RetrogeneDB ID: retro_nleu_2725

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397410.1:1654247..1654869(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZDHHC3
• Ensembl ID: ENSNLEG00000006024
• Aliases: None
• Description: zinc finger, DHHC-type containing 3 [Source:HGNC Symbol;Acc:18470]

Sequence

>retro_nleu_2725
ATGGTGCTGGTCCCTGCCCACCGTTTCAGAGACTCTGAGAGGAAACCAGAGTACCCATAGCTGGAGATGCCTGTCCAATC
TCCCTACCCTGGTCCTGTGAGAACCATGTGGCTTATCCACGATGGCTGTGGCATCGCCTTTGCCATCATCACCTGGTTTC
TGATCCTCTATGTGGAGTCTGTGGTCCTCTTTTTCACGCTGATTCCATCCTGAGACTATGCATACTGCACCATCAATGGA
ATTGTGTTAAACCTGCTGACTTTCTTGGCCCTGGACTCCCACTGCCAGGCCATGCTGACAGACACTGGAGCAGTGCCCAA
ATGAAATGCCACTAAATAATTCATCCAGAGTTTACACATGAAGCCCAGGTATGTGGTATACTCGTGTCCCAGTGCTGCAG
CATCAAGTCTGACCGAGCCTGCCGCTGCAGTGTTTGTAAGGGGTGCATTCGCAGGGTGGACCCCCACTGTCCCTGGGTCG
ATATCTGCATCGAAGAGAACAACCAGAAGTGCTTTGTCCTGTTTATCATGTGCACAGCTCTCATTTCCTTGCCTGCCCTC
ATCGTGGTGGATTCCACTTCCTCGATTGCTGTGAAGAAGATTGCTCAAATCTCCCGAAGCCT

Alignment

ORF - retro_nleu_2725 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.08 %
• Parental protein coverage: 70.57 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MMLIPTHHFRDIERKPEYLQPEKCVPPPYPGPVGTMWFIRDGCGIACAIVTWFLVLYAEFVVLFVMLIPS
          M.L.P.H.FRD.ERKPEY...E..V..PYPGPV.TMW.I.DGCGIA.AI.TWFL.LY.E.VVLF..LIPS
Retrocopy MVLVPAHRFRDSERKPEYP*LEMPVQSPYPGPVRTMWLIHDGCGIAFAIITWFLILYVESVVLFFTLIPS

Parental  RDYVYSIINGIVFNLLAFLALASHCRAMLTDPGAVPKGNATKEFIESLQLKPGQVVYKCP-KCCSIKPDR
          .DY.Y..INGIV.NLL.FLAL.SHC.AMLTD.GAVPK.NATK.FI.SL..KP..VVY.CP..CCSIK.DR
Retrocopy *DYAYCTINGIVLNLLTFLALDSHCQAMLTDTGAVPK*NATK*FIQSLHMKPRYVVYSCP<QCCSIKSDR

Parental  AHHCSVCKRCIRKMDHHCPWVNNCVGENNQKYFVLFTMYIALISLHALIMV-GFHFLHCFEEDWTKCSSF
          A..CSVCK.CIR..D.HCPWV..C..ENNQK.FVLF.M..ALISL.ALI.V.GFHFL.C.EED...CS..
Retrocopy ACRCSVCKGCIRRVDPHCPWVDICIEENNQKCFVLFIMCTALISLPALIVV<GFHFLDCCEED---CSNL

Parental  SPP
          ..P
Retrocopy PKP

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_2725 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000013490	1 retrocopy	retro_ggor_2187,
Loxodonta africana	ENSLAFG00000012733	1 retrocopy	retro_lafr_136,
Nomascus leucogenys	ENSNLEG00000006024	1 retrocopy	retro_nleu_2725 ,
Rattus norvegicus	ENSRNOG00000004344	1 retrocopy	retro_rnor_1688,