RetrogeneDB ID: retro_nleu_1978

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397320.1:10582660..10583574(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TTC4
• Ensembl ID: ENSNLEG00000003044
• Aliases: None
• Description: None

Sequence

>retro_nleu_1978
GACCAGTGGGAAGAGGAATTTGAAAAGGTCCCCCTGATTATAAGAAAGCACCATCAGAAATTGATCCCAGGGAGAATCCT
GACTTGGCTTGTCTCCAGTCAATTATTTTTGATGAGAAGCATTCTCCAGAACAGGCCAAGACCTATAAAGATGAAGGCAA
AGATTATATTAAAGAAAAAGACTACAAGAAAGCTGTAATTTCCTACACTGAAGGATTAAAGAAGAAATGTGCAAATCTTG
ATTTGAATGCTGTCCTTTATACCAACCAGGCAGCAGCACAATACTATCTGGGCAATTTTCATTCTGCTCTCAGTGATGTG
ACAGCTGCCAGAAAGTTAAAACCCTGCTACCTCAAAGCAATAATAAGAGGTGCCTTATGCCATCTGGAACTGAAACACTT
TGCCAAGGCTGTGAACTGATGTGATGAGGGACTGCAGAAAGATGCCAAAGAGAAGAAGCTTCTGGAAATGAGGGCTAAAG
CAGACAAGCTGAAGCTAATTGAACAGAGGGATGTGAGGAAAGCCAACTTGAAAGAAAAGGAGAGGAATCAGAATGAGGCT
TTACTCCAGGATATCAAGGCTAGGAATATCAGGCTCTCTGAAGCTGCCTGTGAGGATGAAGTTTCAGCCTCAGAAGGTCT
AAGTAAGCTTTTCCTGGATGGACTCAGCTCTGAGAACCCCCATGGAGCCAGGGTGAGTCTAGATGACCAGGGCAGGCTGA
GCCGGCCTGTGCTCTTTCTATACCCAGAGTATGCCCAATCGGACTTCATCTCTGCTTTTCATGAGGACTCCAGGTTTACT
GATCATCTAATGGTGATGTTTGGTGAAACACCCTCTTGAGACCTAGAGCAAAAATATTGCCCTGATAATTTGGAGGTCTA
CATTGAGGATGAGGACAGGGCAGAACTGTACCGT

Alignment

ORF - retro_nleu_1978 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.96 %
• Parental protein coverage: 77.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DGWFLEFEKVPLFMTR-APSEIDPRENPDLACLQSIIFDEERSPEEQAKTYKDEGNDYFKEKDYKKAVIS
          D.W..EFEKVPL.....APSEIDPRENPDLACLQSIIFDE..SPE.QAKTYKDEG.DY.KEKDYKKAVIS
Retrocopy DQWEEEFEKVPLIIRK<APSEIDPRENPDLACLQSIIFDEKHSPE-QAKTYKDEGKDYIKEKDYKKAVIS

Parental  YTEGLKKKCADPDLNAVLYTNRAAAQYYLGNFRSALNDVTAARKLKPCHLKAIIRGALCHLELKHFAEAV
          YTEGLKKKCA..DLNAVLYTN.AAAQYYLGNF.SAL.DVTAARKLKPC.LKAIIRGALCHLELKHFA.AV
Retrocopy YTEGLKKKCANLDLNAVLYTNQAAAQYYLGNFHSALSDVTAARKLKPCYLKAIIRGALCHLELKHFAKAV

Parental  NWCDEGLQIDAKEKKLLEMRAKADKLKRIEQRDVRKANLKEKKERNQNEALLQAIKARNIRLSEAACEDE
          N.CDEGLQ.DAKEKKLLEMRAKADKLK.IEQRDVRKANLKE.KERNQNEALLQ.IKARNIRLSEAACEDE
Retrocopy N*CDEGLQKDAKEKKLLEMRAKADKLKLIEQRDVRKANLKE-KERNQNEALLQDIKARNIRLSEAACEDE

Parental  DSASEGLGELFLDGLSSENPHGARLSLDEQGRLSWPVLFLYPEYAQSDFISAFHEDSRFIDHLMVMFGET
          .SASEGL..LFLDGLSSENPHGAR.SLD.QGRLS.PVLFLYPEYAQSDFISAFHEDSRF.DHLMVMFGET
Retrocopy VSASEGLSKLFLDGLSSENPHGARVSLDDQGRLSRPVLFLYPEYAQSDFISAFHEDSRFTDHLMVMFGET

Parental  PSWDLEQKYCPDNLEVYFEDEDRAELYR
          PS.DLEQKYCPDNLEVY.EDEDRAELYR
Retrocopy PS*DLEQKYCPDNLEVYIEDEDRAELYR

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_1978 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000005420	1 retrocopy	retro_ggor_2588,
Macaca mulatta	ENSMMUG00000006754	1 retrocopy	retro_mmul_1616,
Nomascus leucogenys	ENSNLEG00000003044	1 retrocopy	retro_nleu_1978 ,