RetrogeneDB ID: retro_nleu_1225

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397285.1:25428954..25430510(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RFWD2
• Ensembl ID: ENSNLEG00000015420
• Aliases: None
• Description: None

Sequence

>retro_nleu_1225
ATGTCTGGTAGCCACCATGACGGGTCAGACTCCACTGGGACGAGCCCCTGCTCCTCAGCCTCTTTGGTGACTTTTGCCTC
CTTGTCCTTATCGTCTTCCCCATTGCCCCCGCTGTGGCAGCTTCGGCAGTGGTGCTATTGTCCAGCAGGGCGGCCCAGGC
CACCAGCTTGGATAGCCTTGGGGCCCAGTGTGGCCTGTGTTGGTGGTGCCCACCGTGTCAGGCAGTGGCAGGGTGCTGTC
CATAGTCCTGTCCCGGCTCAGCTGCATGCCCAGGCCCAGTGCTGGTATAGGAGGCAGCAGCTGTAGCCTAGGCAGCAGCA
GGAAGCAACCTCTGCTTGCCCCTCCCCTCTCCAACAGGCTCATCAACTCATATAAGGACAACAGCAATGATTTCATATGC
CCCATCTGCTTTGATATGATTGAAGAGGCATACATGACAAAATGTGGCCACAGCTTTTGCTATAAGTATATTCATCAGAG
TTCAGAGGACAATAATAGATGTACCAAGTGTAACTATGTTGTGGACAATACTAACCATCTGTTTCCTAATTTGTTGGTGA
ATGAGCTCATTTTCAAACAGAAGCAAAGATTTGAGGAAAAGAGGTTCAAATCGGACCACTCAGTGAATAGCACCAATGGC
CACAGGTGACAAATATTTCAAGATTTTTTGGGAACTGACCAAGATAACCTTGATTTGGCCAATATCAACCTCATGTTGAA
GTTACTAGTGCAGAAGAAGAAACAACTGGAAGCAGAATCACATGCAGCCCAACTATAGAATCTTACACAATTCCTCAAGA
TTGCAAGAAGAAATAGGAGAGAGCAACTGGGACAGTTCCAGAGGAGCTAGGTGTTTTGGAAGAGGATATTAAAAGAGTGG
AAGAAATGAGTGGCTTATACTCTCCTGGCAGTGAGGATAGCACAGTGCCTCAACTTGAAGCTCCTCCTGCATCACACAGT
AGCATTATGGATTCCACACAATATAGCCAACATCCAGGTTTCAGTGGCAGTTCTTAGACAAAGAAACAGCCTTGATATAA
CAGCACATTAACATCAAAATGAAAATGGTCCACTGCTCATTTTGAAGACCTGGAGCACTGTTACTTTTCTACAAGGATGT
CTCATATCTCAGATGATAGTTGAACTGCAAGCCAATTGGAGGAATTTCAGAAATGCTTGTCCAAGGTTACTCAATATAAA
TCAGTATGAACGTCAGCCACATTATCATGCCCTAGTGATCTCTATAGTGATTCCAGGATAGTCTCTGGTATTGAATTTGA
CCAGGATTGTGACTATTTTGCAATTGCTGAGGTTACAACGAAGATTAAAGTCTATGAATATGGCACAGTCATCCAGGATG
CAGTGGGTATTCATTACCGTGCGAATGAAATGACCTCAATTCCAAAATCAGCTGTATCAGCTGGAGTAGTTATCATAAGA
ACCTGTTAGCTAGCAGTGATTATGAAGGCATTGTTATCCTATGGGATGGATTCACAGAACAGAGGTCAAAGGTCTAACAG
GAGCATGAGAAGAGGTGTTGAAGTGTTTAATTTGAT

Alignment

ORF - retro_nleu_1225 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.42 %
• Parental protein coverage: 71.41 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSGSRQAGSGSAGTSPGSSAASSVTSASSSLSSSPSPP-SVAVSAAAVVSGGVAQAAASGGLG-GPVRPV
          MSGS...GS.S.GTSP.SSA.S.VT.AS.SLSSSP.PP..VA.SA....S...AQA.....LG.GPV.PV
Retrocopy MSGSHHDGSDSTGTSPCSSA-SLVTFASLSLSSSPLPP<AVAASAVVLLSSRAAQATSLDSLG<GPVWPV

