RetrogeneDB ID: retro_nleu_1000

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397278.1:28907422..28908043(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SCAMP1
• Ensembl ID: ENSNLEG00000012775
• Aliases: None
• Description: secretory carrier membrane protein 1 [Source:HGNC Symbol;Acc:10563]

Sequence

>retro_nleu_1000
CTGGATCTCAACAATCCCTTCAAGCCTCCACCAGGCAGTGTGAGGATGCCTAACATACCCAATACACAACCAGCAATAAT
GAAACCAACAGAGAAACATCCAGTTTATACACCGATTGCAAAAAAACATGCGTTGGCCCAAGCTGAACTTCTTAAACACC
AGGAAGAAGTAGAAAGAAAAGATGCAGAATTAGATCATTGGGAATGAGAAATGCAAAACCTCACTCAACATGGTAGAAAA
AATAATTGGCCACTTCTTCTTAGCAGTTTTCCTATAGAACCTTGTTTCTATCAGGATTTTTCTGTTGACATTCCTATAGA
ATTCCAAAAGACAGTAAAGCTTATACACTACTTGTGGATGTTCCATGCTGTAAAACTGTTTCTAAATATCTTCAGATGCT
TGTCTTGGTTTTGTGTTGATTTTGCAAGAGTGGTTGATTTTGGTTTGAGTATCCTGAGGTTCTTGCTTTTTACTCCTTGT
TCATTTGTCTGTTGGTGCAGACTGCTTTATGGAGCTTTCAGGAGGGACAGTTCATTCAGATTCTTTGTATTCTTCTTCAT
CTATATTCGTTAGTTTCCTGTACATGCATTCCAGACTGTAGGATTTCATAATTGGGGCAAT

Alignment

ORF - retro_nleu_1000 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.2 %
• Parental protein coverage: 62.99 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LDEYNPFSDSRTPPPGSVKMPNVPNTQPAIMKPTEEHPAYTQIAKEHALAQAELLKRQEELERKAAELDR
          LD..NPF.....PPPGSV.MPN.PNTQPAIMKPTE.HP.YT.IAK.HALAQAELLK.QEE.ERK.AELD.
Retrocopy LDLNNPFK----PPPGSVRMPNIPNTQPAIMKPTEKHPVYTPIAKKHALAQAELLKHQEEVERKDAELDH

Parental  REREMQSLSQHGRKNNWPPLPSNFPVGPCFYQDFSVDIPVEFQKTVKLMYYLWMFHAVTLFLNIFGCLAW
          .E.EMQ.L.QHGRKNNWP.L.S.FP..PCFYQDFSVDIP.EFQKTVKL..YLWMFHAV.LFLNIF.CL.W
Retrocopy WE*EMQNLTQHGRKNNWPLLLSSFPIEPCFYQDFSVDIPIEFQKTVKLIHYLWMFHAVKLFLNIFRCLSW

Parental  FCVDSARAVDFGLSILWFLLFTPCSFVCWYRPLYGAFRSDSSFRFFVFFFVYICQFAVHVLQAAGFHNWG
          FCVD.AR.VDFGLSIL.FLLFTPCSFVCW.R.LYGAFR.DSSFRFFVFFF.YI..F.VH..Q..GFHNWG
Retrocopy FCVDFARVVDFGLSILRFLLFTPCSFVCWCRLLYGAFRRDSSFRFFVFFFIYIR*FPVHAFQTVGFHNWG

Parental  N
          N
Retrocopy N

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_1000 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
Canis familiaris	ENSCAFG00000032395	1 retrocopy	retro_cfam_227,
Cavia porcellus	ENSCPOG00000008868	1 retrocopy	retro_cpor_174,
Homo sapiens	ENSG00000085365	1 retrocopy	retro_hsap_189,
Gorilla gorilla	ENSGGOG00000015191	1 retrocopy	retro_ggor_269,
Macaca mulatta	ENSMMUG00000016398	1 retrocopy	retro_mmul_396,
Monodelphis domestica	ENSMODG00000019731	1 retrocopy	retro_mdom_964,
Nomascus leucogenys	ENSNLEG00000012775	1 retrocopy	retro_nleu_1000 ,
Tarsius syrichta	ENSTSYG00000014113	1 retrocopy	retro_tsyr_1676,