RetrogeneDB ID: retro_meug_978

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold250642:1380..2709(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBB
• Ensembl ID: ENSMEUG00000015992
• Aliases: None
• Description: tubulin, beta class I [Source:HGNC Symbol;Acc:20778]

Sequence

>retro_meug_978
ATGAGGGAGATCATACCTATTCAGGATGGCCAGTGTGGCAATCAGAGAGGTGCAAAGTTCTGGGAGGTGATCAGTGATGG
ACATGGCATCAATCCCAAAAGCACTTACCATAGGGACAGTGACCTGAAGTTGGACTGAACCTCTACCTACTACAATGAGG
CCACCAGTGGCAAATATGTTCCCGGGCCATACTGATTGATCTTGAGCCTGGAACCATGGACTCTGCTCGTTCTGGACCTT
TTGGCCAGATATTCAGGCCAGACAACGTTTCTTTTGGCCAATCCGGGACAGAAAACAATTAGGCCAAAGGCCACTATACC
AAGAGGCCAGAGATAGTGGATTCAGTCTTGGAAGTGGTACGAAAGGAGGCAGAGAGATGTGATTGCCTGCAAGGCTTCCA
GCTGATCCACTCACTTTGTGGAGGCACAGGCTCAGGGATGGGCACCCCTCCTCATCAGGAAGATCCGAGAAGAGTACCCT
TACCCAATCATGAATAACTTTAATGTGGTTCCATCACCCAAAGTTTCAGATACTGTGGTTGAGCCCTAAGATTCCACCCT
CCCTGTCCACCAGTTAGTAGAAAACACAGATGAAACTTACTGCATTGATAATGAAGCACTTTATGATATCTACTTCTTAA
CCCTAAAGTTGACCACGCCAACCTATTGTGACCTTAACCATCTAGTCTCTGCTACCATGGATGGTATCACTAGATGCCTT
CGTTTTCCTGGTCAGCTCAATGCTGACCTCCGCAAGTTGGCTGTAAACATCGTCCCTTTCCCTCGACTCCACTTCTTTAT
GCCTGGCTTTGCCCACCTCACCAGTCATGGGAGCCAGCAGTACCATGCCCTAACTGTGCCTGAGCTCACCCAGCAAGTCT
TTGATGCCAAGAACATGATGGCAGCATGCGACCCTCGCCATGGGCGATATCTCACCATTGCTGCTGTTTTCCGTGGTCAG
ATGACCATGAAAGAGGTGGCCAAACAAATGCTCAATGTGCAAAACAAAAATAGTAGCTATTTCACTGAGTGGATCCCCAA
CAATGTCAAGACTGCTGTCTGTGATATCCCACCCCATAGGCTCAAGTTGGCTGTCACTTTTATTGGCAACAGCATTTCCA
TCCAGGAGCTCTTCAAGTGCATCTCAAAGCAGTTCATTGCCATGTTCTGCTGAAAGGCCTTCCTCTACTCATACGCAGGG
GAAGGGATGGACAAGATGGAGTTCACCGAGGCTGAGAGAAACATGAATGATCTTGTTTCTGAGTACCAACAGTACTAGGA
TGCCACTGCTGAAGAGGACAAGAATTTCAGTGAGGAGATAGAGGAGGAG

Alignment

ORF - retro_meug_978 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.7 %
• Parental protein coverage: 99.77 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLDRISVYYNEATGGKYVP-RAILVDLE
          MREI..IQ.GQCGNQ.GAKFWEVISD.HGI.P..TYH.DSDL.LD..S.YYNEAT.GKYVP.RAIL.DLE
Retrocopy MREIIPIQDGQCGNQRGAKFWEVISDGHGINPKSTYHRDSDLKLD*TSTYYNEATSGKYVP<RAILIDLE

Parental  PGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSL
          PGTMDS.RSGPFGQIFRPDN..FGQSG..NN.AKGHYT...E.VDSVL.VVRKEAE.CDCLQGFQL.HSL
Retrocopy PGTMDSARSGPFGQIFRPDNVSFGQSGTENN*AKGHYTKRPEIVDSVLEVVRKEAERCDCLQGFQLIHSL

Parental  GGGTGSGMGT-LLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALY
          .GGTGSGMGT.LLI.KIREEYP..IMN.F.VVPSPKVSDTVVEP...TL.VHQLVENTDETYCIDNEALY
Retrocopy CGGTGSGMGT>LLIRKIREEYPYPIMNNFNVVPSPKVSDTVVEP*DSTLPVHQLVENTDETYCIDNEALY

Parental  DICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGS
          DI.F.TLKLTTPTY.DLNHLVSATM.G.T.CLRFPGQLNADLRKLAVN.VPFPRLHFFMPGFA.LTS.GS
Retrocopy DIYFLTLKLTTPTYCDLNHLVSATMDGITRCLRFPGQLNADLRKLAVNIVPFPRLHFFMPGFAHLTSHGS

Parental  QQYRALTVPELTQQVFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNN
          QQY.ALTVPELTQQVFDAKNMMAACDPRHGRYLT.AAVFRG.M.MKEV..QMLNVQNKNSSYF.EWIPNN
Retrocopy QQYHALTVPELTQQVFDAKNMMAACDPRHGRYLTIAAVFRGQMTMKEVAKQMLNVQNKNSSYFTEWIPNN

Parental  VKTAVCDIPPRGLKMAVTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDL
          VKTAVCDIPP..LK.AVTFIGNS..IQELFK.IS.QF.AMF..KAFL..Y.GEGMD.MEFTEAE.NMNDL
Retrocopy VKTAVCDIPPHRLKLAVTFIGNSISIQELFKCISKQFIAMFC*KAFLYSYAGEGMDKMEFTEAERNMNDL

Parental  VSEYQQYQDATAEEEEDFGEEAEEE
          VSEYQQY.DATAEE...F.EE.EEE
Retrocopy VSEYQQY*DATAEEDKNFSEEIEEE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_978 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_978 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000022655	4 retrocopies	retro_ggor_2388, retro_ggor_244, retro_ggor_2519, retro_ggor_2651,
Macropus eugenii	ENSMEUG00000015992	1 retrocopy	retro_meug_978 ,
Macaca mulatta	ENSMMUG00000023684	2 retrocopies	retro_mmul_2501, retro_mmul_375,
Nomascus leucogenys	ENSNLEG00000005348	1 retrocopy	retro_nleu_498,
Otolemur garnettii	ENSOGAG00000032213	1 retrocopy	retro_ogar_2391,
Ochotona princeps	ENSOPRG00000014770	4 retrocopies	retro_opri_1106, retro_opri_237, retro_opri_46, retro_opri_656,
Pan troglodytes	ENSPTRG00000017939	3 retrocopies	retro_ptro_151, retro_ptro_2527, retro_ptro_2677,