ENSGGOG00000009685	1 retrocopy	retro_ggor_1274,
Monodelphis domestica	ENSMODG00000015976	1 retrocopy	retro_mdom_511,
Pongo abelii	ENSPPYG00000018468	2 retrocopies	retro_pabe_1364, retro_pabe_477,
Pan troglodytes	ENSPTRG00000020109	1 retrocopy	retro_ptro_141,
Tarsius syrichta	ENSTSYG00000000732	1 retrocopy	retro_tsyr_1364,