RetrogeneDB ID: retro_dord_791

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_99056:390..769(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDORG00000005801
• Aliases: None
• Description: None

Sequence

>retro_dord_791
ATGTCTATTGGTGTGCCAATGAAAGTCCTGCATGAAGCTGAGGACCATATTATTGCATGTGAGACAAACACTGGTGAGGT
ATATCGAGGAAAGCTCATTGAAGCAGAGGACTCCATGAACTGCCAGATGTCCAACATCACAGTCCTGTACAGAGATGGCC
GAGTGGCACAGCTGGAGCAGCTCTACATCCAAGGCAGCAAGATCCACTTTCTGATTTTCCCTGATACGCTAAAAAATGCA
CCAGTGTTAAAGAGCATGAAAAATAAAAACCCAAGGCTCCAGGGCTGGCTATGGAAAAGCTGCTATTCTGCAGGCCCAAG
TGGCTGCAAGAGCAAGAGGATGTGGAATGGGACGTGGAAACATCTTCGAGAAACAAAGG

Alignment

ORF - retro_dord_791 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.87 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKIRF
          MSIGVP.KVLHEAE.HI..CETNTGEVYRGKLIEAED.MNCQMSNITV.YRDGRVAQLEQ.YI.GSKI.F
Retrocopy MSIGVPMKVLHEAEDHIIACETNTGEVYRGKLIEAEDSMNCQMSNITVLYRDGRVAQLEQLYIQGSKIHF

Parental  LILPDMLKNAPMLKSMKNKN---QSWA-GRGKAAILNAQVAARGRGRGMGRGNIFQKRR
          LI.PD.LKNAP.LKSMKNKN...Q.W..G............ARG.G..MGRGNIF.K.R
Retrocopy LIFPDTLKNAPVLKSMKNKNPRLQGWL>GKAAILQAQVAARARGCG--MGRGNIFEKQR

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_791 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 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013864	1 retrocopy	retro_cfam_173,
Cavia porcellus	ENSCPOG00000012304	1 retrocopy	retro_cpor_297,
Dasypus novemcinctus	ENSDNOG00000018004	1 retrocopy	retro_dnov_2611,
Dipodomys ordii	ENSDORG00000005801	1 retrocopy	retro_dord_791 ,
Otolemur garnettii	ENSOGAG00000012708	3 retrocopies	retro_ogar_1209, retro_ogar_2077, retro_ogar_2235,
Rattus norvegicus	ENSRNOG00000050410	1 retrocopy	retro_rnor_232,
Ictidomys tridecemlineatus	ENSSTOG00000025674	1 retrocopy	retro_itri_651,
Tarsius syrichta	ENSTSYG00000007649	1 retrocopy	retro_tsyr_1489,
Tursiops truncatus	ENSTTRG00000006022	1 retrocopy	retro_ttru_1240,
Vicugna pacos	ENSVPAG00000000241	2 retrocopies	retro_vpac_338, retro_vpac_348,