RetrogeneDB ID: retro_nleu_2307

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397342.1:3176656..3177930(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ME2
• Ensembl ID: ENSNLEG00000011833
• Aliases: None
• Description: Malic enzyme [Source:UniProtKB/TrEMBL;Acc:G1RMD7]

Sequence

>retro_nleu_2307
ATGTTGTCCGGGTTAAGCGTATTTTCCACCACTTGTACTTTCGCATGTCGACATTTGCACATAAAAGAAAAAGGCAAGCC
ACTTATGCTGAATCCAAGAACAAACACGGGAATGGCATTTACTTTACAAGAACGACAAATGCTTGGTCTTCAAGGGCTTC
TACCTCCCCAAATACAGACATAAGATATCTAAGCCTTACGATTCCATAGAAACTTGAAAAAAAATGACTAGCCCTTTGGA
AAAATATATCTACATACAAGAAAGAAATGATAAATTGTTTTATAGAATACTGCAAGATGACCCTGAGAGTTTAATGCCAA
TTGTATATACACCGACGGTTGATCTTGTCTGCTCCCAGTGTGGACACCTCTTTAGAAGACCTAAGGGATTATTTATTTCC
ATCTCAGTCAGAGGTCGTGTTAGATCAATTGTGGATAAGTGGCCAGAAAATCATGTTAAGGCTGTTTTGGTGACTGATGG
AGAGAGAATTCTGGGTCTTGGAGATCTGGGTGTCTATGGAATGGGAATTCCAGTAGGAAAAATTTGTTTGTATACAGTTC
ATCCAGGAATATGGCCTGATAGATGCTTTCTGGTGTGTATTGATGTGGGAACTAATAATATCGCACTCTTAAAAGACACA
TTTTACATGGGCTTGTACCAGAAACGAGATCGCACACAACAGTCTGATGATCTGATTGATGAGTTTATGAAAGCTATTAC
TGACAGATATGGCTGGAACACACTCATTCAATTGGAAGGTTGTGGAAATCACAATGCATTTAGGTTCTTGAGAAAATACC
AATAAAAATATTGAACTTTCAATGATGATATTCAAGGGACAGCTGCAGTAGCTCTAGCAGGTCTTCTTGCAACGCAAAAA
GTTACTAGTAAACCAACCTCTGAACACAAAATCTTATTCTTTGGAGCAGGAGAGATTACTCTTAGAATTGCAAATCTTAT
AGAATGTCTATGGTAGAAAATGACCGTCGGAAGAAAAGGCACAAAAGAAAATCTGGATGTTTGACAAGTATGGTTTATTA
GTTTAGGGGCGGAAAGCAAAAATAGATAGTTAACAGAAACCATTTACTTACCCAGTCCCAGAGAGCATACCTGATACTTT
TGAAGATGCAGTGAATATAATGAAGACTTCAACTACAATTGGAGTTGCAGGTGCTGGCCATCTTTTCACTCCTGATGTTA
TCAGAGCCATTGCCTCTATCAATGAAAGGCCTGTAATATTTGCATTAAGTAATCCTACAGCACAGGCGGAGTGC

Alignment

ORF - retro_nleu_2307 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.45 %
• Parental protein coverage: 73.29 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MLSRLRVVSTTCTLACRHLHIKEKGKPLMLNPRTNKGMAFTLQERQMLGLQGLLPPKIETQDIQALRFHR
          MLS.L.V.STTCT.ACRHLHIKEKGKPLMLNPRTN.GMAFTLQERQMLGLQGLLPP.I.T.DI.ALRFHR
Retrocopy MLSGLSVFSTTCTFACRHLHIKEKGKPLMLNPRTNTGMAFTLQERQMLGLQGLLPPQIQT*DI*ALRFHR

Parental  NLKKM-TSPLEKYIYIMGIQERNEKLFYRILQDDIESLMPIVYTPTVGLACSQYGHIFRRPKGLFISISD
          NL....TSPLEKYIY...IQERN.KLFYRILQDD.ESLMPIVYTPTV.L.CSQ.GH.FRRPKGLFISIS.
Retrocopy NLXXX>TSPLEKYIY---IQERNDKLFYRILQDDPESLMPIVYTPTVDLVCSQCGHLFRRPKGLFISISV

Parental  RGHVRSIVDNWPENHVKAVVVTDGERILGLGDLGVYGMGIPVGKLCLYTACAGIRPDRCLPVCIDVGTDN
          RG.VRSIVD.WPENHVKAV.VTDGERILGLGDLGVYGMGIPVGK.CLYT...GI.PDRC..VCIDVGT.N
Retrocopy RGRVRSIVDKWPENHVKAVLVTDGERILGLGDLGVYGMGIPVGKICLYTVHPGIWPDRCFLVCIDVGTNN

Parental  IALLKDPFYMGLYQKRDRTQQYDDLIDEFMKAITDRYGRNTLIQFEDFGNHNAFRFLRKYREKYCTFNDD
          IALLKD.FYMGLYQKRDRTQQ.DDLIDEFMKAITDRYG.NTLIQ.E..GNHNAFRFLRKY..KY.TFNDD
Retrocopy IALLKDTFYMGLYQKRDRTQQSDDLIDEFMKAITDRYGWNTLIQLEGCGNHNAFRFLRKYQ*KY*TFNDD

Parental  IQGTAAVALAGLLAAQKVISKPISEHKILFLGAGEAALGIANLIV-MSMVENGL-SEQEAQKKIWMFDKY
          IQGTAAVALAGLLA.QKV.SKP.SEHKILF.GAGE..L.IANLI..MSMVEN...SE..AQKKIWMFDKY
Retrocopy IQGTAAVALAGLLATQKVTSKPTSEHKILFFGAGEITLRIANLIE<MSMVENDR<SEEKAQKKIWMFDKY

Parental  GLLVKGRKAKIDSYQEPFTHPAPESIPDTFEDAVNILKPSTIIGVAGAGRLFTPDVIRAMASINERPVIF
          GLLV.GRKAKIDS.Q.PFT.P.PESIPDTFEDAVNI.K.ST.IGVAGAG.LFTPDVIRA.ASINERPVIF
Retrocopy GLLV*GRKAKIDS*QKPFTYPVPESIPDTFEDAVNIMKTSTTIGVAGAGHLFTPDVIRAIASINERPVIF

Parental  ALSNPTAQAEC
          ALSNPTAQAEC
Retrocopy ALSNPTAQAEC

Legend:

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

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_2307 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001929	1 retrocopy	retro_cjac_615,
Homo sapiens	ENSG00000082212	1 retrocopy	retro_hsap_4237,
Gorilla gorilla	ENSGGOG00000010823	1 retrocopy	retro_ggor_2838,
Nomascus leucogenys	ENSNLEG00000011833	1 retrocopy	retro_nleu_2307 ,
Pongo abelii	ENSPPYG00000009163	2 retrocopies	retro_pabe_3402, retro_pabe_3510,