RetrogeneDB ID: retro_nleu_2931

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397490.1:878944..880483(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DEPDC1
• Ensembl ID: ENSNLEG00000009334
• Aliases: None
• Description: None

Sequence

>retro_nleu_2931
TTGTTTCATTTCCTGGTAGTTATTTATGGCTACATCACAGTTTCAGATAGATCCAGTGGGATACATAAAATCCAAGATGA
TCCACAGTCTTCAAAATTCCTTCACTTAAACAATTTGAATTCCTTCAGATCAACTGAGTGCCTTCTTCTCAGTCTGCTTC
ATAGAGAAAAAAAAACAAGAATCAGATTCTACTGAGAGACTACAGATAAGCAATCCAGGATTTCAAGAAAGATGTGCTAA
GAAAATGCAGCTAGTTAATTTAAGAAACAGAAGAGTGAGTGCTAATGACATAATGGGAGGAAGTTGTCGTAATTTAATAG
GGTTAAGTAGTATGCATGATCTATCCTCTAACAGCAAACCAAGGTGCTGTTCTTTGGAAGGAATTGTAGATGTGTCAGGG
AATTCAAGTAAAGAGGCATCCAGTGTCTTTCTTCAATCTTTTCCGAACATGGAAGGACAAAATAATAAACTGTTTTTAGA
GTCTAAGCCCAAATAGGAATTCCTGTTGAATCTCCATTCAGAGGAAAATATTCAAAAGCCATTCAGTGCTGGTTTTAAGA
GAACCTCTACTTTGACTGTTCAAGACCAAGAGGAGTTGTGTAATGGGAAATGCAAGTCAGAACAGCTTTGTAGGTCTCAG
AGTTTGCTTTTAAGAAGTAGTACAAGAAGATTCAGTTATATCAATACACCAGTGGCTGAAATTATCATGAAACCAAATGT
TGGACAAGGCAGCACAAGTGTGCAAACAGCTATGGAAAGTGAACTTGGAGAGTCTAGTGCCACAATCAATGAAAGACTGC
AAAAGTACAATAGAACTTACAGAAGATTCTTTTACTTCCAGCTTCTTCTATGTTGACTGGCACACAAAGTTTGCTGCAAC
CTCATTTAGAGAGGGTTGCCATCAATGCTCTACAGTTATGTTGTTTGTTACTTCCCCCACCAAATCATAGAAAGCTTCAG
CTTTTAATGTGTATGATTTCCCGAATGAGTCAAAATGTTGATATGCCCAAACTTCATGATGCAATGGGTGTGAGATCACT
GTTGATACATACCTTTTCTCAATGTGTGTTATGCTGTGCTGAAGAAGTGGATCTTGATGAGCTTGCTGGAAGATTAGTTT
CTTTCTTAATGGATCATGATCAGGAAATTCTTCAAGTACCCTCTTACTTACAGACTGCAGTGGAAAAACATCTCGACTAC
TGAAAAAAGGGACATATTGAAAATCCTGGAGATGGACTATTTGCTCCTTTGCCAACTTACTCATACTGTAAGCAGATTAG
TGCTCAGGAGTTTGATGAGCAAAAAATTTCTACCTCTCAAGCTGCAATTGCAGAACTTTTAGAAAATATTGTTAAAAACA
GGAGTTTACCTCTAAAGGAGAAAAGAAAAAAACTAAAACGGTTTCAGAAGGAATATCCTTCGATATATCAGAAAAGATTT
CCAACCACGGAGAGTGAAGCAGCACTTTTTGGTGACAAACCTACAGTCAAGCAACCAATGCTGATTTTAAGAAAACCAAA
GTTCCGTAGTCTAAGATAC

Alignment

ORF - retro_nleu_2931 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.07 %
• Parental protein coverage: 63.42 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LFVNILVVCGYITVSDRSSGIHKIQDDPQSSKFLHVNNLNSFKSTECLLL-SLLHREKNKEESDSTERLQ
          LF....V..GYITVSDRSSGIHKIQDDPQSSKFLH.NNLNSF.STEC.LL.S....E....ESDSTERLQ
Retrocopy LFHFLVVIYGYITVSDRSSGIHKIQDDPQSSKFLHLNNLNSFRSTEC-LL>SVCFIEXXXQESDSTERLQ

