RetrogeneDB ID: retro_nleu_2854

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397453.1:1728240..1728857(+)
• Located in intron of: ENSNLEG00000001522

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC35E1
• Ensembl ID: ENSNLEG00000005563
• Aliases: None
• Description: None

Sequence

>retro_nleu_2854
GCTGCCACGCTGTGCTTCTTGCTTCAGAACATTTTCTCCAAAAAGATCTTGGGAGATTTGCAGATCCACCGTCTCCCGCT
GCTCAACATCTTGGGCTGCCACGCTGTCTTTTTTATGATCCCCACCTGGGTCCTGGTGGACCTCTCGGCTTTCCTGGTCA
GCGGCGACTTGACTACGTCTCCCAGTGGCCCTGGATGCTCCTGCTTCTGGCTGTCAGTGGCTTCTGTAACTTTGCCCAGA
ATGTCATCGCCTTCAGCATCCTCAACCTCGTCAGCTCCCTGAGCTATTCAGTCGTCAATGCCACCAAGAGAATAATGGTC
ATCACAGTGTCCCTGATCATGCTGCCCAACCCAGTCACTAGCACCTATGTCCTGGGCATAATGACTGCCGTCCTTGGGGT
CTTCCTCTACAACAAGACCAAGTAAGATGCAAACCAGGAAGTCAGGAAGCACCTCCTCCTGGCACCACAGTGGACCTGAG
CAGCAAGGAGCATCACCAGAGCCCACTGGAGAAGCCCCACCAGTGGCCTCCTCTTCCCCCTGCATGGGGACTATCATGGC
TACAACAATATCTTAACAGACCACTTCCAGTACAGCTGGCAGAGCTACCCAAACTCG

Alignment

ORF - retro_nleu_2854 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.81 %
• Parental protein coverage: 76.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AATLCFSLQNIFSKKVLRDSRIHHLRLLNILGCHAVFFMIPTWVLVDLSAFLVSSDLT-YVYQWPWTLLL
          AATLCF.LQNIFSKK.L.D..IH.L.LLNILGCHAVFFMIPTWVLVDLSAFLVS.DLT.YV.QWPW.LLL
Retrocopy AATLCFLLQNIFSKKILGDLQIHRLPLLNILGCHAVFFMIPTWVLVDLSAFLVSGDLT<YVSQWPWMLLL

Parental  LAVSGFCNFAQNVIAFSILNLVSPLSYSVANATKRIMVITVSLIMLRNPVTSTNVLGMMTAILGVFLYNK
          LAVSGFCNFAQNVIAFSILNLVS.LSYSV.NATKRIMVITVSLIML.NPVTST.VLG.MTA.LGVFLYNK
Retrocopy LAVSGFCNFAQNVIAFSILNLVSSLSYSVVNATKRIMVITVSLIMLPNPVTSTYVLGIMTAVLGVFLYNK

Parental  TKYDANQQARKHLL-PVTSADLSSKERHRTPLEKPH-NGLLFPQHGDYQYGRNNILTDHFQYSRQSYPNS
          TK.DANQ..RKHLL.P.T..DLSSKE.H..PLEKPH..GLLFP.HGDY..G.NNILTDHFQYS.QSYPNS
Retrocopy TK*DANQEVRKHLL<PGTTVDLSSKEHHQSPLEKPH>SGLLFPLHGDY-HGYNNILTDHFQYSWQSYPNS

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_2854 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
Homo sapiens	ENSG00000127526	1 retrocopy	retro_hsap_1170,
Nomascus leucogenys	ENSNLEG00000005563	1 retrocopy	retro_nleu_2854 ,
Pongo abelii	ENSPPYG00000009692	1 retrocopy	retro_pabe_981,
Pan troglodytes	ENSPTRG00000010648	1 retrocopy	retro_ptro_804,