RetrogeneDB ID: retro_nleu_1546

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397298.1:19826020..19826670(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GSTM1
• Ensembl ID: ENSNLEG00000003194
• Aliases: None
• Description: glutathione S-transferase mu 1 [Source:HGNC Symbol;Acc:4632]

Sequence

>retro_nleu_1546
ATGCCCATGACACTGGGGTATGGGGACATTCACGGGCTGGCACATGCCATCCGCCTGCTCCTTGAATACACAGACTCAAG
CTACAAGGAAAAGAAGTACACGATGGGGGACTCTCCTGACTATGACAGAAGCCAGTAGCTGAATGAAAAATTCAAGCTGG
GCCTGGACTTTCCCAATCTGCCCTACTTGTTTGATGGGGCTCACAAGATCACCCAGAGCAATGACATCCTGTGCCACATT
GCCCGCAAGAACAACCTGTGTGAGGAGACAGAAGAGGAGAAGATTTGTGTGGACATTTCAGAGAACCAGACTGTAGACAA
CCTGATGCAGCTGGCCATGATCTGCTATATCCCAGAATTTGAGAAACTGAAGCCAAAGTACCTGGAGGAACTCCCTGAAA
AGCTAAAGCTCTACTCACAGTTTCTGGGGAAGTGGCCATGGTTTGCAGGAGACAAGATCACCTTTGTGGATTTCCTTGCC
TATGACATCCTTGACCTGAACTGTATATTTGACCCCAGCTGCCTGGACGCCTTCCCAAACCTGAAGGACTTCATCTCCCG
AATTGAGGGTTTGAAGAAGATCTCTGCCTACATGAAGTCCAGCCAATGCCTCCGAGGTCCTTTGGGAAGTCAGCTACGTG
GAACAGCAAA

Alignment

ORF - retro_nleu_1546 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.82 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPITLGYWNIRGLAHSIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNLPYLIDGAHKI
          MP.TLGY..I.GLAH.IRLLLEYTDSSY.EKKYTMGD.PDYDRSQ.LNEKFKLGLDFPNLPYL.DGAHKI
Retrocopy MPMTLGYGDIHGLAHAIRLLLEYTDSSYKEKKYTMGDSPDYDRSQ*LNEKFKLGLDFPNLPYLFDGAHKI

Parental  TQSNAILRYIARKHNLCGETEEEKIRVDILENQTMDNHMQLAMICYNPEFEKLKPKYLEELPEKLKLYSE
          TQSN.IL..IARK.NLC.ETEEEKI.VDI.ENQT.DN.MQLAMICY.PEFEKLKPKYLEELPEKLKLYS.
Retrocopy TQSNDILCHIARKNNLCEETEEEKICVDISENQTVDNLMQLAMICYIPEFEKLKPKYLEELPEKLKLYSQ

Parental  FLGKRPWFAGNEITFVDFLVYDVLDFHRIFEPKCLDAFPNLKDFISRFEGLEKISAYMKSSRFL-PRPVF
          FLGK.PWFAG..ITFVDFL.YD.LD...IF.P.CLDAFPNLKDFISR.EGL.KISAYMKSS..L.PR..F
Retrocopy FLGKWPWFAGDKITFVDFLAYDILDLNCIFDPSCLDAFPNLKDFISRIEGLKKISAYMKSSQCL<PRS-F

Parental  TKMAVWGNK
          .K.A.W..K
Retrocopy GKSATWNSK

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_1546 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 6 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003123	7 retrocopies	retro_cjac_1299, retro_cjac_2226, retro_cjac_2463, retro_cjac_2498, retro_cjac_3004, retro_cjac_3084, retro_cjac_811,
Gorilla gorilla	ENSGGOG00000005148	2 retrocopies	retro_ggor_1913, retro_ggor_2459,
Nomascus leucogenys	ENSNLEG00000003194	2 retrocopies	retro_nleu_1546 , retro_nleu_504,
Nomascus leucogenys	ENSNLEG00000003302	1 retrocopy	retro_nleu_1895,
Pongo abelii	ENSPPYG00000001064	2 retrocopies	retro_pabe_2218, retro_pabe_2990,
Pan troglodytes	ENSPTRG00000001061	2 retrocopies	retro_ptro_1859, retro_ptro_2468,