RetrogeneDB ID: retro_dord_302

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_10747:18429..18842(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Stmn2
• Ensembl ID: ENSDORG00000005974
• Aliases: None
• Description: stathmin-like 2 [Source:MGI Symbol;Acc:MGI:98241]

Sequence

>retro_dord_302
GATACTGAGGTGAAGGAACTGGAGGAGCAAGCCTCAGGCCAGGCTTTTGAGCTGATTCTCAACCTTCGGTTGAAAGAATC
TGTTCCTTATTTCCCCCTTTCCCCTCCAAAGAAGACGGATCTTTCCCTGGAGGAAATTGAGAAGAAATTGTATGCTGCAG
AAGAAAGACACAGTCCCATGAAGCTGAGGTCTTACAGCAGCTGTCTGAGAAACGAAAGCATGAGAAAGAAGTGCTTCCGA
AAGCAATAGAAGAGAACAACGATTCCAACAAAATGGCGGAGGAGACACTGACCCACAAGATGGAAACTCACAAAGAAAAT
CCAGAGGCACAAACGGCAGCTAAACTGGAGCGTTTGCACGTGGAAGAGGCGCGGAAAAACAAATTGTCCAAAGATCCTGC
TGCTGAGACTGAA

Alignment

ORF - retro_dord_302 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.68 %
• Parental protein coverage: 77.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DMEVKQINKRASGQAFELILKPPSPVSEAPRTLASPKKKDLSLEEIQKKLEAAEERR-KSQEAQVLKQLA
          D.EVK.....ASGQAFELIL......S.....L..PKK.DLSLEEI.KKL.AAEER...S.EA.VL.QL.
Retrocopy DTEVKELEEQASGQAFELILNLRLKESVPYFPLSPPKKTDLSLEEIEKKLYAAEERH<QSHEAEVLQQLS

Parental  EKREHEREVLQKALEENNNFSKMAEEKLILKMEQIKENREANLAAIIERLQEKERHAAEVRRNKELQVE
          EKR.HE.EVL.KA.EENN...KMAEE.L..KME..KEN.EA..AA..ERL...E..............E
Retrocopy EKRKHEKEVLPKAIEENNDSNKMAEETLTHKMETHKENPEAQTAAKLERLHVEEARKNKLSKDPAAETE

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_302 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000005974	1 retrocopy	retro_dord_302 ,
Mustela putorius furo	ENSMPUG00000001863	1 retrocopy	retro_mputfur_68,
Oryzias latipes	ENSORLG00000008251	1 retrocopy	retro_olat_37,