RetrogeneDB ID: retro_dord_606

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_39735:466..1006(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDORG00000002873
• Aliases: None
• Description: None

Sequence

>retro_dord_606
GGAGCTCCGGGCCCTGGGCCTGGCTCGGGAATGCCTGGCAGCCAAGAGGAGGAGGAAGAGCCGGGACTGGTGGAGAGTGA
TCCAGGGGACAGCACCATTGAGGACTCGGAGCTGGAAGCGATCAAAGTTCACCTCAGGGAGATGGAGGAAGAAGCTGAGA
AGCAAAAGGAGCTACAGAACGAGGTAGGGAAGCAGATGAACATGAGCCCACCTCCAGGCAATGCTGGCCCAGTGATCATG
TCTATTGAAGAGAGGATGGAGGCTGATGCCCACTCCATCTATGTTGGCAATGTGGACTATGGTGCAACAGCAGAAGAGCT
AGAAGCTCCCTTTCATGGCTGTGATTCAGTCAACTGGGTTACCATACTTTGTGACAAATTTAGTGGCCATCCCAAAGGGT
TTGCATATATAGAGTTCTCAGACAAAGAGTCAGTGAGGACTTCCCTGGCCTTAGCTGAGTCCCTTTTTAGAGGAAGACAA
ATCAAGGTGATTCCCAAATTGACCAACAGACCAGACATCAGCACAACAGACGGGGGTTTC

Alignment

ORF - retro_dord_606 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.56 %
• Parental protein coverage: 58.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GAPGPGPGSGAPGSQEEEEEPGLVESDPGDGAIEDPELEAIKARVREMEEEAEKLKELQNEVEKQMNMSP
          GAPGPGPGSG.PGSQEEEEEPGLVESDPGD..IED.ELEAIK...REMEEEAEK.KELQNEV.KQMNMSP
Retrocopy GAPGPGPGSGMPGSQEEEEEPGLVESDPGDSTIEDSELEAIKVHLREMEEEAEKQKELQNEVGKQMNMSP

Parental  PPGNAGPVIMSIEERMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFS
          PPGNAGPVIMSIEERMEADA.SIYVGNVDYGATAEELEA.FHGC.SVN.VTILCDKFSGHPKGFAYIEFS
Retrocopy PPGNAGPVIMSIEERMEADAHSIYVGNVDYGATAEELEAPFHGCDSVNWVTILCDKFSGHPKGFAYIEFS

Parental  DKESVRTSLALDESLFRGRQIKVIPKRTNRPGISTTDRGF
          DKESVRTSLAL.ESLFRGRQIKVIPK.TNRP.ISTTD.GF
Retrocopy DKESVRTSLALAESLFRGRQIKVIPKLTNRPDISTTDGGF

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_606 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 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006884	1 retrocopy	retro_btau_693,
Callithrix jacchus	ENSCJAG00000007960	4 retrocopies	retro_cjac_1263, retro_cjac_2291, retro_cjac_3278, retro_cjac_3836,
Dipodomys ordii	ENSDORG00000002873	1 retrocopy	retro_dord_606 ,
Homo sapiens	ENSG00000100836	1 retrocopy	retro_hsap_4855,
Gorilla gorilla	ENSGGOG00000022683	2 retrocopies	retro_ggor_1454, retro_ggor_3030,
Mustela putorius furo	ENSMPUG00000006775	1 retrocopy	retro_mputfur_496,
Mus musculus	ENSMUSG00000022194	1 retrocopy	retro_mmus_403,
Nomascus leucogenys	ENSNLEG00000015009	2 retrocopies	retro_nleu_2066, retro_nleu_3023,
Otolemur garnettii	ENSOGAG00000008710	1 retrocopy	retro_ogar_797,
Pongo abelii	ENSPPYG00000005663	2 retrocopies	retro_pabe_1645, retro_pabe_3773,
Pan troglodytes	ENSPTRG00000006168	2 retrocopies	retro_ptro_1339, retro_ptro_3232,
Sus scrofa	ENSSSCG00000002023	1 retrocopy	retro_sscr_625,