RetrogeneDB ID: retro_dord_783

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_971:113423..114095(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cdc25a
• Ensembl ID: ENSDORG00000011077
• Aliases: None
• Description: cell division cycle 25A [Source:MGI Symbol;Acc:MGI:103198]

Sequence

>retro_dord_783
TTCCTTTCAGATTTTCCTGGACCTTGGACAGAAAAGAACACCTTGAAAATCCCATGAGGAGGATAAATTATGAGGGTAGA
TTCCTTGCCTTAGAAGATTTTGAGGTATAGACCAGCTTGGAATAGGAGCCATTCTGATTCTCTGGAACATGATATCTTTC
AGCTCATTGACCAGGATGAAAACAAGGAAAAAGAAGCATTTAAGTTTAAGAAGTTCATAAGACCTGCATCTCATGGTTGC
CTGTATGTCCATGGACAAGATGAGGGTAAAGATGACTTCTCACAGAGGCAGAACTCAGCCCCAGCTTGGATGCTTTCTTC
ATAAGAAAGATGTGAGCCAGGGAATTTTGTTCCTCTTTTCACACTCCAGTCACCTGTGACAGCCAGTTTGTCTGATGAGG
ATAATGGCTTCATGGACCTTCTTGATGGAGAGAGTCTGAAGAACGATGTGGAGGCCCCATCGGGCATGGCAAGTCTCTGG
ACAGCACCCATGGTTATGAGAAGAGCTATAAATATTGGCAGTGGGTGGGGGCTGTTTGCCTCCCCTTCCCAGTGTGACTC
CAGCATTCAGTCAGCAATGAAGGGACCAGAACAATCTCAAGTGGAATCTCCACAGGAAAGCACAAAGTGGCAGAAGAGCT
TGGCTGGAATTAGTCCTGGAGGGTCACATAAT

Alignment

ORF - retro_dord_783 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.22 %
• Parental protein coverage: 50.11 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FCLDSPGPLDRKENLENP----VRRINFLPQKLLGCSPALKRSHSDSLDHDIFQLIDQDENKENEVFEFK
          F..D.PGP...K..L..P......R...LP.K.L...PA..RSHSDSL.HDIFQLIDQDENKE.E.F.FK
Retrocopy FLSDFPGPWTEKNTLKIP*GG*IMRVDSLP*KILRYRPAWNRSHSDSLEHDIFQLIDQDENKEKEAFKFK

Parental  KPIRPASRGCLHAHGHDESKDVFTQRQNSAPARMLSSHERDSEPRNFVPLFTPQSPVTASLSDEDDGFMD
          K.IRPAS.GCL..HG.DE.KD.F.QRQNSAPA.MLSS.ER..EP.NFVPLFT.QSPVTASLSDED.GFMD
Retrocopy KFIRPASHGCLYVHGQDEGKDDFSQRQNSAPAWMLSS*ER-CEPGNFVPLFTLQSPVTASLSDEDNGFMD

Parental  LLDGENLKNDEETPSGMASLWTAPLVMRRATNIGNGCRLFDSPSQCVSSTRSAMKRTDRSQEESPQGSTK
          LLDGE.LKND.E.PSGMASLWTAP.VMRRA.NIG.G..LF.SPSQC.SS..SAMK....SQ.ESPQ.STK
Retrocopy LLDGESLKNDVEAPSGMASLWTAPMVMRRAINIGSGWGLFASPSQCDSSIQSAMKGPEQSQVESPQESTK

Parental  RRKSLAGTSPGGSLN
          ..KSLAG.SPGGS.N
Retrocopy WQKSLAGISPGGSHN

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_783 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000011077	2 retrocopies	retro_dord_336, retro_dord_783 ,
Nomascus leucogenys	ENSNLEG00000006390	1 retrocopy	retro_nleu_2333,
Otolemur garnettii	ENSOGAG00000002994	1 retrocopy	retro_ogar_3398,