Parental  LVAPAVSGSGGGAVSTGLSRHSCAARPSAGVGGSSSSLGSGSRKRPLLAP-LCNGLINSYEDKSNDFVCP
          LV.P.VSGSG....S..LSR.SC..RPSAG.GGSS.SLGS.SRK.PLLAP.L.N.LINSY.D.SNDF.CP
Retrocopy LVVPTVSGSGR-VLSIVLSRLSCMPRPSAGIGGSSCSLGS-SRKQPLLAPPLSNRLINSYKDNSNDFICP

Parental  ICFDMIEEAYMTKCGHSFCYKCIHQSLEDNNRCPKCNYVVDNIDHLYPNFLVNELILKQKQRFEEKRFKL
          ICFDMIEEAYMTKCGHSFCYK.IHQS.EDNNRC.KCNYVVDN..HL.PN.LVNELI.KQKQRFEEKRFK.
Retrocopy ICFDMIEEAYMTKCGHSFCYKYIHQSSEDNNRCTKCNYVVDNTNHLFPNLLVNELIFKQKQRFEEKRFKS

Parental  DHSVSSTNGHRWQIFQDLLGTDQDNLDLANVNLMLELLVQKKKQLEAESHAAQLQILMEFLKVARRNKRE
          DHSV.STNGHR.QIFQD.LGTDQDNLDLAN.NLML.LLVQKKKQLEAESHAAQL..L..FLK.ARRN.RE
Retrocopy DHSVNSTNGHR*QIFQDFLGTDQDNLDLANINLMLKLLVQKKKQLEAESHAAQL*NLTQFLKIARRNRRE

Parental  QLEQIQK-ELSVLEEDIKRVEEMSGLYSPVSEDSTVPQFEAPSPSHSSIIDSTEYSQPPGFSGSSQTKKQ
          QL.Q.Q..EL.VLEEDIKRVEEMSGLYSP.SEDSTVPQ.EAP..SHSSI.DST.YSQ.PGFSGSS.TKKQ
Retrocopy QLGQFQR<ELGVLEEDIKRVEEMSGLYSPGSEDSTVPQLEAPPASHSSIMDSTQYSQHPGFSGSS*TKKQ

Parental  PWYNSTLASRRKRLTAHFEDLEQCYFSTRMSRISDDSRTASQLDEFQECLSKFTRYNSVRPLATLSYASD
          P.YNSTL.S..K..TAHFEDLE.CYFSTRMS.ISDDS.TASQL.EFQ.CLSK.T.Y.SV...ATLS..SD
Retrocopy P*YNSTLTSK*KWSTAHFEDLEHCYFSTRMSHISDDS*TASQLEEFQKCLSKVTQYKSV*TSATLSCPSD

Parental  LYNGSSIVSSIEFDRDCDYFAIAGVTKKIKVYEYGTVIQDAVDIHYPENEMT-CNSKISCISWSSYHKNL
          LY..S.IVS.IEFD.DCDYFAIA.VT.KIKVYEYGTVIQDAV.IHY..NEMT..NSKISCISWSSYHKNL
Retrocopy LYSDSRIVSGIEFDQDCDYFAIAEVTTKIKVYEYGTVIQDAVGIHYRANEMT<LNSKISCISWSSYHKNL

Parental  LASSDYEGTVILWDGFTGQRSKVYQEHEKRCWSVDFN
          LASSDYEG.VILWDGFT.QRSKV.QEHEKRC.SV.F.
Retrocopy LASSDYEGIVILWDGFTEQRSKV*QEHEKRC*SV*FD

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_1225 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
Gorilla gorilla	ENSGGOG00000013437	1 retrocopy	retro_ggor_1366,
Macaca mulatta	ENSMMUG00000002072	1 retrocopy	retro_mmul_1342,
Mus musculus	ENSMUSG00000040782	1 retrocopy	retro_mmus_3678,
Nomascus leucogenys	ENSNLEG00000002805	6 retrocopies	retro_nleu_1061, retro_nleu_1179, retro_nleu_1194, retro_nleu_1356, retro_nleu_1379, retro_nleu_2982,
Nomascus leucogenys	ENSNLEG00000015420	1 retrocopy	retro_nleu_1225 ,
Pan troglodytes	ENSPTRG00000001711	1 retrocopy	retro_ptro_1281,