RetrogeneDB ID: retro_nleu_2054

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397325.1:4072327..4073106(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VENTX
• Ensembl ID: ENSNLEG00000002047
• Aliases: None
• Description: None

Sequence

>retro_nleu_2054
ATGCGTCCCTCCTCCTCCCCACCTCGTGGCCGGCAGCAGCCCTCCAGCTTTGGCTCTGTGGACTGGCTCTCCCAGAACAG
CTGCTCAGGGCCGACCCACACCCCCAGTCCTGCCGACGTCTCCCCGGGGAGCCACATTGGCCCGGGCCAGACATCCGGCA
CCCAGAAGCCCCCTCAGGCCGTCAGCATCAAGAAGGCTCGGTCCTCAAATCTGCCTGCGCCGGAGAGGGCCGCGGCTGGG
TTGAGTAAGAAGCCAAACCCCTGGCAGGCCCCCTGTGTAGGCACAGCCTTCACCACCGAGCAGGTCGGCGCCTTGGAGGG
CGTCTTCCAGCACCACCAGGACCTGGGCCCTCTGGAGCCCAGGAAAAGGCTGGCAGGGAGATGCAGCTCTCGGACGTCCA
GACAAAAACCTGGTTTCAAAACCGCCAGATGAAACAGAAACGGTGAATGCAGGACTCCCAGCTGAACAGCCCCTTCTCGG
TGTCTCTCCACGCGCCCCGTGCTTTCCACTCACCGTCTCTGGCCTTGCCAATGGCCTGCAGCTGCCGTGCCCTTGGGCAC
CCCTGCCAGGGCCCCAGGCTCTGATGCTGCCCCCTGGCTCCCTCTGGGGTCTCTGCCAAGTGGAACAAGAGACCCTGGCC
TCTGCGGGGGCTTCCTGTTATGGGCAACCTCTGGCGTACCACCCGCCAAGCCCAGGAAATGGCGTGCGTACGCTGGGACC
AGCCCTGTCCACGGGGCCCTGGGGCCTGTGCGCTCTGCAGGAGACGGGGGGATGCATTT

Alignment

ORF - retro_nleu_2054 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.79 %
• Parental protein coverage: 98.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MRLSSSPPRGRQQPSSFGSVDWLSQSSCSWPTHTPRTADXXXGAFPGRAQTSGAREP-QAVSIKEAGRSS
          MR.SSSPPRGRQQPSSFGSVDWLSQ.SCS.PTHTP..AD...G...G..QTSG...P.QAVSIK.A.RSS
Retrocopy MRPSSSPPRGRQQPSSFGSVDWLSQNSCSGPTHTPSPADVSPGSHIGPGQTSGTQKPPQAVSIKKA-RSS

Parental  NL-APERSVAGLSKKPNNLRAPRVRTAFTTEQVRTLEGVFQHHQYLSPLE-RKRLA-REMQLSEVQIKTW
          NL.APER..AGLSKKPN...AP.V.TAFTTEQV..LEGVFQHHQ.L.PLE.RKRLA.REMQLS.VQ.KTW
Retrocopy NLPAPERAAAGLSKKPNPWQAPCVGTAFTTEQVGALEGVFQHHQDLGPLEPRKRLA<REMQLSDVQTKTW

Parental  FQNRRMKHKRQMQDPQLHSPFSGSLHAPPAFHSPS-SGLANGLQLLCPWAPLPGPQALMLPPGSFWGLCQ
          FQNR.MK.KR.MQD.QL.SPFS.SLHAP.AFHSPS.SGLANGLQL.CPWAPLPGPQALMLPPGS.WGLCQ
Retrocopy FQNRQMKQKR*MQDSQLNSPFSVSLHAPRAFHSPS<SGLANGLQLPCPWAPLPGPQALMLPPGSLWGLCQ

Parental  VEQEGLASAGASCCGQPLASHPPTPGSGLPTLGPALSTGPQGLCALPQT-GDAF
          VEQE.LASAGASC.GQPLA.HPP.PG.G..TLGPALSTGP.GLCAL..T.GDAF
Retrocopy VEQETLASAGASCYGQPLAYHPPSPGNGVRTLGPALSTGPWGLCALQET>GDAF

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_2054 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.

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000151650	4 retrocopies	retro_hsap_1027, retro_hsap_2612, retro_hsap_3973, retro_hsap_4038,
Gorilla gorilla	ENSGGOG00000003340	3 retrocopies	retro_ggor_1830, retro_ggor_2668, retro_ggor_2708,
Macaca mulatta	ENSMMUG00000000543	2 retrocopies	retro_mmul_1477, retro_mmul_2294,
Nomascus leucogenys	ENSNLEG00000002047	5 retrocopies	retro_nleu_2033, retro_nleu_2054 , retro_nleu_635, retro_nleu_664, retro_nleu_905,
Pan troglodytes	ENSPTRG00000003087	4 retrocopies	retro_ptro_1761, retro_ptro_2698, retro_ptro_2736, retro_ptro_702,