RetrogeneDB ID: retro_nleu_1386

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397291.1:20397151..20398218(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSNLEG00000016156
• Aliases: None
• Description: None

Sequence

>retro_nleu_1386
ATGAGGCAGGTGACCCTGTTCCTGAACGGCAGCCCCAAGAACGGAAAGGTGGTTGCTGCATATGGAAGTTTATCTGATTT
GCTTTCTGTGGCCAGCAGTAAACTCGGCATAAAAGCCACCAGTGTGTATAATGGGAAAGGTGGACTGAATGATGACATTG
TTTTGATCAGGGATGATGATGTTTTGTTCTTGTGTGAGGGAGAGCCATTTATTGATCCTCAGACAGATTCTAAGCCTCCT
GAAGGATTGTTAGGATTCCACACAGGCTAGCTAACATTAAATGTTGGAGGGCAGTACTTTACAACTACACGGAGCACTTT
AGTGAATAAATAACCTGACATTATGCTGGACCACATGTTTAAGGACATAGGTGTCTGGGGAAATAAGCAAGATCATAGAG
GAGCTTTCTCAATTGACCAAAGTCCTGAGTACTTAGAACCCATTTTGAACTACTTGCATCATGGACAGCTCATTATAAAT
GATGGTATTGATTTATTGGGTGTGTTAGAAGAAGCAAGATTTTTTGGTATTGACTCATTGATTGAACACCTAGAAGTGGC
AATAAAGAATTCTCAACCACCAGAGGATCATTCACCAATATCCTGAAAGGAATTTGTCCGATTTTTGCCAGCAACTCCAA
CCAAGTCAGAACTGCAATGCCAGGGTTTGAACTTCAGTGGTGCTGACTTTCTTGCTTGGATCTTCGATACATTAACTTCA
AAATCGCCAATTTAAGCTGCTGCAATTTTGCACATGCAAATCTTTGCTGTGCAAATCTTGAACGAGCTGATCTCTCTGGA
TCAGTGCTTGACTGTGCAAATCTCCAGGGAGTCAAGATGCTCTGTTCTAATGCAGAAGGAGCATCTCTGAAACTGTGTAA
TTTTGAGGATCCTTCTGGTCTTAAAGACAATTTGGAAGGTGGTAATCTGAAAGGTGTGGATACGGAAGGAAGTCAGATGA
CAGGAATTAACCTGAGAGTGGCTACCTTAAAAAATGCAAAGTTGAAGAACTGTAACCTCAGAGGAGGAACTCTGACAGGA
ACTGATTTAGAGAATTGTGATCTGTCT

Alignment

ORF - retro_nleu_1386 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.04 %
• Parental protein coverage: 91.52 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRRVTLFLNGSPKNGKVVAVYGTLSDLLSVASSKLGIKATSVYNGKGGLIDDIALIRDDDVLFVCEGEPF
          MR.VTLFLNGSPKNGKVVA.YG.LSDLLSVASSKLGIKATSVYNGKGGL.DDI.LIRDDDVLF.CEGEPF
Retrocopy MRQVTLFLNGSPKNGKVVAAYGSLSDLLSVASSKLGIKATSVYNGKGGLNDDIVLIRDDDVLFLCEGEPF

Parental  IDPQTDSKPPEGLLGFHTDWLTLNVGGRYFTTTRSTLVNKEPDSMLAHMFKDKGVWGNKQDHRGAFLIDR
          IDPQTDSKPPEGLLGFHT..LTLNVGG.YFTTTRSTLVNK.PD.ML.HMFKD.GVWGNKQDHRGAF.ID.
Retrocopy IDPQTDSKPPEGLLGFHTG*LTLNVGGQYFTTTRSTLVNK*PDIMLDHMFKDIGVWGNKQDHRGAFSIDQ

Parental  SPEYFEPILNYLRHGQLIVNDGINLLGVLEEARFFGIDSLIEHLEVAIKNSQPPEDHSPISRKEFVRFLL
          SPEY.EPILNYL.HGQLI.NDGI.LLGVLEEARFFGIDSLIEHLEVAIKNSQPPEDHSPIS.KEFVRFL.
Retrocopy SPEYLEPILNYLHHGQLIINDGIDLLGVLEEARFFGIDSLIEHLEVAIKNSQPPEDHSPIS*KEFVRFLP

Parental  ATPTKSELRCQGLNFSGAD-LSRLDLRYINFKMANLSRCNLAHANLCCANLERADLSGSVLDCANLQGVK
          ATPTKSEL.CQGLNFSGAD.LS.LDLRYINFK.ANLS.CN.AHANLCCANLERADLSGSVLDCANLQGVK
Retrocopy ATPTKSELQCQGLNFSGAD<LSCLDLRYINFKIANLSCCNFAHANLCCANLERADLSGSVLDCANLQGVK

Parental  MLCSNAEGASLKLCNFEDPSGLKANLEGANLKGVDMEGSQMTGINLRVATLKNAKLKNCNLRGATLAGTD
          MLCSNAEGASLKLCNFEDPSGLK.NLEG.NLKGVD.EGSQMTGINLRVATLKNAKLKNCNLRG.TL.GTD
Retrocopy MLCSNAEGASLKLCNFEDPSGLKDNLEGGNLKGVDTEGSQMTGINLRVATLKNAKLKNCNLRGGTLTGTD

Parental  LENCDLS
          LENCDLS
Retrocopy LENCDLS

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_1386 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.

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012157	1 retrocopy	retro_chof_323,
Gorilla gorilla	ENSGGOG00000004480	3 retrocopies	retro_ggor_1309, retro_ggor_2264, retro_ggor_2791,
Macaca mulatta	ENSMMUG00000010151	3 retrocopies	retro_mmul_1083, retro_mmul_1218, retro_mmul_2072,
Nomascus leucogenys	ENSNLEG00000014727	1 retrocopy	retro_nleu_2839,
Nomascus leucogenys	ENSNLEG00000016156	3 retrocopies	retro_nleu_1386 , retro_nleu_2499, retro_nleu_2990,
Pongo abelii	ENSPPYG00000018452	3 retrocopies	retro_pabe_1527, retro_pabe_2725, retro_pabe_3457,