RetrogeneDB ID: retro_nleu_2520

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397366.1:1704380..1704781(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNF8
• Ensembl ID: ENSNLEG00000002743
• Aliases: None
• Description: None

Sequence

>retro_nleu_2520
TCCAAGGCCAAGTATAAGGAGTGAAGGACGGTCTTGGCTGAGGACCAGCTAGCCCAGATGTCAAAGCAGTTGGGCATGTT
CAAGACCAACCTGGAGGAATTTGCCAGCAAGCACACGCAGGAGATCCGGAAGGATCTTGAGTTCCATGTGCAGTTCCAGG
ACATATGTGCAACCTTTGGGGTGGAGCCTTTGGCCTCTGGAAAAGGATTTTGATTTGAGATGCTGGGTTTGAGGGATTTT
TATAAAGAACTAGGTGTCTACATTATCGAAGCGTGCCTGGTGCTGAGCATTGGAGTGGAGGTCCGATAACTCTGGAGGAA
CTATATCAACAGGTGTTAAAAGGAAGGGGTAAGTTCACCCAGGATGTCAGTCAAGATGACCTGATCAGGGCCATCAAGAA
A

Alignment

ORF - retro_nleu_2520 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80. %
• Parental protein coverage: 51.94 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNPEFRVQFQDMCATIGVDPLASGKGF
          ..AKYKE..TVLAEDQLAQMSKQL.MFKTNLEEFASKH.QEIRK..EF.VQFQD.CAT.GV.PLASGKGF
Retrocopy SKAKYKE*RTVLAEDQLAQMSKQLGMFKTNLEEFASKHTQEIRKDLEFHVQFQDICATFGVEPLASGKGF

Parental  WSEMLGVGDFYYELGVQIIEVCLAL-KHRNGGLITLEELHQQVLKGRGKFAQDVSQDDLIRAIKK
          ..EMLG..DFY.ELGV.IIE.CL.L..H..GG.ITLEEL.QQVLKGRGKF.QDVSQDDLIRAIKK
Retrocopy *FEMLGLRDFYKELGVYIIEACLVL<EHWSGGPITLEELYQQVLKGRGKFTQDVSQDDLIRAIKK

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_2520 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 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005062	1 retrocopy	retro_amel_164,
Canis familiaris	ENSCAFG00000016893	1 retrocopy	retro_cfam_1488,
Choloepus hoffmanni	ENSCHOG00000013760	1 retrocopy	retro_chof_1372,
Callithrix jacchus	ENSCJAG00000007322	2 retrocopies	retro_cjac_1175, retro_cjac_1922,
Echinops telfairi	ENSETEG00000000758	1 retrocopy	retro_etel_709,
Felis catus	ENSFCAG00000008944	2 retrocopies	retro_fcat_1291, retro_fcat_574,
Homo sapiens	ENSG00000159210	1 retrocopy	retro_hsap_2394,
Gorilla gorilla	ENSGGOG00000025290	1 retrocopy	retro_ggor_1816,
Macropus eugenii	ENSMEUG00000016638	1 retrocopy	retro_meug_663,
Mustela putorius furo	ENSMPUG00000015356	1 retrocopy	retro_mputfur_1425,
Mus musculus	ENSMUSG00000006058	1 retrocopy	retro_mmus_1050,
Nomascus leucogenys	ENSNLEG00000002743	1 retrocopy	retro_nleu_2520 ,
Oryctolagus cuniculus	ENSOCUG00000009156	2 retrocopies	retro_ocun_814, retro_ocun_996,
Pongo abelii	ENSPPYG00000008911	1 retrocopy	retro_pabe_2161,
Tarsius syrichta	ENSTSYG00000004576	1 retrocopy	retro_tsyr_843,