RetrogeneDB ID: retro_meug_993

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold253250:6..1357(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SHMT2
• Ensembl ID: ENSMEUG00000014334
• Aliases: None
• Description: serine hydroxymethyltransferase 2 (mitochondrial) [Source:HGNC Symbol;Acc:10852]

Sequence

>retro_meug_993
GTATATACAATCATTAAAAAGGAAAATTATCACCAGTAGACTGGGTTGGAACTGATTGCTTCAAAGAATTTTGCAAGTCG
AGCAGTTTGGGAAGCTTTGGGTTCTTGCTTGAATAGTAAGTATTCAGAAGGATTCCCAGGCCAGAGGTATTATGGTGGCA
CCCAGTTTGTGGATGAGTTGGAGATTCTGTGTCAGAAGAGGGCCCTGCAGGTCTATGGCCTGGATCCACAAAGCTGGGGG
TCAATGTTCAGTCATACTCAGGTTCTCCTGCGAATTTTGCTGTGTACACAGCTCTGGTGGAACCACATGGGAGGATTATG
GGTCTAGATCTGCCTGATGGGGGTCACTTCACCCATGGGTTCATGACAGATAAGAAGAAAGTCTCTGCCACTTCCATCTT
CTTTGAGTCCATGCCATATAAGGTAAACCCAGATACTGGCTGCATTGACTATGACATACTAGAAGAAAATGCCCGCTTCT
TCCACCCAAAACTGATCATTGCAGGAATCAGCTCCTATTCCAGGAATCTGGGCTATGGCTGCATACGGAAGATTGCAGAT
AATAATGGGGTGTATCTTATGGCTGACATAGTCCACGTTAGTGGACTGGTAGCCACTGGGGTCATCCCCTCCCCCTTTGA
ACACTGTGATGTGGTGACCACCACCACACACAAAACCCTTCAAGGTTGCCAGGCTGGCATGATCTTCTACAGGAAAAGAG
TGTGCAGTATGGACTCTAAAACAGGCAAAGAGACCATGTACAATCTGGAGTCACTCATTAATTCAGCTTTTTTCCTAGGA
CTTCAGCGAGGGCCTCACAACCATGCCACTGCAGGAGTTGCCATAGCTCTGAAGCAAGCCTTGACACCTGAATTTAAGGC
TTATCAGCAACAGATGGTTGCCAACTGCAAGGCCCTGTCAGTAGCCATGATAGAGTTGGGTTACCACATAGTAACAGGTG
GTTCTGACAACCACTTGATCCTCGTGGACCTACGAAACAAAGGGACAGATGGAGGAAGAGCTGAGAAGGTGCTCAAAGCT
TGTATTCTTGCTTGTAATAAGAACACCTGCCCAGAAGACAAAAGTACATTAAGACCTAGTGGACTGAGACTAGGAACCCC
AGCTCTGACCTTCTGAGGACTGCTAGAAAAAGATTTCCACAAAGTAGCCCATTTATTCACAAAGGAATAGAACTGACTCT
ACAGATTCAGAAAGACCTCAGTCCCCAGGCCACCATGAAAGAATTCAAGGAGAAACTTTTGGGGGATGCGCATTATCAGG
ATATTATCAAGACTATCAGAGAAAAATTGAAGAGCTTTGCAGCTGTTTTTCCCCTACTTGGGATCCCTGAT

Alignment

ORF - retro_meug_993 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.3 %
• Parental protein coverage: 90.87 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MWELLQREKDRQCRGLELIASENFCSRAALEALGSCLNNKYSEGYPGKRYYGGSEIVDEIELLCQRRALE
          .......E...Q..GLELIAS.NF.SRA..EALGSCLN.KYSEG.PG.RYYGG...VDE.E.LCQ.RAL.
Retrocopy VYTIIKKENYHQ*TGLELIASKNFASRAVWEALGSCLNSKYSEGFPGQRYYGGTQFVDELEILCQKRALQ

Parental  AFDLDPDRWG-VNVQPYSGSPANLAAYTAVLQPHDRIMGLDLPDGGHLTHGYMSSVKRISATSIFFESMP
          ...LDP..WG.VNVQ.YSGSPAN.A.YTA...PH.RIMGLDLPDGGH.THG.M...K..SATSIFFESMP
Retrocopy VYGLDPQSWG<VNVQSYSGSPANFAVYTALVEPHGRIMGLDLPDGGHFTHGFMTDKKKVSATSIFFESMP

Parental  YKLNPSTGLIDYDQLALTARLFRPRLIIAGTSAYARLIDYARMREVCDEVKAHLMADMAHISGLVAAKVI
          YK.NP.TG.IDYD.L...AR.F.P.LIIAG.S.Y.R...Y...R...D.....LMAD..H.SGLVA..VI
Retrocopy YKVNPDTGCIDYDILEENARFFHPKLIIAGISSYSRNLGYGCIRKIADNNGVYLMADIVHVSGLVATGVI

Parental  PSPFDYADIVTTTTHKTLRGARAGLIFYRKGVQSVDPKTGKEIPYTFEDRINFAVFPSLQGGPHNHAIAA
          PSPF...D.VTTTTHKTL.G..AG.IFYRK.V.S.D.KTGKE..Y..E..IN.A.F..LQ.GPHNHA.A.
Retrocopy PSPFEHCDVVTTTTHKTLQGCQAGMIFYRKRVCSMDSKTGKETMYNLESLINSAFFLGLQRGPHNHATAG

Parental  VAVALKQXXXXXXXXXXXXXXXXXRAMADALLQRGYSLVSGGTDNHLVLVDLRPKGLDGARAERVLELVS
          VA.ALKQ..................A...A....GY..V.GG.DNHL.LVDLR.KG.DG.RAE.VL....
Retrocopy VAIALKQALTPEFKAYQQQMVANCKALSVAMIELGYHIVTGGSDNHLILVDLRNKGTDGGRAEKVLKACI

Parental  ITANKNTCPGDKSAITPGGLRLGAPALTSRHFREDDFRQVVN-FIDEGVHIGLDVK---NKTGKLQDFKS
          ...NKNTCP.DKS...P.GLRLG.PALT.....E.DF..V...FI..G....L..............FK.
Retrocopy LACNKNTCPEDKSTLRPSGLRLGTPALTF*GLLEKDFHKVAH<FIHKGIELTLQIQKDLSPQATMKEFKE

Parental  FLLNDLETRQRLANLRQRVEDFARAFPMPGFEE
          .LL.D..........R.....FA..FP..G...
Retrocopy KLLGDAHYQDIIKTIREKLKSFAAVFPLLGIPD

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_993 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_993 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000014334	2 retrocopies	retro_meug_77, retro_meug_993 ,
Tursiops truncatus	ENSTTRG00000013079	1 retrocopy	retro_ttru_1882,