RetrogeneDB ID: retro_dord_80

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_2323:36162..36503(-)
• Located in intron of: ENSDORG00000010955

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDORG00000001065
• Aliases: None
• Description: None

Sequence

>retro_dord_80
ATGGCAGCAGAGAAAAAAATGGTAAAAATTAGATCTGAAACACTACAGACCAAGAAGAGACCTGAACAGTTCAATATACC
TGTGGTCTTGGAGAGTAAGAAAGGTGCTTAGGCAGATAGGTTTGGAATTTCTTCTGTTTCAACAAAAGACCTGTCATCTG
ACAACAAGCCTGTGGTTAAAATGGGCCAGCTAAAGGAAAGAGTACAATGATTTGGTTTGTCTCTTCTATCCCTAGAAAGT
CTAAAGATGATTAGAAATTGAAAAAGAGCAAGGAACAATTTGGGATTGTCTCAAGTTCTGCTGGAACTGGAACCATAGAA
GATACAAAGACAAAGTAAAGG

Alignment

ORF - retro_dord_80 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.66 %
• Parental protein coverage: 56.19 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VAAEKKVVKITSEISQTERMQKRAERFNVPVSLESKKAARAARFGISSVPTKGLSSDNKTMVNLDKLKER
          .AAEKK.VKI.SE..QT....KR.E.FN.PV.LESKK.A.A.RFGISSV.TK.LSSDNK..V....LKER
Retrocopy MAAEKKMVKIRSETLQTK---KRPEQFNIPVVLESKKGA*ADRFGISSVSTKDLSSDNKPVVKMGQLKER

Parental  AQRFGLNVSSIS-RKSEDDEKLKKRKERFGIVTSSAGTGTTEDTEAKKR
          .Q.FGL...S.......D....K..KE.FGIV.SSAGTGT.EDT..K.R
Retrocopy VQ*FGLSLLSLE<KSKDD*KLKKS-KEQFGIVSSSAGTGTIEDTKTK*R

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_80 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 18 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011769	2 retrocopies	retro_amel_1602, retro_amel_347,
Bos taurus	ENSBTAG00000020662	1 retrocopy	retro_btau_202,
Callithrix jacchus	ENSCJAG00000007853	8 retrocopies	retro_cjac_1070, retro_cjac_1487, retro_cjac_1801, retro_cjac_2439, retro_cjac_2560, retro_cjac_389, retro_cjac_4139, retro_cjac_731,
Cavia porcellus	ENSCPOG00000011755	1 retrocopy	retro_cpor_1313,
Dipodomys ordii	ENSDORG00000001065	1 retrocopy	retro_dord_80 ,
Erinaceus europaeus	ENSEEUG00000015176	1 retrocopy	retro_eeur_549,
Homo sapiens	ENSG00000205323	1 retrocopy	retro_hsap_3882,
Gorilla gorilla	ENSGGOG00000013217	2 retrocopies	retro_ggor_2613, retro_ggor_2753,
Loxodonta africana	ENSLAFG00000015053	1 retrocopy	retro_lafr_1024,
Microcebus murinus	ENSMICG00000010902	1 retrocopy	retro_mmur_358,
Monodelphis domestica	ENSMODG00000028949	1 retrocopy	retro_mdom_1909,
Mustela putorius furo	ENSMPUG00000000885	1 retrocopy	retro_mputfur_617,
Mus musculus	ENSMUSG00000078427	1 retrocopy	retro_mmus_54,
Nomascus leucogenys	ENSNLEG00000017599	2 retrocopies	retro_nleu_2779, retro_nleu_569,
Procavia capensis	ENSPCAG00000009477	2 retrocopies	retro_pcap_262, retro_pcap_45,
Pongo abelii	ENSPPYG00000004630	2 retrocopies	retro_pabe_3116, retro_pabe_3358,
Pan troglodytes	ENSPTRG00000029747	2 retrocopies	retro_ptro_2644, retro_ptro_2782,
Rattus norvegicus	ENSRNOG00000030520	2 retrocopies	retro_rnor_1326, retro_rnor_471,