RetrogeneDB ID: retro_nleu_1578

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397300.1:8425392..8426690(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000019050
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSMC2
• Ensembl ID: ENSNLEG00000009274
• Aliases: None
• Description: None

Sequence

>retro_nleu_1578
ATGCCAGATTACCTTGGTGCCCATCAGCGGAAGACCAAAGAAGATGAGAAGGACGACAAGCTCATCCAAGTTCTGGATGA
GGCGGATATTGTCTTGCTGAAAACTTATGGTCAGAGCACTTACTCTAGGCAGATCAAGCAAGTCGAAGATGGCATTCAGC
AACTTCTCAAGAAAATTAATGAGCTCATTGGTATTAAGGAATCTGACACTGGCCTGGCCCCACCAGCACTCTGGGATTTG
GCTGCAGATAAGCAGACACTCCAGAGTAAACAGCCTTTACAGGTTGCCAGGTGTACAAAGATAATCAATGCTGATTCAGA
GGACCCAAAATACATTGTCAATGTAAAGCGGTTTGCCAAGTTTGTGATGGACTTTAGTGATCAGGTGGCACCCACTGACA
TTGAAGAAGGGATGAGAGTAGGTGTGGACCGAAATAAATATCAAATTCACATTCCATTGCCTCCTAAGACTGACCCAACA
GTTACCACGATGCAGGTGGAGGAAAAACCTGATGTCACATACAGTAATGTCAGTGACTGTAAGGAGCAGATTGAGAAATT
GCGAGAAGTAGTTGAAACCCCATTACTTCATCCAGACAGGTTTGTGAATCTCAGCATTGAGGCTCCCAAGGGCATGCTGC
TCTTTAATCCACCCAGTACAGGAAGACACTCTGTGTGCAGGCAGTTGCTAATCAGACTGATGCGTGCTTCATTCGAGTTA
TTGGATCTGAGCAGTACAGAAATATGTCAGTTAGAGGGCTCAAATGGTTAATGAGCCCTTTGAAATGGCCAGAACAAAAA
AAGCCTGCCTTATCTTCTTTGATGAAATTGATGCTATTGGAGGGGCTCGGTTTGATGACGGTGCTAGAGGTGACAATGAA
GTGCAGAGAACAATGTTGGAACTGATCAATCAGCTTGATGGTTTTGATCCTCGAGGCAATATTAAAGTGCTGATGGCCAC
TAACTGACCTGATAATTTGGATCCAGCACTGATGAGGCCAGGGAGATTAGATAGAAAAAATTGAATTTAGCTTGCCCGAT
CTAAAGGGTCGGACCCACATCTTTAAGATTCATGCTCATTCAATGAGTGTTGAAAGACATATCAGATTTGAATTGTTAGC
ACGACTGTGTCCAAATGGCACTGCTGCTGAGATTAGAAGTGTCTGCACAGAAGCTGGTATGTTTGCCATCAGAGCACGGC
GAAAAATTGCTACTGAGAAGGATTTCTTGGAAGCTGTAAATAATGTCATTAAGTCTTATGCCAAATTCAGTGCTACTCCT
CGCTACATGACATACAAC

Alignment

ORF - retro_nleu_1578 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.45 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPDYLGADQRKTKEDEKDDKPIRALDEGDIALLKTYGQSTYSRQIKQVEDDIQQLLKKINELTGIKESDT
          MPDYLGA.QRKTKEDEKDDK.I..LDE.DI.LLKTYGQSTYSRQIKQVED.IQQLLKKINEL.GIKESDT
Retrocopy MPDYLGAHQRKTKEDEKDDKLIQVLDEADIVLLKTYGQSTYSRQIKQVEDGIQQLLKKINELIGIKESDT

Parental  GLAPPALWDLAADKQTLQSEQPLQVARCTKIINADSEDPKYIINVKQFAKFVVDLSDQVAPTDIEEGMRV
          GLAPPALWDLAADKQTLQS.QPLQVARCTKIINADSEDPKYI.NVK.FAKFV.D.SDQVAPTDIEEGMRV
Retrocopy GLAPPALWDLAADKQTLQSKQPLQVARCTKIINADSEDPKYIVNVKRFAKFVMDFSDQVAPTDIEEGMRV

