RetrogeneDB ID: retro_nleu_891

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397275.1:25614175..25615191(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000015375
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SDCCAG3
• Ensembl ID: ENSNLEG00000008186
• Aliases: None
• Description: None

Sequence

>retro_nleu_891
GATGACAAATTTGAAGATCTTGAAGAGGCAAATCCATTCTCCTTTAAAGAGCTTCTGAAGACCAAGAACCTCGGCCTGTC
AAAAGAGGACCCAGCCAGCAGCATTTATGCAAAGGAAGCCTCGAGGCATTCACTGGGACTTGACCACAACTCCTCAGCCT
CCCAAACCGGGGGGGTATGGCCTGGAGTATCAGCAGCCATTTTTCGAGGACCCGACAGGGGCCGGTGACCTCCTGAATAA
GGAGGAGGATGAGGACACCTGATGGAGTGGGGCCTACCTGCCGTCCGCCATCCAGCAGACTCACCCCGAGAGGGTCCCTG
CCAGCACGTGGCCCTGCAGCACATACCTTTCCTTTTTCTCCACCCCGTCGGAGCTGGCAGGGCCTGAGTCTCTGCCCCCG
TGGGTGTTGAGTGACACTGATTCTCGTGTCTCTGGCCTCTCCGGCAGGGAGTCCTAGCGCAGACTTTGCGGCTCATGGAG
AGTCTCCGGGATACAGGCGCCTGCGGACGCTGCAGATAAGTTACGACGCACTGAAAGATGAAAATTCTAAGCTGAGAAGA
AAGCTGAATGAGGTTCAGAGCTTCTCTGAAGCTCAAACAGAAATGGTGAAGACACTTGAGCGGAAATTAGAAGCAAAAAT
GATCAAGGAGGAAAGCGACTACCACGACTTGGAGTCGGTGGTTCAGCAGGTGGAGCAGAACCTGGAGCTGATGACCAAAC
GGGCTGTAAAGGCAGAAAACCACGTCGTGAAACTGAAACAGGAAATCAATTTGCTCCAGGCGCAGGTCTCCAACTTCCAG
CGAGAGAATGAAGCCCTGTGGTGCGGCCAGGGCACCAGACTGACAGTGGTGAAGCAGAACGCCGACGTGGCCTTGCAGAA
CCTCCGCGTGGCCATGAACAGCGCACAGGCTTCCATTAAGCAACTGGTTTCCAGAGCTGAGACACTGAATCTTGTTGCCG
AAATCCTTAAATCTATAGACAGAATTTCTGAAATTAAAGACGAGGAGGAAGACTCT

Alignment

ORF - retro_nleu_891 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.04 %
• Parental protein coverage: 77.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DDRFEDLEEANPFSFKEFLKTKNLGLSKEDPASRIYAKEASRHSLELDHNSPPSQTGG-YGLEYQQPFFE
          DD.FEDLEEANPFSFKE.LKTKNLGLSKEDPAS.IYAKEASRHSL.LDHNS..SQTGG.YGLEYQQPFFE
Retrocopy DDKFEDLEEANPFSFKELLKTKNLGLSKEDPASSIYAKEASRHSLGLDHNSSASQTGG>YGLEYQQPFFE

Parental  DPTGASDLLDEEEDEDTGWSGAYLPSAIEQTHPERVPAGT-SPCS-TYPSFFSTPSEPAGPESLPPWALS
          DPTGA.DLL..EEDEDT.WSGAYLPSAI.QTHPERVPA.T..P...T.P..FS.P.......SL.P....
Retrocopy DPTGAGDLLNKEEDEDT*WSGAYLPSAIQQTHPERVPAST>GPAAHTFP--FSPPRRSWQGLSLCPRGC*

Parental  DTDSRVSPASPAGSPSADFASHGESLGDRHLWTLQISYEALKDENSKLRRKLNEVQSFSEAQTEMVRTLE
          .T...VS.ASPAGSPSADFA.HGES.G.R.L.TLQISY.ALKDENSKLRRKLNEVQSFSEAQTEMV.TLE
Retrocopy VTLILVSLASPAGSPSADFAAHGESPGYRRLRTLQISYDALKDENSKLRRKLNEVQSFSEAQTEMVKTLE

Parental  RKLEAKMIKEESDYQDLESVVQQVEHNLELMTKRAVKAENHVVKLKQEISLLQAQVSNFQRENEALRCGQ
          RKLEAKMIKEESDY.DLESVVQQVE.NLELMTKRAVKAENHVVKLKQEI.LLQAQVSNFQRENEAL.CGQ
Retrocopy RKLEAKMIKEESDYHDLESVVQQVEQNLELMTKRAVKAENHVVKLKQEINLLQAQVSNFQRENEALWCGQ

Parental  GASLTVVKQNADVALQSLRVVMNSAQTSIQQLVSGAETLNLVAELLKSIDRISEIKDEEEDS
          G..LTVVKQNADVALQ.LRV.MNSAQ.SI.QLVS.AETLNLVAE.LKSIDRISEIKDEEEDS
Retrocopy GTRLTVVKQNADVALQNLRVAMNSAQASIKQLVSRAETLNLVAEILKSIDRISEIKDEEEDS

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_891 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000165689	1 retrocopy	retro_hsap_1944,
Gorilla gorilla	ENSGGOG00000010905	1 retrocopy	retro_ggor_1414,
Mus musculus	ENSMUSG00000026927	3 retrocopies	retro_mmus_1545, retro_mmus_3492, retro_mmus_711,
Nomascus leucogenys	ENSNLEG00000008186	1 retrocopy	retro_nleu_891 ,
Otolemur garnettii	ENSOGAG00000015872	1 retrocopy	retro_ogar_3418,
Pongo abelii	ENSPPYG00000019772	2 retrocopies	retro_pabe_1612, retro_pabe_256,
Pan troglodytes	ENSPTRG00000021555	1 retrocopy	retro_ptro_1300,
Rattus norvegicus	ENSRNOG00000018876	2 retrocopies	retro_rnor_1215, retro_rnor_2770,