RetrogeneDB ID: retro_pabe_1323

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:85857198..85857624(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VAPA
• Ensembl ID: ENSPPYG00000009006
• Aliases: None
• Description: Vesicle-associated membrane protein-associated protein A [Source:UniProtKB/Swiss-Prot;Acc:Q5R601]

Sequence

>retro_pabe_1323
ACAATTTTTGCTCCACTAAACACTTCAGATATGGAAGCTGTGTGGAAAAAGGCAAAACCTCATGAATTAATGGATTCCAA
ATTGAGATGTGTATTTGAAATGCCCAATGAAAATGATAAACTGAATGACATGGAACCTAGCAAAGCTGTTCCACTGAATG
CATCTAAACAAGATGGACCCATGCCAAAACCACACAGTGTTTCACTTAATGATACCGAAACAAGGAAACTAATAGAAGAG
TGTAAAAGACTTCAGGGAGAAATGATGAAGCTATCAGAAGAAAATCGACACCTGAGAGATGAAGGTTTAAGGCTCAGAAA
GGTAGCACATTCGGATAAACCTGGATCAACCTCAACTGCGTCCTTCAGAGATGTCACCAGTCCTCTTCCTTCACTTCTTG
TTGTAATTGCAGCCATTTTCACTGGA

Alignment

ORF - retro_pabe_1323 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.8 %
• Parental protein coverage: 57.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TIFAPPNTSDMEAVWKEAKPDELMDSKLRCVFEMPNENDKLNDMEPSKAVPLNASKQDGPMPKPHSVSLN
          TIFAP.NTSDMEAVWK.AKP.ELMDSKLRCVFEMPNENDKLNDMEPSKAVPLNASKQDGPMPKPHSVSLN
Retrocopy TIFAPLNTSDMEAVWKKAKPHELMDSKLRCVFEMPNENDKLNDMEPSKAVPLNASKQDGPMPKPHSVSLN

Parental  DTETRKLMEECKRLQGEMMKLSEENRHLRDEGLRLRKVAHSDKPGSTSTASFRDNVTSPLPSLLVVIAAI
          DTETRKL.EECKRLQGEMMKLSEENRHLRDEGLRLRKVAHSDKPGSTSTASFRD.VTSPLPSLLVVIAAI
Retrocopy DTETRKLIEECKRLQGEMMKLSEENRHLRDEGLRLRKVAHSDKPGSTSTASFRD-VTSPLPSLLVVIAAI

Parental  FIG
          F.G
Retrocopy FTG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	10.51 RPM	59.27 RPM
SRP007412_cerebellum	8.15 RPM	101.17 RPM
SRP007412_heart	7.74 RPM	40.85 RPM
SRP007412_kidney	7.16 RPM	41.14 RPM
SRP007412_liver	28.89 RPM	37.95 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1323 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1323 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1323 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000008965	1 retrocopy	retro_mluc_542,
Monodelphis domestica	ENSMODG00000021442	1 retrocopy	retro_mdom_57,
Pongo abelii	ENSPPYG00000009006	1 retrocopy	retro_pabe_1323 ,
Rattus norvegicus	ENSRNOG00000014765	1 retrocopy	retro_rnor_266,