RetrogeneDB ID: retro_nleu_2454

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397357.1:1964168..1964747(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMED2
• Ensembl ID: ENSNLEG00000001652
• Aliases: None
• Description: None

Sequence

>retro_nleu_2454
GTGGTGACGCTCGCTGAGCTGCTGTTGCTCCAGACCACTCTCCTGACCATGGTCTTGGGCTATTTCATCAGCATCCACGC
ACATGAGGAGTGCTTCAGTGAGTCACCTCAGGCACCAAGATGGGCCTCATCTTCGAAGGTGGCTTCCTGGGCATCAACGT
GGAGATTACAGGACCTAAGAATAAAAGGATTTATAAAGGAGACAAAGAATCCAGTGGGAAATACACATTTTCTGCTCACA
TGGATGGAACACATAAATTTTGTTTTAGTAACCGAGTGTCCACCATGACTCCAAAGATAGTGATATTCACCATTGATATT
GGGGAGGCTCCAAAAGGAGAAGACATGGAAACAGAAGCTCACCAGAACAAACTAGAAGAAATGATCAGTGAGCTGGCTGT
GGCCATGACAGCTGTACAGCACGAAGAGGAATACATGAAAGTCTGGGAGAGGACACACAGAGCCATTAGTGACAACACAA
ACAGCCCAGTCGTCCTTCGGTCGTTCTTTGAAGCTCTTGTTCATGACACTGGGACACATCTACCACCTGAAGAGATTTTT
TGAAGTCCAGAGGGTTGTT

Alignment

ORF - retro_nleu_2454 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.79 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVTLAELLVLLAALLATVSGYFVSIDAHAEECFFER-VTSGTKMGLIFEVAEGGFLDIDVEITGPDNKGI
          .VTLAELL.L...LL..V.GYF.SI..HA.E..F...VTSGTKMGLIF...EGGFL.I.VEITGP.NK.I
Retrocopy VVTLAELLLLQTTLLTMVLGYFISI--HAHEECFSE<VTSGTKMGLIF---EGGFLGINVEITGPKNKRI

Parental  YKGDRESSGKYTFAAHMDGTYKFCFSNRMSTMTPKIVMFTIDIGEAPKGQDMETEAHQNKLEEMINELAV
          YKGD.ESSGKYTF.AHMDGT.KFCFSNR.STMTPKIV.FTIDIGEAPKG.DMETEAHQNKLEEMI.ELAV
Retrocopy YKGDKESSGKYTFSAHMDGTHKFCFSNRVSTMTPKIVIFTIDIGEAPKGEDMETEAHQNKLEEMISELAV

Parental  AMTAVKHEQEYMEVRERIHRASKQ-TQTTRGFRWSFLEVFFFICQTGQIYYLKRFFEVRRVV
          AMTAV.HE.EYM.V.ER.HRA....TQT........L...F.....G.IY.LKRFFEV.RVV
Retrocopy AMTAVQHEEEYMKVWERTHRAISD>TQTAQSSFGRSLKLLFM--TLGHIYHLKRFFEVQRVV

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_2454 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 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015262	2 retrocopies	retro_amel_1923, retro_amel_337,
Bos taurus	ENSBTAG00000039630	2 retrocopies	retro_btau_52, retro_btau_819,
Choloepus hoffmanni	ENSCHOG00000012728	6 retrocopies	retro_chof_104, retro_chof_1277, retro_chof_2323, retro_chof_2601, retro_chof_2709, retro_chof_981,
Callithrix jacchus	ENSCJAG00000020466	1 retrocopy	retro_cjac_1392,
Echinops telfairi	ENSETEG00000000556	2 retrocopies	retro_etel_2109, retro_etel_2154,
Homo sapiens	ENSG00000086598	1 retrocopy	retro_hsap_2793,
Gorilla gorilla	ENSGGOG00000028536	1 retrocopy	retro_ggor_1943,
Macaca mulatta	ENSMMUG00000031491	2 retrocopies	retro_mmul_1439, retro_mmul_613,
Mustela putorius furo	ENSMPUG00000001598	1 retrocopy	retro_mputfur_1241,
Mus musculus	ENSMUSG00000029390	2 retrocopies	retro_mmus_1361, retro_mmus_3262,
Nomascus leucogenys	ENSNLEG00000001652	2 retrocopies	retro_nleu_2454 , retro_nleu_2794,
Otolemur garnettii	ENSOGAG00000009192	1 retrocopy	retro_ogar_2548,
Pongo abelii	ENSPPYG00000005090	3 retrocopies	retro_pabe_1919, retro_pabe_2227, retro_pabe_3597,