RetrogeneDB ID: retro_dord_473

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_21157:13345..14803(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Wwp2
• Ensembl ID: ENSDORG00000007924
• Aliases: None
• Description: WW domain containing E3 ubiquitin protein ligase 2 [Source:MGI Symbol;Acc:MGI:1914144]

Sequence

>retro_dord_473
GAGTCTTTGCCATCAGGATGGGAACAGAGAAAGGACCCTCATGGTAGAACCTATTATGTAGATCATAATACTCGAACTAC
CACATGGGAGAGACCACAACCTTTACCCCCAGGTTGGGAAAGAAGAGTTGATGAGCGTGGGAGAGTGTGCTATGTGGATC
ATAACACCAGAACAACAACATAGCAGCGTCCCACCATGGAGTCTGTTCGAAACTTTGAACAGTGGCAATCTCAGCGGAAC
CAATTGCAGGGAGCTATGCAACAGTTCAACCAACGATACCTCTGTTCGGCTTCAATGTTGGCTGCAGAAAATGACCCGTA
TGGACCTTTACCACCAGGTTGGGAAAAAAGAGTGGATTCAACTGACAGGGTTTACTTTGTGAATCACAATACAAAAACAG
CCCAGTGGGAAGATCCTAGGACTCAAGGCTTACAAAATGAAGAACCTCTGCCAGAAGGCTGAGAAATTAGGTATACTCGG
GAAGGTGTTAGGTATTTTGTTGATCATAACACAAGGACAACAACATTCAAAGATCCTCGAAATGGGAAGTCATCTGTAAC
AAAAGGTGGTCCACAGATTGCTTATGAACGCAGCTTTAGGTGGAAACTTGCTCACTTCCGTTATTTGTGCCAGTCTAATG
CACTTCCCAGTCATGTAAAGATCAATGTGTCCTGGCAGACGTTATTTGAAGATTCCTTCCAACAGATTATGGCATTAAAA
CCATATGACTTGAGGAGGCGATTATATGTAATATTTAGAGGAGAAGAAGGACTTGATTATGGAGGTCTGGCAAGAGAATG
GTTTTTCTTGCTTTCACATGAAGTTTTGAACCCAATGTATTGCTTATTTGAATATGCGGGCAAAAACAACTATTGTCTAC
AGATAAATCCAGCATCAACCATAAATCCAGACCATCTTTCGTATTTCTGTTTCATTGGTCGCTTTATTGCAATGGCACTA
TTTCCTGGGAAGTTTATTCATACTGGTTTCTCTTTACCATTCTACAAGCCATATGCTAAGTAAAAAACTTACTATAAAGG
ATCTGGAGCCCATTGATACTGAATTTTATAACTCTCTTATCTGGATAAGGGATAACAACATAGAAGAATGTGGCTTAGAA
ATGTACTTTTCTGTTGACATGGAGATTTTAGGAAAAGTCACTTCACATGACCTAAAGTTGGGAGGTTCCAATATTCTGGT
GACTGAGGAAAACAAAGATGAATATATTGGCTTAATGACAGAATGGCGTTTTTCTCGAGGAGTACAAGAACAGACCAAAG
CTTTCCTTGATGGTTTTAATGAAGTTTTTCCCCTTCAGTGGCTACAATACTTTGATGAAAAAGAATTGGAGGTTATGTTG
TGTGGCATGCACGAGGTTAACTTGACAGATTGGCAGAGAAATACAGTTTATCGACATTATACAGAAACAGCAAGCAAATT
ATTTGGTTTTGGGCAGTT

Alignment

ORF - retro_dord_473 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.8 %
• Parental protein coverage: 57.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DALPAGWEQRELPNGRVYYVDHNTKTTTWERP--LPPGWEKRTDPRGRFYYVDHNTRTTT-WRPTAEYVR
          ..LP.GWEQR..P.GR.YYVDHNT.TTTWERP..LPPGWE.R.D.RGR..YVDHNTRTTT..RPT.E.VR
Retrocopy ESLPSGWEQRKDPHGRTYYVDHNTRTTTWERPQPLPPGWERRVDERGRVCYVDHNTRTTT*QRPTMESVR

Parental  NYEQWQSQRNQLQGAMQHFSQRFLYQSSSASTDHDPLGPLPPGWEKRQDN-GRVYYVNHNTRTTQWEDPR
          N.EQWQSQRNQLQGAMQ.F.QR.L...S......DP.GPLPPGWEKR.D...RVY.VNHNT.T.QWEDPR
Retrocopy NFEQWQSQRNQLQGAMQQFNQRYLCSASMLAAENDPYGPLPPGWEKRVDSTDRVYFVNHNTKTAQWEDPR

Parental  TQGMIQEPALPPGWEMKYTSEGVRYFVDHNTRTTTFKDPRPGFESGTKQGSPGAYDRSFRWKYHQFRFLC
          TQG...E..LP.G.E..YT.EGVRYFVDHNTRTTTFKDPR.G..S.TK.G...AY.RSFRWK...FR.LC
Retrocopy TQGLQNEEPLPEG*EIRYTREGVRYFVDHNTRTTTFKDPRNGKSSVTKGGPQIAYERSFRWKLAHFRYLC

Parental  HSNALPSHVKISVSRQTLFEDSFQQIMNMKPYDLRRRLYIIMRGEEGLDYGGIAREWFFLLSHEVLNPMY
          .SNALPSHVKI.VS.QTLFEDSFQQIM..KPYDLRRRLY.I.RGEEGLDYGG.AREWFFLLSHEVLNPMY
Retrocopy QSNALPSHVKINVSWQTLFEDSFQQIMALKPYDLRRRLYVIFRGEEGLDYGGLAREWFFLLSHEVLNPMY

Parental  CLFEYAGKNNYCLQINPASSINPDHLTYFRFIGRFIAMALYHGKFIDTGFTLPFYK-RMLNKRPTLKDLE
          CLFEYAGKNNYCLQINPAS.INPDHL.YF.FIGRFIAMAL..GKFI.TGF.LPFYK..ML.K..T.KDLE
Retrocopy CLFEYAGKNNYCLQINPASTINPDHLSYFCFIGRFIAMALFPGKFIHTGFSLPFYK>HMLSKKLTIKDLE

Parental  SIDPEFYNSIVWIKENNLEECGLELFFIQDMEILGKVTTHELKEGGESIRVTEENKEEYIMLLTDWRFTR
          .ID.EFYNS..WI..NN.EECGLE..F..DMEILGKVT.H.LK.GG..I.VTEENK.EYI.L.T.WRF.R
Retrocopy PIDTEFYNSLIWIRDNNIEECGLEMYFSVDMEILGKVTSHDLKLGGSNILVTEENKDEYIGLMTEWRFSR

Parental  GVEEQTRAFLDGFNEVAPLEWLRYFDEKELELMLCGMQEIDMSDWQKNTIYRHYT-KNSKQIQWFWQV
          GV.EQT.AFLDGFNEV.PL.WL.YFDEKELE.MLCGM.E....DWQ.NT.YRHYT..NSKQI.WFW.V
Retrocopy GVQEQTKAFLDGFNEVFPLQWLQYFDEKELEVMLCGMHEVNLTDWQRNTVYRHYT<RNSKQIIWFWAV

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_473 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000007924	1 retrocopy	retro_dord_473 ,