RetrogeneDB ID: retro_pvam_388

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2891:88036..88668(-)
• Located in intron of: ENSPVAG00000011155

Retrocopy information

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

Parental gene information

• Parental gene symbol: ERP29
• Ensembl ID: ENSPVAG00000012400
• Aliases: None
• Description: endoplasmic reticulum protein 29 [Source:HGNC Symbol;Acc:13799]

Sequence

>retro_pvam_388
ATGGCTGCCACCATTCTCCACGCCACTTCTCTCTCCCTACTATTTCCCCGTCTCCTGTTCTTTCTGTTCCTCTTCGCTCC
ACAGGGTGGCAGCGGCCTGCATACCAAGGGTCCCCTTTCCCTGGATACAGTCACTTTCTACAAGGTCATTCCCAAAAGCA
AATTCGTCTTGGTGATGTTTGACACTCACTATCTCTACAGTGAGAAGCAGGATGAGTTCAAGCATCTGGCTGAAAACTTG
GCCTCCAGCGATGATCTCCTGGTGGCAGAGGTGGGGATCTCAGATTATGGTGACAAGCTGAATATGGAGCTGAATGAGAA
ATACAAATTGGACAAAGAGAACTACCCCGTCTTCTACCTCTTCCGGGATGGGAACTTTGAGAACCCAATCCTGCACAAGG
GGGCAGTTAAGGTTGGAGCCATCCAGTGCTGGCTAAAGGGGCATGGGGTCTACCTAGGTTTGTCTGGTTGCCTGCCTACA
TATGATGCCCTTGCTGAAGAGTTCATCAAGGCCTCTGGCGTGGAGGCCTGCCAGGCCCTCTCAAAGCGGGGACAGGACAA
CCTTGCAAGTGTGAAGGAGATTGAGAAGTGAGAGCTGAGTAATACCTGAAGATCATGGGGAAGGTCTTAGAC

Alignment

ORF - retro_pvam_388 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.96 %
• Parental protein coverage: 80.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAAILRAASLSPLFPLLLFLLFLSAPQGGSGLHTKGALPLDTVTFYKVIPKSKFVLVKFDTQYPYGEKQ
          MAA.IL.A.SLS.LFP.LLF.LFL.APQGGSGLHTKG.L.LDTVTFYKVIPKSKFVLV.FDT.Y.Y.EKQ
Retrocopy MAATILHATSLSLLFPRLLFFLFLFAPQGGSGLHTKGPLSLDTVTFYKVIPKSKFVLVMFDTHYLYSEKQ

Parental  DEFKRLAENSASSDDLLVAEVGISDYGDKLNMELSEKYKLDKENYPVFYLFRDGDFENPVLYSGAVKVGA
          DEFK.LAEN.ASSDDLLVAEVGISDYGDKLNMEL.EKYKLDKENYPVFYLFRDG.FENP.L..GAVKVGA
Retrocopy DEFKHLAENLASSDDLLVAEVGISDYGDKLNMELNEKYKLDKENYPVFYLFRDGNFENPILHKGAVKVGA

Parental  IQRWLKGHGVYLGMPGCLPTYDNLAGEFIKASGVEARQALLKQGQDNLASVKETER-KWAEQYLKIMGKV
          IQ.WLKGHGVYLG..GCLPTYD.LA.EFIKASGVEA.QAL.K.GQDNLASVKE.E....AE.YLKIMGKV
Retrocopy IQCWLKGHGVYLGLSGCLPTYDALAEEFIKASGVEACQALSKRGQDNLASVKEIEK<VRAE*YLKIMGKV

Parental  LD
          LD
Retrocopy LD

Legend:

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

Expression

RNA-Seq

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq

Pteropus vampyrus was not studied using ChIP-Seq data.

EST

Pteropus vampyrus was not studied using EST data.

TSS

Pteropus vampyrus was not studied using FANTOM5 data.

Lab

retro_pvam_388 was not experimentally validated.

Homology

Retrocopy orthology:

Pteropus vampyrus 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000089248	1 retrocopy	retro_hsap_2488,
Nomascus leucogenys	ENSNLEG00000000031	1 retrocopy	retro_nleu_276,
Pongo abelii	ENSPPYG00000004971	1 retrocopy	retro_pabe_1829,
Pan troglodytes	ENSPTRG00000005468	1 retrocopy	retro_ptro_1441,
Pteropus vampyrus	ENSPVAG00000012400	1 retrocopy	retro_pvam_388 ,