RetrogeneDB ID: retro_nleu_55

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397393.1:1602943..1603672(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000018189
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: VAPB
• Ensembl ID: ENSNLEG00000009351
• Aliases: None
• Description: VAMP (vesicle-associated membrane protein)-associated protein B and C [Source:HGNC Symbol;Acc:12649]

Sequence

>retro_nleu_55
ATGGCGAAGGTGGAGCAGGTCCTGAGCCTTGAGCCGCAGCACGAGCTCAAATTCCGAGGTCCCTTCACCGATGTTGTCAC
CACCAACCTAAAGCTTGGCAACCCGACAGACCGAAATGTGTGTTTTAAGGTGAAGACTGCAGCACCAAGTAGGTACTGTG
TGAGGCCCAACAGCGGAATCATCGATGCAGGGGCGTCAGTTAATGTATCTGTGATGTTACAGCCTTTCAATTATGATCGC
AATGAGAAAAGTAAACACAAGTTTATGGTTCAGTCTATGTTTGCTCCAACTGACACTTCAGATATGGAAGCAGTATGGAA
GGAGGCAAAACCAGAAGACCTTATGGATTCAAAACTTAGATGTGTGTTTGAATTGCCAGCAGAGAATGATAAACCACATG
ATGTAGAAATAAATAAAATTATATCCACAACTGCATCAAAGACAGAAACACCAATAGTGTCTAAGTCTCTGAGTTCTTCT
TTGGATGACACCGAAGTTAAGAAGGTTATGGAAGAATGTAAGACGCTGCAAGGTGAAATTCAGAGGCTATGGGAGGAGAA
CAAGCAGTTCAAGGAAGAAGATGGACTGCAGATGAGGAAGACAGTGCAGAGCAACAGCCCCATTTCAGCATTAGACCCAA
CTGGGAAGGAAGAAGGCCTTAGCACCTGGCTCTTGGCTCTGGTGGTTTTGTTCTTTATCGTTGGTGTAATTATTGGGAAG
ATTGCCTTG

Alignment

ORF - retro_nleu_55 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.47 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAKVEQVLSLEPQHELKFRGPFTDVVTTNLKLGNPTDRNVCFKVKTTAPRRYCVRPNSGIIDAGASINVS
          MAKVEQVLSLEPQHELKFRGPFTDVVTTNLKLGNPTDRNVCFKVKT.AP.RYCVRPNSGIIDAGAS.NVS
Retrocopy MAKVEQVLSLEPQHELKFRGPFTDVVTTNLKLGNPTDRNVCFKVKTAAPSRYCVRPNSGIIDAGASVNVS

Parental  VMLQPFDYDPNEKSKHKFMVQSMFAPTDTSDMEAVWKEAKPEDLMDSKLRCVFELPAENDKPHDVEINKI
          VMLQPF.YD.NEKSKHKFMVQSMFAPTDTSDMEAVWKEAKPEDLMDSKLRCVFELPAENDKPHDVEINKI
Retrocopy VMLQPFNYDRNEKSKHKFMVQSMFAPTDTSDMEAVWKEAKPEDLMDSKLRCVFELPAENDKPHDVEINKI

Parental  ISTTASKTETPIVSKSLSSSLDDTEVKKVMEECKRLQGEVQRLREENKQFKEEDGLRMRKTVQSNSPISA
          ISTTASKTETPIVSKSLSSSLDDTEVKKVMEECK.LQGE.QRL.EENKQFKEEDGL.MRKTVQSNSPISA
Retrocopy ISTTASKTETPIVSKSLSSSLDDTEVKKVMEECKTLQGEIQRLWEENKQFKEEDGLQMRKTVQSNSPISA

Parental  LAPTGKEEGLSTRLLALVVLFFIVGVIIGKIAL
          L.PTGKEEGLST.LLALVVLFFIVGVIIGKIAL
Retrocopy LDPTGKEEGLSTWLLALVVLFFIVGVIIGKIAL

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_55 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017424	1 retrocopy	retro_btau_1010,
Dasypus novemcinctus	ENSDNOG00000012711	1 retrocopy	retro_dnov_206,
Echinops telfairi	ENSETEG00000017229	1 retrocopy	retro_etel_1235,
Macropus eugenii	ENSMEUG00000009788	1 retrocopy	retro_meug_842,
Monodelphis domestica	ENSMODG00000016549	1 retrocopy	retro_mdom_919,
Nomascus leucogenys	ENSNLEG00000009351	1 retrocopy	retro_nleu_55 ,