RetrogeneDB ID: retro_nleu_759

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397272.1:2849677..2850150(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDC4
• Ensembl ID: ENSNLEG00000006698
• Aliases: None
• Description: Syndecan [Source:UniProtKB/TrEMBL;Acc:G1R4N6]

Sequence

>retro_nleu_759
GGGCCAAACTTCTCCAGATGTCTACTGGAAGACTCTGGATGTGGGTGTGGGGGGCAGGAACCTGATGACTCTGAGCTGTC
TGGCTCTGGAGATATTGGTGAGTCAAGGGACCCCAAGATGATCCCTGAAGTGATCCAACCCTTGGTGCTTCTAGATAACC
ACATCCCTGAGAGGGCAGGGCCTGGGAACCTGGTCCCACTGAAACCAAGGAACTAGAGGAGAATGAGGTCATCCCCAGGA
GGATCTCTGTGGGGGACCAGGATGTGTCCAATAAGGCACCCATGTCCAACACTGCCCAGGGCAGCAACATCTTTGAGAGA
ATGGAAGTCGTGGCAGTCCTGACTGTGGACAGCATCGTGGGCATCCTCTCTGCTGTTTTCCTGATCCTGCTTCTGGTGAA
CCATATGAAGAAGGATGAAGGCAGAAACAACCTGAGCAGGAAGCCCATCTACTAAAAAGCCCCTAGCAATGAG

Alignment

ORF - retro_nleu_759 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.82 %
• Parental protein coverage: 81.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRYFSGALPDDEDVVGPGQESDDFELSGSGDMGMEDDLEDSMIGPEVIHPLVPLDNHIPERAGSGSQVP-
          G..FS..L..D......GQE.DD.ELSGSGD.G......D....PEVI.PLV.LDNHIPERAG.G..VP.
Retrocopy GPNFSRCLLEDSGCGCGGQEPDDSELSGSGDIG---ESRDPKMIPEVIQPLVLLDNHIPERAGPGNLVP<

Parental  TEPKKLEENEVIPKRISPIEESEDVSNKVSMSSTVQGSNLFERTEVLAALIVGGIVGILFAVFLILLLMY
          TE.K.LEENEVIP.RIS......DVSNK..MS.T.QGSN.FER.EV.A.L.V..IVGIL.AVFLILLL..
Retrocopy TETKELEENEVIPRRISVGDQ--DVSNKAPMSNTAQGSNIFERMEVVAVLTVDSIVGILSAVFLILLLVN

Parental  RMKKKDEGSYDLGKKPIYKKAPTNE
          .M.KKDEG...L..KPIY.KAP.NE
Retrocopy HM-KKDEGRNNLSRKPIY*KAPSNE

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_759 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000124145	1 retrocopy	retro_hsap_2579,
Gorilla gorilla	ENSGGOG00000004153	1 retrocopy	retro_ggor_1614,
Macropus eugenii	ENSMEUG00000000817	1 retrocopy	retro_meug_1994,
Nomascus leucogenys	ENSNLEG00000006698	1 retrocopy	retro_nleu_759 ,