RetrogeneDB ID: retro_nleu_2033

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397324.1:1647905..1648697(+)
• Located in intron of: ENSNLEG00000001342

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_2033
ATGCATCCCTCCTCCTCCTCACCTTGTGGCCGGCAGCAGCCCTCTAGCTTTGGCTCCATGGACTGGCTCTCCCAAAGCAG
TTGCTCAGGGCCGACCCACACCCCCAGGCCTGCCGAGGTCTCCCTGGGGAGCCTCCCTGGCCCGGGCCAGGCATCCGGCC
CCGAGGAGCCCCCTCAGGCCGTCAGCATCAAGGAGGCTAGGTCCTCAAATCCGCCTCTGCCAGAGAGAGCCATGGCTGGG
TTGAGTAAAGGGCTAAACGCCTGGTGGGCCCCCCTGCGTCCACACAGCCTTCACCACGGAGCAGGTCTGTGGCTTGGAGG
GCATCTTCCGGCACCACCAGTACCTGGGCCCTCTGGAGTGGAAGAGGCTGGCCAGAGAAATGCAGCTGTCGGAGGTCCAG
ATAAAAACCTGGTTTCAAAATCGCCAGATGAAACACAAATGGCAAATGCAGGACTCCCAGCTGAACAGCCCCTTCTCGGG
GTCACTGCACGCACCCCTGGCTTTCCACTCACCATCTTCTGGCCTTGCCAATGGCCTGCACCTGCTGTGCCCTTGGGCAC
CCCTGCCTGGGCCCCAGGCTCTGATGCTGTCCCCTGACTCCTTCTGGGGTCTCTGCCAAGTGGAACAAGAGGCCCTGGCA
TCTGAGTGGGCCTCCTGCTGCGGGCAGCCTCTGGCGTACCACCCCCCAAAGCCCAGGAAGTGGCATGCATACGCTGGGAC
CAGCCCTGTCCATGGGGCCCTGGGGCCTGGTGTGCTCTGCTGGACACAGGATGCATTTTGAGGAAATGCCTC

Alignment

ORF - retro_nleu_2033 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.44 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MRLSSSPPRGRQQPSSFGSVDWLSQSSCSWPTHTPRTADXXXGAFPGRAQTSGAREP-QAVSIKEAGRSS
          M..SSS.P.GRQQPSSFGS.DWLSQSSCS.PTHTPR.A....G..PG..Q.SG..EP.QAVSIKEA..S.
Retrocopy MHPSSSSPCGRQQPSSFGSMDWLSQSSCSGPTHTPRPAEVSLGSLPGPGQASGPEEPPQAVSIKEARSSN

Parental  NLAPERSVAGLSKKPNNLRAPR-VRTAFTTEQVRTLEGVFQHHQYLSPLERKRLAREMQLSEVQIKTWFQ
          ...PER..AGLSK..N...AP..V.TAFTTEQV..LEG.F.HHQYL.PLE.KRLAREMQLSEVQIKTWFQ
Retrocopy PPLPERAMAGLSKGLNAWWAPL>VHTAFTTEQVCGLEGIFRHHQYLGPLEWKRLAREMQLSEVQIKTWFQ

Parental  NRRMKHKRQMQDPQLHSPFSGSLHAPPAFHSPSSGLANGLQLLCPWAPLPGPQALMLPPGSFWGLCQVEQ
          NR.MKHK.QMQD.QL.SPFSGSLHAP.AFHSPSSGLANGL.LLCPWAPLPGPQALML.P.SFWGLCQVEQ
Retrocopy NRQMKHKWQMQDSQLNSPFSGSLHAPLAFHSPSSGLANGLHLLCPWAPLPGPQALMLSPDSFWGLCQVEQ

Parental  EGLASAGASCCGQPLASHPP-TPGSGLPTLGPALSTGPQGL-CALPQTGDAFEEAL
          E.LAS..ASCCGQPLA.HPP..PGSG..TLGPALS.GP.GL.CAL..TG......L
Retrocopy EALASEWASCCGQPLAYHPP>SPGSGMHTLGPALSMGPWGL>CALLDTGCILRKCL

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_2033 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 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,