RetrogeneDB ID: retro_nleu_1912

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397315.1:2039510..2040724(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000018842
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_nleu_1912
CCCCTCAGGAGGGAGAACTTCCATCGAACGAAATGGAGAGCAAAAGACCGCGACTGCTGGAGGAAGCAGACAAGCAGAAA
AAGACAGTCAGAGCGGGACTCAGTGCACCTTCCATGCTACGAAAGAACCAGCTAGGTTTCCTCAGATTCGCCAACTATTG
CCGTTTAGCTCGCGAGCTGCGTGTAAGCTGCATGCAGAGGAAAAAGGTCCAGATTCATAGCTGGGATCCCTCCTCTTTGG
CAAGCGACCGATTTAACCGCATACTGGCGAATACCAACACTGACCAGCTCTTCACAGTGAACCAAGTCGAAGCTGGAGGC
TCCAAGTACGGCATCATCACCATGCGAGGCCTGACGACCCCTGAGCTCCGGGTATACCCTCACAAAAGCCTCTACGTTCC
TAATCGGAAGGTGAATTCTATGTGCTGGGCCTCACTGAATCACTTGGATTCCCACCTTCTGCTGTGCTTCGTGGGACTTG
CAGGTATTCCAAGCTGTGCCGTGCTGCTCCCAGCGTCACTGTTCGTAGGTAGCTACCCAGGAATACGTCGGCCTGGCATG
CTCTGCAGTTTCCAGATCCCTGATGCCTGGTCCTGTGCCTGGTCCCTGAGCATCCACGCATATCACTGCTTCAGTACAGG
CTTGTCTCAGCAGGTCCTGTTGACCAACGTGGTAACGGGACACCAGCAGTCATTTGGGACTAGCAGTGATGTCTTGGCCC
AGCAGTTTGCAATCATGACTCCTTTGCTGTTTAATGGCTGTCGCTCTGGGGAGATCTTTGGCATTGATCTGCGCTGTGGA
AATCAAGGCAGGGGGTGGAAGGCCATTTGCCTGTCCCATGATTCAGCAGTGACCTCTCTGCAAATCCTCCAAGAAGGGCA
ATTCCTGGTGGCATCAGACATGACTGGAACGATCAAGCTGTGGGACTTGAGGGCCACTAAATGTGTAACACAGTACGAAG
GTCATGTGAATAACTCCGCCTACCTGCCCCTGCATGTGAACGAGGAAGAAGGAGTCGTGGCGGCCGTGGGCCAGGACTGC
TATACGAGAATCTGGAGCCTCCGTCATGGCCACCTGCTCACAACCATACCCTCCCCATACCCCGCCTCAGAGAACGACAT
TCCCAGTGTGGCCTTCTCTTCTCGCCTCGGGGGCTTCCGAGGAGCACCAGGGCTGCTCATGGCTGTCCGGGAGGACCTTT
ATTGTTTCTCCTAC

Alignment

ORF - retro_nleu_1912 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.65 %
• Parental protein coverage: 81.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PLTKESIRQ-KEMESKRLWLLQEEDRQKKIARMGFNASSMLRKSQLGFLNVTNYCHLAHELRLSCMERRK
          PL..E......EMESKR..LL.E.D.QKK..R.G..A.SMLRK.QLGFL...NYC.LA.ELR.SCM.R.K
Retrocopy PLRRENFHR<NEMESKRPRLLEEADKQKKTVRAGLSAPSMLRKNQLGFLRFANYCRLARELRVSCMQRKK

Parental  VQIRSLDPSALASDRFNLILADTNSDRLFTVNDVKVGGSKYGIINLQSLKTPTLKVFMHENLYFTNRKVN
          VQI.S.DPS.LASDRFN.ILA.TN.D.LFTVN.V..GGSKYGII....L.TP.L.V..H..LY..NRKVN
Retrocopy VQIHSWDPSSLASDRFNRILANTNTDQLFTVNQVEAGGSKYGIITMRGLTTPELRVYPHKSLYVPNRKVN

Parental  SVCWASLNHLDSHILLCLMGLAETPGCATLLPASLFVNSHPGIDRPGMLCSFRIPGAWSCAWSLNIQANN
          S.CWASLNHLDSH.LLC..GLA..P.CA.LLPASLFV.S.PGI.RPGMLCSF.IP.AWSCAWSL.I.A..
Retrocopy SMCWASLNHLDSHLLLCFVGLAGIPSCAVLLPASLFVGSYPGIRRPGMLCSFQIPDAWSCAWSLSIHAYH

Parental  CFSTGLSRRVLLTNVVTGHRQSFGTNSDVLAQQFALMAPLLFNGCRSGEIFAIDLRCGNQGKGWKATRLF
          CFSTGLS..VLLTNVVTGH.QSFGT.SDVLAQQFA.M.PLLFNGCRSGEIF.IDLRCGNQG.GWKA..L.
Retrocopy CFSTGLSQQVLLTNVVTGHQQSFGTSSDVLAQQFAIMTPLLFNGCRSGEIFGIDLRCGNQGRGWKAICLS

Parental  HDSAVTSVRILQDEQYLMASDMAGKIKLWDLRTTKCIRQYEGHVNEYAYLPLHVHEEEGILVAVGQDCYT
          HDSAVTS..ILQ..Q.L.ASDM.G.IKLWDLR.TKC..QYEGHVN..AYLPLHV.EEEG...AVGQDCYT
Retrocopy HDSAVTSLQILQEGQFLVASDMTGTIKLWDLRATKCVTQYEGHVNNSAYLPLHVNEEEGVVAAVGQDCYT

Parental  RIWSLHDARLLRTIPSPYPASKADIPSVAFSSRLGGSRGAPGLLMAVGQDLYCYSY
          RIWSL....LL.TIPSPYPAS..DIPSVAFSSRLGG.RGAPGLLMAV..DLYC.SY
Retrocopy RIWSLRHGHLLTTIPSPYPASENDIPSVAFSSRLGGFRGAPGLLMAVREDLYCFSY

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_1912 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,