RetrogeneDB ID: retro_nleu_635

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397269.1:9497489..9498265(+)
• 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_635
ATGTGTCTCTCCTCCTCCCCACCTCGTGGCTGGCAGCAGCCCTCCAGCTTTGGCTCCATGGACTGGCTCTCCCCGAGCAG
CTGCTCAGGGTCGACCCACACCCCTAGGCCTGCCGACGTCTCCCCCAGGAGCCTCCCTGGCCCGAGCCAGACATTCGGCA
ACCGGGAGCCCCCTCAGACTGTCAGTACCAAGGAGGCTAGCTCTTCAAATCTACATGCGCCGGAGAGGACTGTTGCTGGG
TTGAGTAAGGAGCCAAACCTCTAGCTGGCCCCCGGTGTCCGCGCAGCCTTCACCACGGAGCAGGTCCGCGCCTTGGAAGG
CGTCTTCCGGCACCACCAGTACCTGGGCCCTCTGGAGCGGAAGAGGCTGGCCAGGGAGACGCAGCTCTCAGAGGTCCAGA
TAAAAACCTGGTTTCAAAATCGCCGGATGAAACACAAACGACAAATGCAGGACTCCCAGCTAAACGGCGCCTTCTCGGGG
TCTCTCCACGGGCCCCCTGCTTTCCATTCACCATCTTCTGGCCTTGCCAATGGCCTGCAGCTGCTGTGCCCTTGGGCACC
CCTGCCTGGGCCCCCTGGCTGCCCCTTGGCTCCTTCTGGGGTCTGCGACAAATGGATGAAGAGGCCCTGGCCTCTTCGTG
GGCTTCCTGCTGCGGGCAGCTTCTGGCGTACCACCCCCCACGCCCAGGAAGTGGCGAGCATACGCTGGGACCAGCCCTGT
CCACGGGGCCCTGGGGCCTTTGTGCTCTACCAGAGACAGGTGATGCATTTGAGGAA

Alignment

ORF - retro_nleu_635 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.34 %
• Parental protein coverage: 99.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRLSSSPPRGRQQPSSFGSVDWLSQSSCSWPTHTPRTADXXXGAFPGRAQTSGAREP-QAVSIKEAGRSS
          M.LSSSPPRG.QQPSSFGS.DWLS.SSCS..THTPR.AD......PG..QT.G.REP.Q.VS.KEA..S.
Retrocopy MCLSSSPPRGWQQPSSFGSMDWLSPSSCSGSTHTPRPADVSPRSLPGPSQTFGNREPPQTVSTKEASSSN

Parental  NLAPERSVAGLSKKPNNLRAPRVRTAFTTEQVRTLEGVFQHHQYLSPLERKRLAREMQLSEVQIKTWFQN
          ..APER.VAGLSK.PN...AP.VR.AFTTEQVR.LEGVF.HHQYL.PLERKRLARE.QLSEVQIKTWFQN
Retrocopy LHAPERTVAGLSKEPNL*LAPGVRAAFTTEQVRALEGVFRHHQYLGPLERKRLARETQLSEVQIKTWFQN

Parental  RRMKHKRQMQDPQLHSPFSGSLHAPPAFHSPSSGLANGLQLLCPWAPLPGPQALMLPPGSFWGLC-QVEQ
          RRMKHKRQMQD.QL...FSGSLH.PPAFHSPSSGLANGLQLLCPWAPLPGP....L.P....G.C.....
Retrocopy RRMKHKRQMQDSQLNGAFSGSLHGPPAFHSPSSGLANGLQLLCPWAPLPGPPGCPLAPS---GVC<RQMD

Parental  EGLASAGASCCGQPLASHPP-TPGSGLPTLGPALSTGPQGLCALPQTGDAFEE
          E.........C...L....P..PGSG..TLGPALSTGP.GLCALP.TGDAFEE
Retrocopy EEALASSWASCCGQLLAYHPPRPGSGEHTLGPALSTGPWGLCALPETGDAFEE

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_635 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,