RetrogeneDB ID: retro_nleu_2217

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397335.1:8819702..8820210(+)
• Located in intron of: ENSNLEG00000016826

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL35
• Ensembl ID: ENSNLEG00000002756
• Aliases: None
• Description: None

Sequence

>retro_nleu_2217
ATAGCTGCCTCTGCCTTTGCCAGTGCAGTGAGAGCAGCTTCAGGAATCTTAAGGCCTCTGAATATTTTGGCATCTTCAGC
CTACCAAAACTGTGTCAAAAATGCCTCTCTTATTTCTGCATTGTCCACTGGACGTTTTAGTCATATTCAGACACCGGTTG
TTTCCTCCACTCCCACACTTACTGCATCTGAGAGAAACCTGACATGTGGGCATACTTCAGCGATCCTTAATAGAGTGGCC
CCCTTGCTTCCAAGTGTCTTGAAGCTGCCAGTCAGATCTCTAACATGCGTCAGTACACGAAAAGGCAAGAGAAAGATTGT
GAAAGCCGTCATCTATAGGTTTCTTCGACTTCATTGTGGCCTTTGGATGAGAAGGGCTGGTTATAAGAAAAAATTATGGA
AAAAGGCACCTGCAAGAAAAAAGCAATTGAGGGAATTTGTATTCTGCAATGAAACCCAGAGTAAACTCTTAAGATAAAAT
GACATTGTCCTTCTGGAAGAGGCGAAAC

Alignment

ORF - retro_nleu_2217 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.72 %
• Parental protein coverage: 81.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAASAFAGAVRAASGILRPLNILASSTYRNCVKNASLISAWSTGRFSHIQTPVVSSTPRLTTSERNLTCG
          .AASAFA.AVRAASGILRPLNILASS.Y.NCVKNASLISA.STGRFSHIQTPVVSSTP.LT.SERNLTCG
Retrocopy IAASAFASAVRAASGILRPLNILASSAYQNCVKNASLISALSTGRFSHIQTPVVSSTPTLTASERNLTCG

Parental  HTSAILNRVAPVLPSVVKLPVRFLTYFSARKGKRKTVKAVIYRFLRLHCGLWVRRKAGYKKKLWKKTPAR
          HTSAILNRVAP.LPSV.KLPVR.LT..S.RKGKRK.VKAVIYRFLRLHCGLW.RR.AGYKKKLWKK.PAR
Retrocopy HTSAILNRVAPLLPSVLKLPVRSLTCVSTRKGKRKIVKAVIYRFLRLHCGLWMRR-AGYKKKLWKKAPAR

Parental  KKRLREFVFCNKTQSKLL-DKMTTSFWKRRN
          KK.LREFVFCN.TQSKLL.DKMT.SFWKRRN
Retrocopy KKQLREFVFCNETQSKLL>DKMTLSFWKRRN

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_2217 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 10 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019467	1 retrocopy	retro_cjac_203,
Dasypus novemcinctus	ENSDNOG00000008329	1 retrocopy	retro_dnov_404,
Macropus eugenii	ENSMEUG00000004773	1 retrocopy	retro_meug_1703,
Mus musculus	ENSMUSG00000052962	1 retrocopy	retro_mmus_1777,
Nomascus leucogenys	ENSNLEG00000002756	4 retrocopies	retro_nleu_1103, retro_nleu_1362, retro_nleu_2217 , retro_nleu_781,
Otolemur garnettii	ENSOGAG00000004048	1 retrocopy	retro_ogar_2600,
Pongo abelii	ENSPPYG00000012214	5 retrocopies	retro_pabe_1817, retro_pabe_2837, retro_pabe_3724, retro_pabe_541, retro_pabe_595,
Rattus norvegicus	ENSRNOG00000008546	1 retrocopy	retro_rnor_1399,
Tupaia belangeri	ENSTBEG00000015366	10 retrocopies	retro_tbel_1143, retro_tbel_146, retro_tbel_2647, retro_tbel_289, retro_tbel_2892, retro_tbel_3789, retro_tbel_3828, retro_tbel_428, retro_tbel_4379, retro_tbel_627,
Tarsius syrichta	ENSTSYG00000007713	2 retrocopies	retro_tsyr_1128, retro_tsyr_264,