RetrogeneDB ID: retro_nleu_1362

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397291.1:4824865..4825372(+)
• Located in intron of: ENSNLEG00000000920

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_1362
ATGGCTGCCTCTGCCTTTGCCAGTGCAGTGAGAGCAGCTTCAGGAATCTTATAGCCCCTGAATATTTTGGCATTTTCAGC
CTACCAAAACTGTGTCAAGAATGCCTCTCTTATTTCTGCATTGTGCACTGGACATTTTAGTCATATTCAGACACCAGTTG
TTTCCTCTGCTCCCAGACTTACCACATCTGTCAGAAACCTGACATGTGGGCATCCTGCGGTAATCTTTAATAGAGTGGCC
CCCTTACTTCCAAGTGTCCTGAAGCTGCCAGTCAGATCCCTAACATTCGTTTGTACACGAAAAGGCAAGAGAAAGACCGT
GAAAGCTGTCATCTATAGGTTTCTTCGACTTCATTCTGGCCTTTGGTTGAAGAGAAAGGCTGGTTATAAGTAAAAATTAC
GGAAAAAGACCCTTGCAAGAAAAAAGCGATTGAGGGAATCTGTGTTCTGCAGTAAGATCCAGAGTAAACTCTTAGATAAA
ATGATGATGTCCTTCTGGAAGAGGCAA

Alignment

ORF - retro_nleu_1362 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.47 %
• Parental protein coverage: 81.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAASAFAGAVRAASGILRPLNILASSTYRNCVKNASLISAWSTGRFSHIQTPVVSSTPRLTTSERNLTCG
          MAASAFA.AVRAASGIL.PLNILA.S.Y.NCVKNASLISA..TG.FSHIQTPVVSS.PRLTTS.RNLTCG
Retrocopy MAASAFASAVRAASGIL*PLNILAFSAYQNCVKNASLISALCTGHFSHIQTPVVSSAPRLTTSVRNLTCG

Parental  HTSAILNRVAPVLPSVVKLPVRFLTYFSARKGKRKTVKAVIYRFLRLHCGLWVRRKAGYKKKLWKKTPAR
          H...I.NRVAP.LPSV.KLPVR.LT....RKGKRKTVKAVIYRFLRLH.GLW..RKAGYK.KL.KKT.AR
Retrocopy HPAVIFNRVAPLLPSVLKLPVRSLTFVCTRKGKRKTVKAVIYRFLRLHSGLWLKRKAGYK*KLRKKTLAR

Parental  KKRLREFVFCNKTQSKLLDKMTTSFWKRR
          KKRLRE.VFC.K.QSKLLDKM..SFWKR.
Retrocopy KKRLRESVFCSKIQSKLLDKMMMSFWKRQ

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_1362 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 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,