RetrogeneDB ID: retro_nleu_2070

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397326.1:5417747..5418964(+)
• Located in intron of: ENSNLEG00000006116

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIGA
• Ensembl ID: ENSNLEG00000009352
• Aliases: None
• Description: None

Sequence

>retro_nleu_2070
GTCATCCGTGCTTATGGAAATCGAAAAGGCATCCATTACCTCACTAATGACCTCAAAGTCTATTACTTGCCTCTGAAAGT
CATGTATAACCAGTCTATGGCTAGGACCCTCTTTCACAGTCTGCCATTGCTCAAGTACATATTTGTTCAGGAGACAGTCA
CAATAATCCATTCACATAGTTCATTTTCTGCCATGGCCCATGATGTTCTCTTCCATGCCAAGACAATGGGGCTTCAAACA
GTCTTAACAGACCATTCCCTTTCTGGATTTGCTAAGTCCGTTCAGTGCTTACAAACAAACTTCTAACTGTGTCTGTTTGT
GACACAAGCCATATCATTTGCATTTCTTATACTAGTAAGGAAAATACCATACTACGAGCAGCACTGATTCCTGAAATAGT
GTCTGTCATTTCTAATGCTGTAGATCCCACTGACTTCACTCCAGACCCATTTAGAAGGCATGATAGTGTAACTGTTGTTG
TCAGCAGACTTGTTTACAGAAAAGGAACCAATTTGCTTAGTGGTATTATACCCAAACTCTTGTCAGAAATATTCAGATTT
AAATTTCATAATTGGAGGAGAGGGACCAAAGAGAATCATTTTGCAAGAAGTTCCGGAAAGATACCGGTTGCACGACAGGG
TGCATCTTTTGGGAGCTTTACAACACAAGAATATTAGGAGTGTCTTAGTTCAAGGACGTATTTTTCTTAATACCTCCCTT
ACTGAAGCATTCTGCATGGCAATTGTGGAGGCAGCCAGCTGTGGTTTACAGCTTGTAAGTACCAGGCATAGGGAATTCCT
GAGGTGCTTCCAGAAAATCTTACTATTTTATGAGAAACTTCAGTAAAATCTTTGTGTGAGGGATTGGAAAAAGCTATTTT
CCAACTGAAGTCAGGGGCATTGCTGGCTCCAGAAAATATCCATAACATAGTAAAGACTTTCTACACCTGGAGGAATGTTG
TGGCGAGAACTGAAAAAGTGTATGACCGAGTATCGGTGGAATCTGTGTTGCCAATGGACAAACAACTGGACAGACTTATT
TCTCACTGTGGACCAGTAACAGGCTACATCTTTGCTTTGTTGTCTGTTTTCAACTTCCTCTTCCTCATTTTCTTGAGATG
GATGACTCCAGATTCTATCATTGATACTGGAATAGATGCCACTGGGCCAAGGGGTGCCTGGACTCATATATGTTCTCACA
GTAAAAGGGGGTGAGAA

Alignment

ORF - retro_nleu_2070 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.37 %
• Parental protein coverage: 84.09 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VTHAYGNRKGIRYLTNGLKVYYLPLKVMYNQSTATTLFHSLPLLRYIFVRERVTVIHSHSSFSAMAHDAL
          V..AYGNRKGI.YLTN.LKVYYLPLKVMYNQS.A.TLFHSLPLL.YIFV.E.VT.IHSHSSFSAMAHD.L
Retrocopy VIRAYGNRKGIHYLTNDLKVYYLPLKVMYNQSMARTLFHSLPLLKYIFVQETVTIIHSHSSFSAMAHDVL

Parental  FHAKTMGLQTVFTDHSLFGFAD-VSSVLTNKLLTVSLCDTNHIICVSYTSKENTVLRAALNPEIVSVIPN
          FHAKTMGLQTV.TDHSL.GFA..V.SVLTNKLLTVS.CDT.HIIC.SYTSKENT.LRAAL.PEIVSVI.N
Retrocopy FHAKTMGLQTVLTDHSLSGFAK<VRSVLTNKLLTVSVCDTSHIICISYTSKENTILRAALIPEIVSVISN

Parental  AVDPTDFTPDPFRRHDSITIVVVSRLVYRKGIDLLSGIIPEL-CQKYPDLNFIIGGEGPKRIILEEVRER
          AVDPTDFTPDPFRRHDS.T.VVVSRLVYRKG..LLSGIIP.L.CQKY.DLNFIIGGEGPKRIIL.EV.ER
Retrocopy AVDPTDFTPDPFRRHDSVT-VVVSRLVYRKGTNLLSGIIPKL>CQKYSDLNFIIGGEGPKRIILQEVPER

Parental  YQLHDRVRLLGALEHKDVRNVLVQGHIFLNTSLTEAFCMAIVEAASCGLQVVSTR-VGGIPEVLPENLII
          Y.LHDRV.LLGAL.HK..R.VLVQG.IFLNTSLTEAFCMAIVEAASCGLQ.VSTR...GIPEVLPENL.I
Retrocopy YRLHDRVHLLGALQHKNIRSVLVQGRIFLNTSLTEAFCMAIVEAASCGLQLVSTR<A*GIPEVLPENLTI

Parental  LCEPSVKSLCEGLEKAIFQLKSGTLPAPENIHNIVKTFYTWRNVAERTEKVYDRVSVEAVLPMDKRLDRL
          L.E.SVKSLCEGLEKAIFQLKSG.L.APENIHNIVKTFYTWRNV..RTEKVYDRVSVE.VLPMDK.LDRL
Retrocopy L*ETSVKSLCEGLEKAIFQLKSGALLAPENIHNIVKTFYTWRNVVARTEKVYDRVSVESVLPMDKQLDRL

Parental  ISHCGPVTGYIFALLAVFNFLFLIFLRWMTPDSVIDVAIDATGPQGAWTNNYSHSKRGSE
          ISHCGPVTGYIFALL.VFNFLFLIFLRWMTPDS.ID..IDATGP.GAWT...SHSKRG.E
Retrocopy ISHCGPVTGYIFALLSVFNFLFLIFLRWMTPDSIIDTGIDATGPRGAWTHICSHSKRG*E

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_2070 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006415	1 retrocopy	retro_chof_2311,
Homo sapiens	ENSG00000165195	1 retrocopy	retro_hsap_1050,
Gorilla gorilla	ENSGGOG00000007293	1 retrocopy	retro_ggor_828,
Nomascus leucogenys	ENSNLEG00000009352	1 retrocopy	retro_nleu_2070 ,
Ochotona princeps	ENSOPRG00000015381	1 retrocopy	retro_opri_1065,
Pongo abelii	ENSPPYG00000020142	1 retrocopy	retro_pabe_876,
Pan troglodytes	ENSPTRG00000021684	1 retrocopy	retro_ptro_716,
Rattus norvegicus	ENSRNOG00000003554	1 retrocopy	retro_rnor_2566,