RetrogeneDB ID: retro_nleu_937

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397276.1:21483659..21484217(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TM2D3
• Ensembl ID: ENSNLEG00000000529
• Aliases: None
• Description: None

Sequence

>retro_nleu_937
GCAGTGAAAGTACGAAAATTCCACCTTTTATGTTCAAGCAATGGTTTGTGCAGCAGGTATTCAGCAGAATTTATAGACTG
CACAACAAATGTCCCCTGTGTCTATGGGAAGCTTGTCACTTTTGACTGTGCAATGAAACCTTCTGTTGCCTGTGTTGATT
AGGAGTTAAAATCCCAAAGTAACTTTATCATCAATGTGACTTGATTTTGCTGGAAGCTTCCAGAAACAGAATATGAATGT
TTCAATTCTACCAACTGCATGAGGTCCTGTCCTCAACGGCATCACACTGCCAACTGCATGATAAACACATTCATGACTTG
GGTAACTACTTTATTCAAAATGCTGTACTGAAATTGGGCTGGAGGCTATAAGTGGTCTATTGCTCTGGCTCTAAGTATCA
CCCTTGGTGGTTTTGGAGCAGACCATTTCTACCTCGACCAGTGGCAAGAAGGCCTTGGCAAGCTCTTCAGCTTCAGTGGC
CTGGAAATATGGACACTAATAGACATCTTGCTAATTGGAGTTGGCTACATTGGACCAGCAGATGGCTCTTCATACATT

Alignment

ORF - retro_nleu_937 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.32 %
• Parental protein coverage: 76.92 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  STEIPPYVMKCPSNGLCSRLPADCIDCTTNFSCIYGKPVTFDCAVKPSVTCVDQDFKSQKNFIINMTCRF
          ..........C.SNGLCSR..A..IDCTTN..C.YGK.VTFDCA.KPSV.CVD...KSQ.NFIIN.T..F
Retrocopy AVKVRKFHLLCSSNGLCSRYSAEFIDCTTNVPCVYGKLVTFDCAMKPSVACVD*ELKSQSNFIINVT*-F

Parental  CWQLPETDYECTNSTSCMTVSCPRQRYPANCTVRDHVHCLGNRTFPKMLYCNWTGGYKWSTALALSITLG
          CW.LPET.YEC.NST.CM..SCP.....ANC............T..KMLY.NW.GGYKWS.ALALSITLG
Retrocopy CWKLPETEYECFNSTNCMR-SCPQRHHTANCMINTFMTWV--TTLFKMLY*NWAGGYKWSIALALSITLG

Parental  GFGADRFYLGQWREGLGKLFSFGGLGIWTLIDVLLIGVGYVGPADGSLYI
          GFGAD.FYL.QW.EGLGKLFSF.GL.IWTLID.LLIGVGY.GPADGS.YI
Retrocopy GFGADHFYLDQWQEGLGKLFSFSGLEIWTLIDILLIGVGYIGPADGSSYI

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_937 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017340	1 retrocopy	retro_cjac_3233,
Homo sapiens	ENSG00000184277	1 retrocopy	retro_hsap_1138,
Gorilla gorilla	ENSGGOG00000011598	1 retrocopy	retro_ggor_887,
Macaca mulatta	ENSMMUG00000000277	1 retrocopy	retro_mmul_884,
Mustela putorius furo	ENSMPUG00000010985	1 retrocopy	retro_mputfur_313,
Nomascus leucogenys	ENSNLEG00000000529	1 retrocopy	retro_nleu_937 ,
Pan troglodytes	ENSPTRG00000007515	1 retrocopy	retro_ptro_775,
Tarsius syrichta	ENSTSYG00000004536	1 retrocopy	retro_tsyr_1116,