RetrogeneDB ID: retro_nleu_1317

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397288.1:18677184..18677928(-)
• Located in intron of: ENSNLEG00000016369

Retrocopy information

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

Parental gene information

• Parental gene symbol: ASS1
• Ensembl ID: ENSNLEG00000012500
• Aliases: None
• Description: None

Sequence

>retro_nleu_1317
CGAGTGGTTCACTGAGCCATGAAGACAGATTCCAGGCATCAGGAATTGCACCTCCAATCCCAGATGCTATGTTCAGCAAA
AGCTCCATGGTTCTGGCCTACAGTGGTGGCCTGGACACCTCCTGCATCCTCGTGTGGCTGAAGGAACAAGGCTATGACAT
CATTGCCTACCTGGACAACATCGGCCAGAAGGAAGACTTCAAGTAAGCCAAGAAGAAGGCACTGAACCTTGGGTCCAAAA
AGGTGTTCATTGAGGACGTCAGCAAGGAGTTTGTGGAGGGAGTTCATCTGGCCGGCCATCCAGTCCAGTGCACTGTGTGA
GGACTGCTACCTCCTGGGCCCCTCTCTTCCCGGGCCCTGCATCACCCGCAAACAAGTGGAAATTGCTCGGTGGGAGGGGG
CCAAGTATGTGTCCCACAGTGCCATGGGAAAGGGGAACAATCAGGTCTGGTTTGAGCTCACCTGCTACTCGCTGGCCCCG
CAGATTAAGGTCATTGCTCCTAGGAGGATCCCCGAGTTCCACAACCAGTTCAAGGGCCACAGTGATCTGATGGAATATGC
AGAGAAACATGGGATTCCCATCCCAGTCACTCTGAAGCACCCATGGAACATGGACGAGAACCTCATGCACAACAACTATG
AGGCTGGAATCTTGGAGAACCCCAAGAACCAAGCACCTTCAGGTCTCTACATGAAGATCCAGGAACCAGCCAAAGCCCCC
AACACCCCCAACATTCTCAAGATT

Alignment

ORF - retro_nleu_1317 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.6 %
• Parental protein coverage: 57.01 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RVVHCTVKTDSRRWEL-TPPIPDAMSSKGSVVLAYSGGLDTSCILVWLKEQGYDVIAYLANIGQKEDFEE
          RVVH...KTDSR..EL..PPIPDAM.SK.S.VLAYSGGLDTSCILVWLKEQGYD.IAYL.NIGQKEDF..
Retrocopy RVVH*AMKTDSRHQEL<APPIPDAMFSKSSMVLAYSGGLDTSCILVWLKEQGYDIIAYLDNIGQKEDFK*

Parental  ARKKALKLGAKKVFIEDVSREFVE-EFIWPAIQSSALYEDRYLLGTSLARPCIARKQVEIAQREGAKYVS
          A.KKAL.LG.KKVFIEDVS.EFVE.EFIWPAIQSSAL.ED.YLLG.SL..PCI.RKQVEIA..EGAKYVS
Retrocopy AKKKALNLGSKKVFIEDVSKEFVE>EFIWPAIQSSALCEDCYLLGPSLPGPCITRKQVEIARWEGAKYVS

Parental  HGATGKGNDQVRFELSCYSLAPQIKVIAPWRMPEFYNRFKGRNDLMEYAKQHGIPIPVTPKNPWSMDENL
          H.A.GKGN.QV.FEL.CYSLAPQIKVIAP.R.PEF.N.FKG..DLMEYA..HGIPIPVT.K.PW.MDENL
Retrocopy HSAMGKGNNQVWFELTCYSLAPQIKVIAPRRIPEFHNQFKGHSDLMEYAEKHGIPIPVTLKHPWNMDENL

Parental  MHISYEAGILENPKNQAPPGLYTKTQDPAKAPNTPDILEI
          MH..YEAGILENPKNQAP.GLY.K.Q.PAKAPNTP.IL.I
Retrocopy MHNNYEAGILENPKNQAPSGLYMKIQEPAKAPNTPNILKI

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_1317 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 8 parental genes, and 68 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020554	3 retrocopies	retro_cjac_1219, retro_cjac_4038, retro_cjac_4209,
Homo sapiens	ENSG00000130707	14 retrocopies	retro_hsap_2247, retro_hsap_2885, retro_hsap_3109, retro_hsap_3175, retro_hsap_3252, retro_hsap_3564, retro_hsap_3824, retro_hsap_4149, retro_hsap_4182, retro_hsap_4648, retro_hsap_4743, retro_hsap_4934, retro_hsap_820, retro_hsap_985,
Gorilla gorilla	ENSGGOG00000010228	8 retrocopies	retro_ggor_1346, retro_ggor_1675, retro_ggor_2134, retro_ggor_2403, retro_ggor_2574, retro_ggor_2787, retro_ggor_671, retro_ggor_787,
Myotis lucifugus	ENSMLUG00000006066	2 retrocopies	retro_mluc_1058, retro_mluc_1304,
Mus musculus	ENSMUSG00000076441	1 retrocopy	retro_mmus_135,
Nomascus leucogenys	ENSNLEG00000012500	13 retrocopies	retro_nleu_1088, retro_nleu_1245, retro_nleu_1317 , retro_nleu_1381, retro_nleu_1390, retro_nleu_1424, retro_nleu_1701, retro_nleu_1792, retro_nleu_220, retro_nleu_253, retro_nleu_2680, retro_nleu_2764, retro_nleu_625,
Pongo abelii	ENSPPYG00000019692	13 retrocopies	retro_pabe_1963, retro_pabe_2390, retro_pabe_2637, retro_pabe_2696, retro_pabe_2937, retro_pabe_3069, retro_pabe_3197, retro_pabe_3422, retro_pabe_3460, retro_pabe_3521, retro_pabe_3522, retro_pabe_731, retro_pabe_834,
Pan troglodytes	ENSPTRG00000021473	14 retrocopies	retro_ptro_1590, retro_ptro_1951, retro_ptro_2101, retro_ptro_2199, retro_ptro_2268, retro_ptro_2421, retro_ptro_2602, retro_ptro_2821, retro_ptro_2836, retro_ptro_3064, retro_ptro_3158, retro_ptro_3298, retro_ptro_571, retro_ptro_762,