RetrogeneDB ID: retro_meug_354

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold10419:17028..17931(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ALDH1A1
• Ensembl ID: ENSMEUG00000008847
• Aliases: None
• Description: aldehyde dehydrogenase 1 family, member A1 [Source:HGNC Symbol;Acc:402]

Sequence

>retro_meug_354
GGAAAGTTTTTCTCATATACAAGGCATGAACCTATTGGTGTTTGTGGTCAAATCATTCCTAGGAATTTCCCTTTGATTAT
GCTTATGTGGCAAATTGCACCTGCCTTTTGCTGTGGAAACACCATAATTGTCAAACCAGCAGAACAGAGCCCACTAACTG
CTCTTTATGCAGCATTGTTAATTAAAGAGGCAAGATTTCCATGAGGAGTAGTCAATATTGTGCCTGGTTATGGACTCACG
GCAGGAGCAGTCATTTCTTCTCACATGGATGCAGATAAAGTAGCCTTCACAGGGTCCGCAGAGGTTGGCCTACTAATTAA
GGAGACAGGTGGGAAGACCAACCTAAAAAGGGTTTCCCTGGAACTGGGAGGAAAGAGCCCTTGCATTGTATTTGCTGATG
CTGACATGCATAATGTTGTGGAATTTGTGCACTTTGGATTAGTTTTCCACCAGGGCCAGTGCTGCACTGCTGCATTAAGG
CTTTTTTGTGAAAAAGTCCATTTACAATGAGTTTGTTCGGAGGAGCATATAGCATGCCCAGAAATACACACTGGGGAATC
CTCTGAACCCAGAAGTATACCAAGGCCCTCAGAATGATAAAAAGAGCAGTATACCAAAGTGCTTGACCTCACTGAGAGTG
GGAAGAAGGAAGGAGCCACATTGGAATGTGGAGAAAGACCATGGGGAGACAAAGATTACTTCATTCAGCCCACAGTTTTC
TCCAATGTTACTGATGAGATGTGCATTGCCAAAGAAGAGATTTTTGGACCAGTCGAACAAATCATGAAGTTTAAGACTAT
CGCTGAAGTAGTCAAGAGAACCAACAACACCCATTATGGTTTATCAGCGAGCATTTTTAGCAGAGATCTTGATAAGGTCT
TGACAGTTTCTTCTACCCTTCAA

Alignment

ORF - retro_meug_354 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.93 %
• Parental protein coverage: 60.12 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GKFFSYTRHEPVGVCGQIIPWNFPLVMFIWKIGPALCCGNTVVVKPAEQTPLSALYAASLIKEAGFPPGV
          GKFFSYTRHEP.GVCGQIIP.NFPL.M..W.I.PA.CCGNT..VKPAEQ.PL.ALYAA.LIKEA.FP.GV
Retrocopy GKFFSYTRHEPIGVCGQIIPRNFPLIMLMWQIAPAFCCGNTIIVKPAEQSPLTALYAALLIKEARFP*GV

Parental  VNIVPGYGPTAGAAISSHMDIDKVAFTGSTEVGKLIKEAAGKSNLKRVTLELGGKSPCIIFADADLDNAV
          VNIVPGYG.TAGA.ISSHMD.DKVAFTGS.EVG.LIKE..GK.NLKRV.LELGGKSPCI.FADAD..N.V
Retrocopy VNIVPGYGLTAGAVISSHMDADKVAFTGSAEVGLLIKETGGKTNLKRVSLELGGKSPCIVFADADMHNVV

Parental  EFAHHGVFYHQGQCCIAASRIF-VEESIYDEFVHRSVERAKKYTL-GDPLNPR-VQQGPQIDKDQYNKIL
          EF.H.G...HQGQCC.AA.R.F.V..SIY.EFV.RS...A.KYTL.G....PR.........K.QY.K.L
Retrocopy EFVHFGLVFHQGQCCTAALRLF>VKKSIYNEFVRRSI*HAQKYTL<GESSEPRSIPRPSE**KEQYTKVL

Parental  DLIESGKKEGAKLECGGGPWGDKGFFIQPTVFSNVTDEMRIAKEEIFGPVQQIMKFKTIDEVIKRANNTH
          DL.ESGKKEGA.LECG..PWGDK..FIQPTVFSNVTDEM.IAKEEIFGPV.QIMKFKTI.EV.KR.NNTH
Retrocopy DLTESGKKEGATLECGERPWGDKDYFIQPTVFSNVTDEMCIAKEEIFGPVEQIMKFKTIAEVVKRTNNTH

Parental  YGLSAGIFTKDLDKAITVSSALQ
          YGLSA.IF..DLDK..TVSS.LQ
Retrocopy YGLSASIFSRDLDKVLTVSSTLQ

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_354 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_354 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 4 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000031532	1 retrocopy	retro_lafr_1162,
Macropus eugenii	ENSMEUG00000002553	3 retrocopies	retro_meug_1574, retro_meug_1848, retro_meug_802,
Macropus eugenii	ENSMEUG00000008847	1 retrocopy	retro_meug_354 ,
Tupaia belangeri	ENSTBEG00000001455	7 retrocopies	retro_tbel_2156, retro_tbel_2326, retro_tbel_3836, retro_tbel_3843, retro_tbel_3945, retro_tbel_3951, retro_tbel_4329,