Parental  ISNPGFQERRAKKMQLVNLRNRRVSAHDIMGGSCHNLIGLSSMHDLSSNSKPRCCSLEGIVDVSGNSSKE
          ISNPGFQER.AKKMQLVNLRNRRVSA.DIMGGSC.NLIGLSSMHDLSSNSKPRCCSLEGIVDVSGNSSKE
Retrocopy ISNPGFQERCAKKMQLVNLRNRRVSANDIMGGSCRNLIGLSSMHDLSSNSKPRCCSLEGIVDVSGNSSKE

Parental  ASSVFHQSFPNIEGQNNKLFLESKPKQEFLLNLHSEENIQKPFSAGFKRTSTLTVEDQEELCNGKCKSKQ
          ASSVF.QSFPN.EGQNNKLFLESKPK.EFLLNLHSEENIQKPFSAGFKRTSTLTV.DQEELCNGKCKS.Q
Retrocopy ASSVFLQSFPNMEGQNNKLFLESKPK*EFLLNLHSEENIQKPFSAGFKRTSTLTVQDQEELCNGKCKSEQ

Parental  LCRSQSLLLRSSIRRNSYINTPVAEIIMKPNVGQGSTSVQTAMESELGESSATINKRL-CKSTIELSENS
          LCRSQSLLLRSS.RR.SYINTPVAEIIMKPNVGQGSTSVQTAMESELGESSATIN.RL..K....L....
Retrocopy LCRSQSLLLRSSTRRFSYINTPVAEIIMKPNVGQGSTSVQTAMESELGESSATINERL<AKVQ*NLQKIL

Parental  LLPASSVLTGTQSLLQPHLERVAIDALQLCCLLLPPPNRRKLQLLMRMISRMSQNVDMPKLHDAMGTRSL
          LLPASS.LTGTQSLLQPHLERVAI.ALQLCCLLLPPPN.RKLQLLM.MISRMSQNVDMPKLHDAMG.RSL
Retrocopy LLPASSMLTGTQSLLQPHLERVAINALQLCCLLLPPPNHRKLQLLMCMISRMSQNVDMPKLHDAMGVRSL

Parental  MIHTFSRCVLCCAEEVDLDELLAGRLVSFLMDHHQEILQVPSYLQTAVEKHLDYLKKGHIENPGDGLFAP
          .IHTFS.CVLCCAEEVDLDE.LAGRLVSFLMDH.QEILQVPSYLQTAVEKHLDY.KKGHIENPGDGLFAP
Retrocopy LIHTFSQCVLCCAEEVDLDE-LAGRLVSFLMDHDQEILQVPSYLQTAVEKHLDY*KKGHIENPGDGLFAP

Parental  LPTYSYCKQISAQEFDEQKVSTSQAAIAELLENIIKNRSLPLKEKRKKLKQFQKEYPLIYQKRFPTTESE
          LPTYSYCKQISAQEFDEQK.STSQAAIAELL....................FQKEYP.IYQKRFPTTESE
Retrocopy LPTYSYCKQISAQEFDEQKISTSQAAIAELLXXXXXXXXXXXXXXXXXXXRFQKEYPSIYQKRFPTTESE

Parental  AALFGDKPTIKQPMLILRKPKFRSLRY
          AALFGDKPT.KQPMLILRKPKFRSLRY
Retrocopy AALFGDKPTVKQPMLILRKPKFRSLRY

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_2931 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013839	1 retrocopy	retro_cpor_735,
Homo sapiens	ENSG00000024526	2 retrocopies	retro_hsap_1545, retro_hsap_4206,
Gorilla gorilla	ENSGGOG00000016316	1 retrocopy	retro_ggor_1176,
Macaca mulatta	ENSMMUG00000017766	1 retrocopy	retro_mmul_1176,
Mus musculus	ENSMUSG00000028175	1 retrocopy	retro_mmus_3028,
Nomascus leucogenys	ENSNLEG00000009334	1 retrocopy	retro_nleu_2931 ,
Otolemur garnettii	ENSOGAG00000000934	1 retrocopy	retro_ogar_1907,
Pongo abelii	ENSPPYG00000001248	1 retrocopy	retro_pabe_3441,
Pan troglodytes	ENSPTRG00000000847	2 retrocopies	retro_ptro_1041, retro_ptro_2855,