RetrogeneDB ID: retro_nleu_1537

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397298.1:1443781..1444844(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM43
• Ensembl ID: ENSNLEG00000010889
• Aliases: None
• Description: None

Sequence

>retro_nleu_1537
GCATCGGTTTTGAATGTCAAGGAATCCAAAGCTTTGAAAGAACAGTTGTAGTTGCTGGTCTTCCGTTTGTCCTCTGTAGT
GATCAATTATTGGCCATATTAGTGAAAAGGCACTTCCAAGATATTAAGAATGAGGGTGGAGATGTCGAAGATGTGATATA
TCCAACAAGAATCCCAGGGAGTTGCATCTGTAATATGCAAAGAAAAAAAGTTGCGAAGAATGTCATCAGATATAAGAAAT
GCCAGCTAACAAGGAAGGCTGGACATGCTGAACTCACAGTCTCTCATTTTAGTGACAAGATCTTCAGCTCTGTAAATGCT
ATCTTTGATCTTTCTGTTTTTGGAAGTGAGGTTACTGGGGAAATTCTGGTAATGAACCTGAAAAAGAAATTCCCAACTTT
AAGCTTCAGTCCTTTGGAAGCCAATGGAAGACTCTCCATGGAAGGATGATTTCTAGCTGTCAACGAGGCTCGAATAATCT
TTGCAAGTCAAAGTAAGTTCTCTTTTATAAAAAAAAAAAAAGACAAATTTTACCAGTGAGAGGGATAAAGTAGAATAAAT
AGAGCCCCCAGAGGAATGTACAGAGAGGCGATAACTCTTTGGAGTCAGTCTGGACCTTAGTACGTGAGACTACTAGAAGT
GGAGAAATACTTCGCTCAACACAGATGTTTTTCTTTACCTGAAACAGAAATGTGGATTTTTTGAAAATACACTGAACAAA
TTCCATATTCTGAGTCAGAAGAGAGTGGACGGTGAAATGACCACAATTTGTCTAAAAAGTACTCAAGCTGGTTCTCAACC
AAACAATCCAAAACATGTAAATGAGCTCATTGAGGAATGGTCACATGCTCTTCATTTAGAGCTTAGAAAAGAGACATTTA
TTCTGGGGGAAAAAAAAGGAAAATAGAGAGAAAATCATTAAATGGGCATATGAACAATTAAGTTTGAGATATCTTGGAGT
CCTAATTAACCTTTGTAGGACACTCATTGACATTATAGGATCTTCTTCTGACACTTACCTATTTTTAAAAGGGGTCATGA
AATTAATAGGGCAAAAGGTTAGT

Alignment

ORF - retro_nleu_1537 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.08 %
• Parental protein coverage: 99.72 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  ASVLNVKESKAP-ERTVVVAGLPVDLFSDQLLAILVKSHFQDIKNEGGDVEDVIYPTR-TKGVAYVIFKE
          ASVLNVKESKA..ERTVVVAGLP..L.SDQLLAILVK.HFQDIKNEGGDVEDVIYPTR...GVA.VI.KE
Retrocopy ASVLNVKESKAL<ERTVVVAGLPFVLCSDQLLAILVKRHFQDIKNEGGDVEDVIYPTR>SQGVASVICKE

Parental  KK-VAENVIRQKKHWLARKARHAELTVSHFSDKIFISVNAILDLSVFGKEVILETLVKDLKKKIPSLSFS
          KK.VA.NVIR.KK..L.RKA.HAELTVSHFSDKIF.SVNAI.DLSVFG.EV..E.LV..LKKK.P.LSFS
Retrocopy KK<VAKNVIRYKKCQLTRKAGHAELTVSHFSDKIFSSVNAIFDLSVFGSEVTGEILVMNLKKKFPTLSFS

Parental  SLKPNGRISVEGSFLAFK-RLKESLLVRAYSLLKKDR--NFTSE-GRKWNRQNPQRNLQRSSNSMASVRT
          .L..NGR.S.EG.FLA...RL..SL.V...SLL......NFTSE.G.K.N...PQRN.QR..NS..SV.T
Retrocopy PLEANGRLSMEG*FLAVN>RLE*SLQVKVSSLLXXXXXTNFTSE>GIK*NK*SPQRNVQRGDNSLESVWT

Parental  LVPETARSGEML-VLDTDVFLYLKHKCGSYESTLKKFHILSQEKVDGEITTICLKNIQVGSQPNNVNHVK
          LV.ET.RSGE.L..L.TDVFLYLK.KCG..E.TL.KFHILSQ..VDGE.TTICLK..Q.GSQPNN..HV.
Retrocopy LVRETTRSGEIL<SLNTDVFLYLKQKCGFFENTLNKFHILSQKRVDGEMTTICLKSTQAGSQPNNPKHVN

Parental  ELIEEWSHALYLK-LRKETFILEGKENREKRMIKRACEQLSSRYLEVLINFYRTHIDIIGSSSDTYLFKK
          ELIEEWSHAL.L..L.K...............IK.A.EQLS.RYL.VLIN..RT.IDIIGSSSDTYLF.K
Retrocopy ELIEEWSHALHLE>LEKRHLFWGXXXXXREKIIKWAYEQLSLRYLGVLINLCRTLIDIIGSSSDTYLFLK

Parental  GVMKLIGQKVS
          GVMKLIGQKVS
Retrocopy GVMKLIGQKVS

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_1537 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003125	1 retrocopy	retro_cjac_1396,
Nomascus leucogenys	ENSNLEG00000010889	1 retrocopy	retro_nleu_1537 ,