RetrogeneDB ID: retro_nleu_1937

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397317.1:12313621..12314979(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLTSCR2
• Ensembl ID: ENSNLEG00000003143
• Aliases: None
• Description: None

Sequence

>retro_nleu_1937
CTCGAAATGCGGCGCATTTCGGTGGACCCAGCGCTGAGGCAGCGGCGGCGAGGCCCAAGAAATAAGAAGTGGGGCTGGCG
GCGGCTTGCTCAGGAAGCCGCTGGGGCTGGAGGTTGACCAATTCCTGGAACACGTGCGGCCACAGGAGCGCACGAGCGGT
GGCTTGTTGTCAGAGGCCCCACATGAAAAACTCTTCTTTGTGGACACCGGCTCCAAGGAAAAAGGGCTAAGAAGAGAACC
AAAGTCCACAAGAAGTCACTGCTTCTCAAGAAACCCCTTCGCGTTCACCTCATCCTTGAGAACACATCCAAAGTCCCTGC
CCCCAAAGACGTCCTCGCCCACCAGGTCCCCAATGCCAAGAAGCTCAGGCGGAAGGAGCAGCTATGGGAGAAGCTGGCCA
AGCAGGGCGAGCTGCCCCGGGAGGTGCGCAGGGCCCAGACCCGGCTCCTCAACCCTCCCGCAGCCAGGGCCCCAGGACAC
CGTGGAGCGGCCCTTCTACGACCTCTGGGCCTCAGACAACCCCCGGACAGGCCGTTGTTTGGCCAGGATGAGTTTTTCCT
GGAGCAGACCAAGAAGGAAGGAGTGAAGCGGCCACCACGCCTGCACACCAGGCCGTCCCAGGCACCCGCCGTGGAGGTGG
CGCCTGCCGGAGCTTCCTCCAACCCGTCCTTTGAAGACCACCAGACCCTGCTCTCAGCGGCCCACGAGGTGGAGTTGCAG
CGGCAGAAGGAGGCGGAGAGGCTGGAGCGGCAGCTGGCTCTGCCCGCCACAGAGCAGGCCGCTACCCAGGAGTCCACGTT
CCAGGAGCTGTGCGAGGGGCTGCTGGAGGAGTCGGATGGTGAGGGGGAGCCAGGCCAGGGCGAGGGGCCGGAGGCTGGGG
ATGCCGAGGTCTGTCCCACGTCCGCCCGCCTGGTCGCCACAGAGAAGAAGACGGAGCAGCAGCGGCGGCGGGAGTAGGCT
GCGCGCAGGCTGCGGGTACAGCAGGCCGCGTTGCTGGCTGCCCGGCTCCGGCTCCGGCACTAGCAGGTGTTCCCGCTGCG
CGGATCAAGGCCCAGGTGGCCCTGAGGTTGGCGGAGCTGGCGCGGCGGCGGAGGCAGCGGCAGGCACGGCGGGAGGCCGA
GGCTGACAAGGCCCGAAGGCTGGGGCGGCTCAAGTACCAGGCAGCTGACATCGACGTGCAGCTGAGCTGGGAGCTGACAG
ACTCGCTCAGGACCCTGAAGCCCGAGGGCAACATCCTTCGAGACCGGTTCAGGAGCTTCCAGAGGAGGAATAGGATCGAT
CCTCGAGAGAGAGCCAAGTTCAAACGTAAGTAGAAGGTGAAGCTGGTGGAGAAGCGGGCGTTCCGCGGGATCCAGTTG

Alignment

ORF - retro_nleu_1937 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.38 %
• Parental protein coverage: 95.4 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LGLRPTSVDPALRRRRRGPRNKKRGWRRLAQE-PLGLEVDQFLEDVRLQERTSGGLLSEAPNEKLFFVDT
          L..R..SVDPALR.RRRGPRNKK.GWRRLAQE.PLGLEVDQFLE.VR.QERTSGGLLSEAP.EKLFFVDT
Retrocopy LEMRRISVDPALRQRRRGPRNKKWGWRRLAQE>PLGLEVDQFLEHVRPQERTSGGLLSEAPHEKLFFVDT

Parental  GSKEKGL-TKKRTKVQKKSLLLKKPLRVDLILENTSKVPAPKDVLAHQVPNAKKLRRKEQLWEKLAKQGE
          GSKEKGL..K......K..LL.KKPLRV.LILENTSKVPAPKDVLAHQVPNAKKLRRKEQLWEKLAKQGE
Retrocopy GSKEKGL<KKRTKVHKKSLLL-KKPLRVHLILENTSKVPAPKDVLAHQVPNAKKLRRKEQLWEKLAKQGE

Parental  LPREVRRAQARLLNPPAARAKPGPQDTVERPFYDLWASDNPLDRPLVGQDEFFLEQTKKKGVKRPSRLHT
          LPREVRRAQ.RLLNPPAARA.........RP.......D.PL.....GQDEFFLEQTKK.GVKRP.RLHT
Retrocopy LPREVRRAQTRLLNPPAARAPGHRGAALLRPLGLRQPPDRPL----FGQDEFFLEQTKKEGVKRPPRLHT

Parental  KPSQAPAVEVAPAGASYNPSFEDHQTLLSAAHEVELQRQKEAEKLERQLALPATEQAATQESTFQELCEG
          .PSQAPAVEVAPAGAS.NPSFEDHQTLLSAAHEVELQRQKEAE.LERQLALPATEQAATQESTFQELCEG
Retrocopy RPSQAPAVEVAPAGASSNPSFEDHQTLLSAAHEVELQRQKEAERLERQLALPATEQAATQESTFQELCEG

Parental  LLEESDGEGEPGQGEGPEAGDAEVGPMPARLAATEKKTEQQRRREKAVRRLRVQQAALRAA--RLRHQEL
          LLEESDGEGEPGQGEGPEAGDAEV.P..ARL.ATEKKTEQQRRRE.A.RRLRVQQAAL.AA..RLRH...
Retrocopy LLEESDGEGEPGQGEGPEAGDAEVCPTSARLVATEKKTEQQRRRE*AARRLRVQQAALLAARLRLRH*QV

Parental  FRLRG-IKAQVALRLAELARRRRQRQARREAEADKPRRLGRLKYQAPDIDVQLSSELTDSLRTLKPEGNI
          F.LRG.IKAQVALRLAELARRRRQRQARREAEADK.RRLGRLKYQA.DIDVQLS.ELTDSLRTLKPEGNI
Retrocopy FPLRG<IKAQVALRLAELARRRRQRQARREAEADKARRLGRLKYQAADIDVQLSWELTDSLRTLKPEGNI

Parental  LRDRFKSFQRRNMIEPRERAKFKRKYKVKLVEKRAFREIQL
          LRDRF.SFQRRN.I.PRERAKFKRK.KVKLVEKRAFR.IQL
Retrocopy LRDRFRSFQRRNRIDPRERAKFKRK*KVKLVEKRAFRGIQL

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_1937 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000105373	1 retrocopy	retro_hsap_1528,
Macropus eugenii	ENSMEUG00000002525	2 retrocopies	retro_meug_1136, retro_meug_1713,
Nomascus leucogenys	ENSNLEG00000003143	1 retrocopy	retro_nleu_1937 ,
Pongo abelii	ENSPPYG00000010181	3 retrocopies	retro_pabe_1270, retro_pabe_653, retro_pabe_662,
Pan troglodytes	ENSPTRG00000011215	1 retrocopy	retro_ptro_1035,
Rattus norvegicus	ENSRNOG00000013023	1 retrocopy	retro_rnor_1107,