RetrogeneDB ID: retro_dord_56

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_1549:98809..99172(+)
• Located in intron of: ENSDORG00000003496

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tax1bp3
• Ensembl ID: ENSDORG00000013801
• Aliases: None
• Description: Tax1 (human T cell leukemia virus type I) binding protein 3 [Source:MGI Symbol;Acc:MGI:1923531]

Sequence

>retro_dord_56
TCGAGATGTCCTACATCTATGGTTACCACCGCGGTGCACAGAGTTGAAATTCGCAAGCTGTGCCAAGGTGGGAACTTAAT
CCTTGGCTTCAGCATTGGAGGTGGGACTGACCAAGATCTCTCCCAGAATCCCTTCTCAGAAGATAAGACAGACAAGGGCA
TTTATGTCACATAGGTATCTGAAGGAGGACCTGGGGAAATTGCTGGGCTGCAGATTAGAGACAAGATCATGCAGGTAAAT
GGCTGGGACATGACCGTGATGACACATGACCAGGTCTGGAAGTGGCTCACCAAGCGCTCAGAAGAAGTGGTGCGTCTGCT
GGTGACAAGGCAGTCACTGCAGAAGGCCGTGCAGCAGTCCATG

Alignment

ORF - retro_dord_56 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.64 %
• Parental protein coverage: 97.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SYIPGQPVTAVVQRVEIHKLRQGENLILGFSIGGGIDQDPSQNPFSEDKTDKGIYVTRVSEGGPAEIAGL
          S..P...VT..V.RVEI.KL.QG.NLILGFSIGGG.DQD.SQNPFSEDKTDKGIYVT.VSEGGP.EIAGL
Retrocopy SRCPTSMVTTAVHRVEIRKLCQGGNLILGFSIGGGTDQDLSQNPFSEDKTDKGIYVT*VSEGGPGEIAGL

Parental  QIGDKIMQVNGWDMTMVTHDQARKRLTKRSEEVVRLLVTRQSLQKAVQQSM
          QI.DKIMQVNGWDMT..THDQ..K.LTKRSEEVVRLLVTRQSLQKAVQQSM
Retrocopy QIRDKIMQVNGWDMTVMTHDQVWKWLTKRSEEVVRLLVTRQSLQKAVQQSM

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_56 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000013801	2 retrocopies	retro_dord_56 , retro_dord_728,
Myotis lucifugus	ENSMLUG00000026421	1 retrocopy	retro_mluc_221,
Mus musculus	ENSMUSG00000040158	1 retrocopy	retro_mmus_1929,
Oryctolagus cuniculus	ENSOCUG00000023903	1 retrocopy	retro_ocun_781,
Sus scrofa	ENSSSCG00000017866	1 retrocopy	retro_sscr_365,
Ictidomys tridecemlineatus	ENSSTOG00000022920	1 retrocopy	retro_itri_134,