RetrogeneDB ID: retro_nleu_2499

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397362.1:1626120..1627283(-)
• Located in intron of: ENSNLEG00000016270

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_2499
ATGAGGCGGGTGACCCTGTTCCTGAATGGCAGCTCCAAGAACGGAAAGGTGGTTGCTGTATACGGAACTTTATCTGATTT
GCTTTCTGTGGCCAGCAGTAAACTCGGCATAAAAGCCACCAGTGTGTACAATGAGAAAGGTGGACTGATTGATGATATTG
CTTTGATCAGGGATGATGACGTTTTGTGTGTGAGGGAGAGCCATTTATTGATCTTCAGACAGATTCTAAGCCTCCTGAAG
GATTGTTAGGATTCCACATAGAATGGCTAACATTAAATGTTGGAGGGAGGTACTTTACAACTACACGGAGCACTTTAGTG
AATAAAGAACCTGACAGTATGCTGGCCCACATGCTTAAGGACAGAGGTATCTGGGGAAATAAGCAAGATCACAGAGGAAC
TTTCTTAATTGACCAAAGTCCTGAGTACTTTGAACCCATTTTGAACTACTTGTGTCATGGACAGCTCATTGTAAATGATG
GCATTAATTTATTGGGTGTGTTAGAAGAAGCAAGATTTTTTGGTATTGACTCACTGATTGAACACCTAGAAATGGCAATA
ACGAATTCTCAACCACCAGAGGATCATTCACCAATATCTCAAAAGGAATTTGTCCAATTTTTGCTAGCAACTCCAACCAA
GTCAGAACTGTGATGCCAGAGTTTGAACTTCAGTGGTGCTGATCTTTCTCGTTAGGACCTTCGATACATTAACTTCAAAA
TGGCCAATTTAAGCTGCTGCAATCTTGCACATGCAAATCTTTACTGTGCAAATCTTGAATGAGCTGATCTCTCTGGATCA
GTGTTTGACTGTGCAAATCTCCAGGGAGTCAAGATGCTCTGTTCTAATGCAGAAGGAGCATCCCTGAAACTGTGTAATTT
TGAGGATCCTTCTGGTCTTAAAGCCAATTTAGAAGGTGCTAATCTGAAAGGTGTGGATATGGAAGGAAGTCAGATGACAG
GAATTAACCTGAGAGCGGCTACCTTAAAAAATGCAAAGTTGAAGAACTGTAACCTCAGAGGAGCAACTCTGGCAGGAACC
AATTTAGAGAACTGTGATCTGTCTGGGTGTGATCTTCAAGAAGCCAACTTGAGAGGGTCCACCATGAAGGGAGCTATATT
TGAAGAGATGCTGACACTACTATACATGTCGCAAAATGTCAGA

Alignment

ORF - retro_nleu_2499 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.54 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRRVTLFLNGSPKNGKVVAVYGTLSDLLSVASSKLGIKATSVYNGKGGLIDDIALIRDDDVL-FVCEGEP
          MRRVTLFLNGS.KNGKVVAVYGTLSDLLSVASSKLGIKATSVYN.KGGLIDDIALIR.DD...FVCEGEP
Retrocopy MRRVTLFLNGSSKNGKVVAVYGTLSDLLSVASSKLGIKATSVYNEKGGLIDDIALIR-DDDV<FVCEGEP

Parental  FIDPQTDSKPPEGLLGFHTDWLTLNVGGRYFTTTRSTLVNKEPDSMLAHMFKDKGVWGNKQDHRGAFLID
          FID.QTDSKPPEGLLGFH..WLTLNVGGRYFTTTRSTLVNKEPDSMLAHM.KD.G.WGNKQDHRG.FLID
Retrocopy FIDLQTDSKPPEGLLGFHIEWLTLNVGGRYFTTTRSTLVNKEPDSMLAHMLKDRGIWGNKQDHRGTFLID

Parental  RSPEYFEPILNYLRHGQLIVNDGINLLGVLEEARFFGIDSLIEHLEVAIKNSQPPEDHSPISRKEFVRFL
          .SPEYFEPILNYL.HGQLIVNDGINLLGVLEEARFFGIDSLIEHLE.AI.NSQPPEDHSPIS.KEFV.FL
Retrocopy QSPEYFEPILNYLCHGQLIVNDGINLLGVLEEARFFGIDSLIEHLEMAITNSQPPEDHSPISQKEFVQFL

Parental  LATPTKSELRCQGLNFSGADLSRLDLRYINFKMANLSRCNLAHANLCCANLERADLSGSVLDCANLQGVK
          LATPTKSEL.CQ.LNFSGADLSR.DLRYINFKMANLS.CNLAHANL.CANLE.ADLSGSV.DCANLQGVK
Retrocopy LATPTKSEL*CQSLNFSGADLSR*DLRYINFKMANLSCCNLAHANLYCANLE*ADLSGSVFDCANLQGVK

Parental  MLCSNAEGASLKLCNFEDPSGLKANLEGANLKGVDMEGSQMTGINLRVATLKNAKLKNCNLRGATLAGTD
          MLCSNAEGASLKLCNFEDPSGLKANLEGANLKGVDMEGSQMTGINLR.ATLKNAKLKNCNLRGATLAGT.
Retrocopy MLCSNAEGASLKLCNFEDPSGLKANLEGANLKGVDMEGSQMTGINLRAATLKNAKLKNCNLRGATLAGTN

Parental  LENCDLSGCDLQEANLRGSNVKGAIFEEMLTPLHMSQSVR
          LENCDLSGCDLQEANLRGS..KGAIFEEMLT.L.MSQ.VR
Retrocopy LENCDLSGCDLQEANLRGSTMKGAIFEEMLTLLYMSQNVR

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_2499 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 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,