RetrogeneDB ID: retro_nleu_833

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397274.1:33176088..33177306(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000019002
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DCAF4
• Ensembl ID: ENSNLEG00000002449
• Aliases: None
• Description: None

Sequence

>retro_nleu_833
CCTGTCACGAGGAACATTCCGCAGGAGGAAATGGAGGCTGAAAGGCTGCGACTCCTCGAGGAAGAGGCCAAGCAGAAAAA
GGTAGCCAGAATGGGATTTAATGCATCTTCCATGCTCCGAAAAAGCCAGCTAGGTTTCCTCAACGTCATCAGTTACTCCC
GTTTAGCCAACGAGCTGCGTGTGAGCTGCATGGAGCGGAAAAAGGTCCAAATTCGGAGCTTAGATCCCTCGTCTTTGGCG
AGCGACCGATTTAACTTCATTCTGGCGAGTACCAACAGCGACCAGCTCTTCGTAGTGAACCAGGTCGAAGTGGAAGGCTC
CAAGTACGGCATCATCAGCCTGCGAACTCTGAAGATCCCTTCGTTCCACGTGTACGTGCTCAGAAACCTCTACGTCCCCG
ACCGGAAGGTGAAGTCCCTGTGCTGGGCCTCGCTGAACCAGTTGGACTCTCACGTTCTGCTGTGCTTCGAGGGAATCACA
GATGCTACAAGCCGTGCAGTGCTGCTCCCAGCGTCGCGGTTCTTAAGTGTTCACACAAGAGTAAACCAGCCTGGCATGTT
CTGCAGTTTCCAGATCCCAGAGGCCTGGTCCTGTGCCTGGTCCCTCAACACCCGGGCATATCACTGCTTTAGTGCAGGCT
TGTCTCAGCAGGTCCTGTTGACCAACGTGGCGACGGGACACCAGCAGTCATTTGGTACCAGCAGTGATGTCTTGGCCCAG
CAGTTTGCTAATACGGCTCCTTTGCTGTTTAATGGCTGTCGCTCCGGGGAAATCTTTGCCATTGATCTGCGTTGTAGAAA
TCGAGGCAAGGGGTGGAGGGCCACTCGCCTGTTCCATGACTCAGCAGTGACCTCTGTGCAAATCCTCCAAGAAGAGCAAT
GCCTGATGGCGTCAGACATGACTGGAAAGATCAAGCTGTGGGATCTGAGGGCCACTAAATGTATAAGGCAGTACGAAGGT
CACGTGAATGAGTCCGCCTATCTGCCCCTGCATGTGCACGAGGAAGAGGGAATCGTGGTGGCAGTGGGCCAGGACTGCTA
CACGAGAATCTGGAGCCTCCATGATGCCCACCTGCTCAGAACGATTCCTTCCCCGTACTCTGCCTCCGAGGACGACATTC
CCAGCGTGGCCTTCGCTTCTCGGCTCGGGGGCATCCGGGGAGCAGCACCAGGGCTGCTCATGGCTGTCCGGCAGGACCTT
TATTGTTTCCCCTTCAGC

Alignment

ORF - retro_nleu_833 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.18 %
• Parental protein coverage: 82.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PLTKESIRQKEMESKRLWLLQEEDRQKKIARMGFNASSMLRKSQLGFLNVTNYCHLAHELRLSCMERRKV
          P.T...I.Q.EME..RL.LL.EE..QKK.ARMGFNASSMLRKSQLGFLNV..Y..LA.ELR.SCMER.KV
Retrocopy PVTR-NIPQEEMEAERLRLLEEEAKQKKVARMGFNASSMLRKSQLGFLNVISYSRLANELRVSCMERKKV

Parental  QIRSLDPSALASDRFNLILADTNSDRLFTVNDVKVGGSKYGIINLQSLKTPTLKVFMHENLYFTNRKVNS
          QIRSLDPS.LASDRFN.ILA.TNSD.LF.VN.V.V.GSKYGII.L..LK.P...V....NLY...RKV.S
Retrocopy QIRSLDPSSLASDRFNFILASTNSDQLFVVNQVEVEGSKYGIISLRTLKIPSFHVYVLRNLYVPDRKVKS

Parental  VCWASLNHLDSHILLCLMGLAETPGCATLLPASLFVNSHPGIDRPGMLCSFRIPGAWSCAWSLNIQANNC
          .CWASLN.LDSH.LLC..G.......A.LLPAS.F...H.....PGM.CSF.IP.AWSCAWSLN..A..C
Retrocopy LCWASLNQLDSHVLLCFEGITDATSRAVLLPASRFLSVHTRVNQPGMFCSFQIPEAWSCAWSLNTRAYHC

Parental  FSTGLSRRVLLTNVVTGHRQSFGTNSDVLAQQFALMAPLLFNGCRSGEIFAIDLRCGNQGKGWKATRLFH
          FS.GLS..VLLTNV.TGH.QSFGT.SDVLAQQFA..APLLFNGCRSGEIFAIDLRC.N.GKGW.ATRLFH
Retrocopy FSAGLSQQVLLTNVATGHQQSFGTSSDVLAQQFANTAPLLFNGCRSGEIFAIDLRCRNRGKGWRATRLFH

Parental  DSAVTSVRILQDEQYLMASDMAGKIKLWDLRTTKCIRQYEGHVNEYAYLPLHVHEEEGILVAVGQDCYTR
          DSAVTSV.ILQ.EQ.LMASDM.GKIKLWDLR.TKCIRQYEGHVNE.AYLPLHVHEEEGI.VAVGQDCYTR
Retrocopy DSAVTSVQILQEEQCLMASDMTGKIKLWDLRATKCIRQYEGHVNESAYLPLHVHEEEGIVVAVGQDCYTR

Parental  IWSLHDARLLRTIPSPYPASKADIPSVAFSSRLGGSRG-APGLLMAVGQDLYCYSYS
          IWSLHDA.LLRTIPSPY.AS..DIPSVAF.SRLGG.RG.APGLLMAV.QDLYC...S
Retrocopy IWSLHDAHLLRTIPSPYSASEDDIPSVAFASRLGGIRGAAPGLLMAVRQDLYCFPFS

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_833 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 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013878	1 retrocopy	retro_cpor_293,
Homo sapiens	ENSG00000119599	2 retrocopies	retro_hsap_101, retro_hsap_92,
Gorilla gorilla	ENSGGOG00000003815	2 retrocopies	retro_ggor_2026, retro_ggor_2743,
Macaca mulatta	ENSMMUG00000003625	2 retrocopies	retro_mmul_152, retro_mmul_264,
Nomascus leucogenys	ENSNLEG00000002449	2 retrocopies	retro_nleu_1912, retro_nleu_833 ,
Pan troglodytes	ENSPTRG00000006507	2 retrocopies	retro_ptro_2774, retro_ptro_46,