RetrogeneDB ID: retro_nleu_674

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397269.1:24642593..24643283(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RFC3
• Ensembl ID: ENSNLEG00000001169
• Aliases: None
• Description: None

Sequence

>retro_nleu_674
ATGAGCTTCTGGGTGGACAAGTACCAGCCCTAATCCTTGGGATGGATGGAGTATCGCAGGGAGCAGGCAGCCCAGCTGTA
CAACCTGGTGCAGGGTGGTGAGTTTCCTCACCTTTAAGTGTATGGACCATCAGGTGCTGGAAAAAAGACAAGTGCTATGT
GTGTTCTACACGAACTTTATGGTGTTGGAGTGGAAAAATTGAGAATTAAATATCAGACCATCAGGACTCCATCTAAAAAA
ATTGAAATTAGCACCACTGCAAATAATTACCACCTTGAAGTTAATCCCAGTGGTGCTGGAAATATTGATGAGGTAGTAAT
TCAAAGATGTTGAAAACAGTGGCTCAGTCACAGCAACTTGAAACAAACTGTCAGATATTTTAAAATGGTATTATTGACAG
AAGTTGACAAACTCATTAAAGATGCTCAACATGCCTTGTATGCCTTGTAAAGAACCATGGAAAAGTATATGTCCACCTGC
AGATTGATCTTGTGCTACAATTCTACATCTAATGTGATACCACCTATTTGTAGTAGGTGCTTGGCAGTTTGTGTGCCTGC
TCCCAGCATTGGAGATATTTACCATGTGTTGTGTACTGTGTACAAGAAGGAAGATCTGAATCTTCCTTCACAACTGACTC
ATAGACTTGCAGAGAAGTCCTGCAGAAATCTCAGAAAAGCCCTGCTTATG

Alignment

ORF - retro_nleu_674 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.43 %
• Parental protein coverage: 64.33 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLWVDKYRPCSLGRLDYHKEQAAQLRNLVQCGDFPHLLVYGPSGAGKKTRIMCILRELYGVGVEKLRIE
          MS.WVDKY.P.SLG...Y..EQAAQL.NLVQ.G.FPHL.VYGPSGAGKKT..MC.L.ELYGVGVEKLRI.
Retrocopy MSFWVDKYQP*SLGWMEYRREQAAQLYNLVQGGEFPHL*VYGPSGAGKKTSAMCVLHELYGVGVEKLRIK

Parental  HQTITTPSKKKIEISTIASNYHLEVNPSDAGNSDRVVIQEMLKTVAQSQQLETNSQRDFKVVLLTEVDKL
          .QTI.TPSKK.IEIST.A.NYHLEVNPS.AGN.D.VVIQ...K.......L.....R.FK.VLLTEVDKL
Retrocopy YQTIRTPSKK-IEISTTANNYHLEVNPSGAGNIDEVVIQRC*KQWLSHSNLK-QTVRYFKMVLLTEVDKL

Parental  TKDAQHALR---RTMEKYMSTCRLILCCNSTSKVIPPIRSRCLAVRVPAPSIEDICHVLSTVCKKEGLNL
          .KDAQHAL....RTMEKYMSTCRLILC.NSTS.VIPPI.SRCLAV.VPAPSI.DI.HVL.TV.KKE.LNL
Retrocopy IKDAQHALYAL*RTMEKYMSTCRLILCYNSTSNVIPPICSRCLAVCVPAPSIGDIYHVLCTVYKKEDLNL

Parental  PSQLAHRLAEKSCRNLRKALLM
          PSQL.HRLAEKSCRNLRKALLM
Retrocopy PSQLTHRLAEKSCRNLRKALLM

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_674 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018380	1 retrocopy	retro_cjac_1611,
Cavia porcellus	ENSCPOG00000008739	1 retrocopy	retro_cpor_405,
Myotis lucifugus	ENSMLUG00000014088	1 retrocopy	retro_mluc_1754,
Mustela putorius furo	ENSMPUG00000001885	1 retrocopy	retro_mputfur_1073,
Nomascus leucogenys	ENSNLEG00000001169	1 retrocopy	retro_nleu_674 ,
Pongo abelii	ENSPPYG00000005272	1 retrocopy	retro_pabe_2420,
Tupaia belangeri	ENSTBEG00000004725	1 retrocopy	retro_tbel_4191,
Tarsius syrichta	ENSTSYG00000009501	2 retrocopies	retro_tsyr_1772, retro_tsyr_331,