RetrogeneDB ID: retro_dord_559

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_32251:8867..9983(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Wee2
• Ensembl ID: ENSDORG00000015156
• Aliases: None
• Description: WEE1 homolog 2 (S. pombe) [Source:MGI Symbol;Acc:MGI:3027899]

Sequence

>retro_dord_559
AGAAAACGATTACTTCAATCAACAAGCAAGAGGAAATACTGTAATCCTGAAGAAATTGAAGCAGAGAAAGACAAAAAAGA
AAGGCTGCTTCCAATGAAAAGTATCCTACAACAAATCAACATGGCTTCTCGGTATGAAACAGAATTTTTTGAAATAGAAA
AAATTGGAGTTGGGGCATTTGGTACAGTCTACAAGTGCATTAAGAAGTTGGATGGATGTGTTTATGCAATCAAGTGCTCC
AAAAAAACTTTTTCAGATGTATCAAGTGAAAATTTGGATTTGCATGAAGTTTATGCTCATGCAGTTCTTGGGCATCACCC
CAATGTTGTACGTTACTATTCCTCATGGACAGAAGGTGATTATGTGATCATTCAAAATGAATACTGCAATGGTGGGAGCT
TGCAGGTTGCTGTATCTCAAAACACTAAGTCTGGTAGTCATTTCCAAGAATCAAACCTCAAAGATATACTCCATCAGATT
TCTCTGGGGCTCAAGTACATCCACAGTGCTGGCATGGTGCACCTTGATATAAAGCCTAGTAACATCTTCATTTGTCATAA
CATGCAAAATGTTTCATTTGAAGGACCAGAAGAGGTTGAAAATGAAGATGATTGGTTTCTCTCTGCCAGTGTGATATATA
AAATTGGTGACTTGGGCCATGTGACCTCAATAAGAAAACCCAAAGTAGAAGAAGGAGATAGTTGCTTTCTGGCTAATGAG
ATTTTACAAGAGAATTATGAACACCTTCCCAAAGCAGATATATTTGCTTTAGGATTAACAATTGCAGCAGCTGCTGGAGC
ATCATTACCTGCTGCTGGTGATGAGTGGTATCACATCCGCAAGGGTAACATTCCCTACATTCCTCAGGAACTCTCAGATG
ATTTTTGCAATTTGCTAAAGAAAATGATCCACACTGATCCACAGGAGAGACCATCTGCCACAGCTCTCTCCAGAAGTCAA
GTTCTCTGGCCATTATTTGCTGAAACAGCGGAGCTCCAGCAGCAGCTCAACTTGGAAAAGTCTAAGATAGCCACACTAGA
AAAGAAACTCAGAGAAGCGCAGCAGACACAGTTCCCCCAAGATGATTCTGAGGACTGGGGACCGCAAAAGAACAAG

Alignment

ORF - retro_dord_559 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.93 %
• Parental protein coverage: 66.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RKLIHHSKGKRKTQGDLEGTSAEEGKAEQGRPAKKSLLEEINMASRYAKEFLEVEKLGVGAFGTVYKCIK
          RK....S..KRK.....E...AE..K.E...P.K.S.L..INMASRY..EF.E.EK.GVGAFGTVYKCIK
Retrocopy RKRLLQSTSKRKYCNP-EEIEAEKDKKERLLPMK-SILQQINMASRYETEFFEIEKIGVGAFGTVYKCIK

Parental  RLDGCIYAIKYSTRTFSGLSNXXXXLHEVYAHAVLGHHPHVVRY-SSWTEDDHVIIQNEYCNGGSLQAAI
          .LDGC.YAIK.S..TFS..S.....LHEVYAHAVLGHHP.VVRY.SSWTE.D.VIIQNEYCNGGSLQ.A.
Retrocopy KLDGCVYAIKCSKKTFSDVSSENLDLHEVYAHAVLGHHPNVVRYYSSWTEGDYVIIQNEYCNGGSLQVAV

Parental  SKNTKAGNHFQEPKLKDMLLQITLGLKYIHNAGMVHMDIKPSNIFICHNMQSDSPEGPEEAENEADWFLS
          S.NTK.G.HFQE..LKD.L.QI.LGLKYIH.AGMVH.DIKPSNIFICHNMQ..S.EGPEE.ENE.DWFLS
Retrocopy SQNTKSGSHFQESNLKDILHQISLGLKYIHSAGMVHLDIKPSNIFICHNMQNVSFEGPEEVENEDDWFLS

Parental  ASVIYKIGDLGHVTSISKPKVEEGDICFLANEILQENYRYLPKADIFSLGLTMAVAAGAQSLPANGEEWH
          ASVIYKIGDLGHVTSI.KPKVEEGD.CFLANEILQENY..LPKADIF.LGLT.A.AAGA.SLPA.G.EW.
Retrocopy ASVIYKIGDLGHVTSIRKPKVEEGDSCFLANEILQENYEHLPKADIFALGLTIAAAAGA-SLPAAGDEWY

Parental  HIRRGNLPSIPQELSEDFYQLLQNMIHPDPEERPSAAALARSQVLRPSLGTTEELQQQLDLEKSKIAALE
          HIR.GN.P.IPQELS.DF..LL..MIH.DP.ERPSA.AL.RSQVL.P....T.ELQQQL.LEKSKIA.LE
Retrocopy HIRKGNIPYIPQELSDDFCNLLKKMIHTDPQERPSATALSRSQVLWPLFAETAELQQQLNLEKSKIATLE

Parental  RELREAQQAQSSQGDIPQGHPSDSE
          ..LREAQQ.Q..Q.D.....P....
Retrocopy KKLREAQQTQFPQDDSEDWGPQKNK

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_559 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004658	1 retrocopy	retro_btau_932,
Callithrix jacchus	ENSCJAG00000013627	1 retrocopy	retro_cjac_936,
Dipodomys ordii	ENSDORG00000015156	1 retrocopy	retro_dord_559 ,
Gorilla gorilla	ENSGGOG00000009609	1 retrocopy	retro_ggor_705,
Ochotona princeps	ENSOPRG00000009103	2 retrocopies	retro_opri_358, retro_opri_841,
Pongo abelii	ENSPPYG00000018066	1 retrocopy	retro_pabe_684,
Pan troglodytes	ENSPTRG00000028383	1 retrocopy	retro_ptro_601,