RetrogeneDB ID: retro_nleu_352

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397263.1:21969947..21970957(-)
• Located in intron of: ENSNLEG00000006056

Retrocopy information

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

Parental gene information

• Parental gene symbol: API5
• Ensembl ID: ENSNLEG00000017956
• Aliases: None
• Description: None

Sequence

>retro_nleu_352
CTATCAATGCAGTTAGACCTCTGTGAGGATGAAGATGTATCTATCCGACGTCAAGCAATTAAAGAACTGCCTCAATTTAC
CACTGGAGAAAATCTTCTTCGAGTGGCAGATACACTAATGCAACTTTTGGAGACAGATGGCTCTGCAGAATTTAACCTAG
TGAACAATGCCCTGTTAAGTGTATTTAATATGGATGGAAAAGGGACTTTAGGTTCATTGTTCAGCCAAATAATTCAAGGA
GAGGACATTGTTAGAGAACGAGCAATTAAATTCCTTTCTACAAAACTTAAGACTTTACCAGATGAAATATTAACAAAGGA
AGTGGAAGAGCTTATACTAACTGAATCCAAACACGTCCTAGAAGATGTGACTCGTGAAGAATTTGTTCTATTCATGAAAT
ACTGTCTGGGTTAAAAAGCTTACAGACAGTAAGTGGAAGACAGCAACTTGTAAAGCTGGTGGCCGAACAGGCTGACATAG
AACAGACCTTCAGTCCCTCGGATCCTGAGTGTGTGGACAGGCTCTTACAGTGCACTCGGCAGGCAGTACCCTTCTTCTCT
AAAACTGTCCATTCCACAAGGTTTGTGACATATTTCTGTGAGCAGGTCCTCCCTAACCTTAGTATCTTGACTACTGCAGT
GGAAGGTCTTGATATACAGTTGGAGGTATTGAAATTGTTGGTGGAGATGAGTTCATTTTGTGGTGACATTGAAAAACTAG
AAACAAATTTAAGGAAACTATTGGTTAAGTTATTGGAATACATGCCCCTCCCTCCAGAAGAAGCAGAAAATGGAGAGAAT
GGTGGTGATGAAGAACCCAAGCTACAGTTCAGTTATGTGGAATGTTTGTTGTACAGTTTTCACCAGTTGGGTCAAAAACT
TCCAGATTTCTTAACAGCCAAACTGAATGCAAAAAAACTCAAAGATTTCAAAATCAGGCTGCAATACTTTGCACGAGGCC
TGCAAGTTTATATCAGACAACTTCGCTTAGCTCTCCAGGGTGAAACGGGT

Alignment

ORF - retro_nleu_352 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.35 %
• Parental protein coverage: 64.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  INAQLDLCEDEDVSIRRQAIKELPQFATGENLPRVADILTQLLQTDDSAEFNLVNNALLSIFKMDAKGTL
          ...QLDLCEDEDVSIRRQAIKELPQF.TGENL.RVAD.L.QLL.TD.SAEFNLVNNALLS.F.MD.KGTL
Retrocopy LSMQLDLCEDEDVSIRRQAIKELPQFTTGENLLRVADTLMQLLETDGSAEFNLVNNALLSVFNMDGKGTL

Parental  GGLFSQILQGEDIVRERAIKFLSTKLKTLPDEVLTKEVEELILTESKKVLEDVTGEEFVLFMK-ILSGLK
          G.LFSQI.QGEDIVRERAIKFLSTKLKTLPDE.LTKEVEELILTESK.VLEDVT.EEFVLFMK.ILSGLK
Retrocopy GSLFSQIIQGEDIVRERAIKFLSTKLKTLPDEILTKEVEELILTESKHVLEDVTREEFVLFMK<ILSGLK

Parental  SLQTVSGRQQLVELVAEQADLEQTFNPSDPDCVDRLLQCTRQAVPLFSKNVHSTRFVTYFCEQVLPNLGT
          SLQTVSGRQQLV.LVAEQAD.EQTF.PSDP.CVDRLLQCTRQAVP.FSK.VHSTRFVTYFCEQVLPNL..
Retrocopy SLQTVSGRQQLVKLVAEQADIEQTFSPSDPECVDRLLQCTRQAVPFFSKTVHSTRFVTYFCEQVLPNLSI

Parental  LTTPVEGLDIQLEVLKLLAEMSSFCGDMEKLETNLRKLFDKLLEYMPLPPEEAENGENAGNEEPKLQFSY
          LTT.VEGLDIQLEVLKLL.EMSSFCGD.EKLETNLRKL..KLLEYMPLPPEEAENGEN.G.EEPKLQFSY
Retrocopy LTTAVEGLDIQLEVLKLLVEMSSFCGDIEKLETNLRKLLVKLLEYMPLPPEEAENGENGGDEEPKLQFSY

Parental  VECLLYSFHQLGRKLPDFLTAKLNAEKLKDFKIRLQYFARGLQVYIRQLRLALQGKTG
          VECLLYSFHQLG.KLPDFLTAKLNA.KLKDFKIRLQYFARGLQVYIRQLRLALQG.TG
Retrocopy VECLLYSFHQLGQKLPDFLTAKLNAKKLKDFKIRLQYFARGLQVYIRQLRLALQGETG

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_352 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000166181	2 retrocopies	retro_hsap_2350, retro_hsap_4893,
Gorilla gorilla	ENSGGOG00000002358	2 retrocopies	retro_ggor_1784, retro_ggor_3055,
Myotis lucifugus	ENSMLUG00000013546	1 retrocopy	retro_mluc_245,
Nomascus leucogenys	ENSNLEG00000017956	1 retrocopy	retro_nleu_352 ,
Pan troglodytes	ENSPTRG00000003516	2 retrocopies	retro_ptro_1720, retro_ptro_3261,