Parental  GVDRNKYQIHIPLPPKIDPTVTMMQVEEKPDVTYSDVGGCKEQIEKLREVVETPLLHPERFVNLGIEPPK
          GVDRNKYQIHIPLPPK.DPTVT.MQVEEKPDVTYS.V..CKEQIEKLREVVETPLLHP.RFVNL.IE.PK
Retrocopy GVDRNKYQIHIPLPPKTDPTVTTMQVEEKPDVTYSNVSDCKEQIEKLREVVETPLLHPDRFVNLSIEAPK

Parental  GVLLFGPPGTG-KTLCARAVANRTDACFIRVIGSE-LVQKYVGEGARMVRELFEMARTKKACLIFFDEID
          G.LLF.PP.TG.KTLC..AVAN.TDACFIRVIGSE..VQKYV...A.MV.E.FEMARTKKACLIFFDEID
Retrocopy GMLLFNPPSTG<KTLCVQAVANQTDACFIRVIGSE<AVQKYVS*RAQMVNEPFEMARTKKACLIFFDEID

Parental  AIGGARFDDGAGGDNEVQRTMLELINQLDGFDPRGNIKVLMATNRPDTLDPALMRPGRLDR-KIEFSLPD
          AIGGARFDDGA.GDNEVQRTMLELINQLDGFDPRGNIKVLMATN.PD.LDPALMRPGRLDR.KIEFSLPD
Retrocopy AIGGARFDDGARGDNEVQRTMLELINQLDGFDPRGNIKVLMATN*PDNLDPALMRPGRLDR>KIEFSLPD

Parental  LEGRTHIFKIHARSMSVERDIRFELLARLCPNSTGAEIRSVCTEAGMFAIRARRKIATEKDFLEAVNKVI
          L.GRTHIFKIHA.SMSVER.IRFELLARLCPN.T.AEIRSVCTEAGMFAIRARRKIATEKDFLEAVN.VI
Retrocopy LKGRTHIFKIHAHSMSVERHIRFELLARLCPNGTAAEIRSVCTEAGMFAIRARRKIATEKDFLEAVNNVI

Parental  KSYAKFSATPRYMTYN
          KSYAKFSATPRYMTYN
Retrocopy KSYAKFSATPRYMTYN

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_1578 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 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000005729	1 retrocopy	retro_etel_1316,
Homo sapiens	ENSG00000161057	2 retrocopies	retro_hsap_2705, retro_hsap_3980,
Gorilla gorilla	ENSGGOG00000009167	3 retrocopies	retro_ggor_1885, retro_ggor_2672, retro_ggor_2673,
Myotis lucifugus	ENSMLUG00000008853	1 retrocopy	retro_mluc_1642,
Macaca mulatta	ENSMMUG00000003432	2 retrocopies	retro_mmul_1538, retro_mmul_2299,
Monodelphis domestica	ENSMODG00000017238	1 retrocopy	retro_mdom_868,
Mustela putorius furo	ENSMPUG00000018268	3 retrocopies	retro_mputfur_1025, retro_mputfur_232, retro_mputfur_387,
Nomascus leucogenys	ENSNLEG00000009274	2 retrocopies	retro_nleu_1578 , retro_nleu_2042,
Otolemur garnettii	ENSOGAG00000005164	2 retrocopies	retro_ogar_2198, retro_ogar_2309,
Pongo abelii	ENSPPYG00000017883	2 retrocopies	retro_pabe_2257, retro_pabe_2412,
Pan troglodytes	ENSPTRG00000019553	2 retrocopies	retro_ptro_1826, retro_ptro_2702,
Tarsius syrichta	ENSTSYG00000000666	4 retrocopies	retro_tsyr_1031, retro_tsyr_1272, retro_tsyr_1857, retro_tsyr_2178,
Vicugna pacos	ENSVPAG00000008921	1 retrocopy	retro_vpac_44,