RetrogeneDB ID: retro_pvam_725

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_999:342023..342458(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAR1B
• Ensembl ID: ENSPVAG00000012433
• Aliases: None
• Description: SAR1 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:10535]

Sequence

>retro_pvam_725
GTGACCTTCACATTTGACTGGATTTACAGTGGTTTCAGCAATGTGCTACAGTTTTTAGGGTCCTATAAAAAAAAAACTGG
TAAATTGGTATTTCTTGGCTTGGATAATACAGGGAAAAGAATATTGCTACACATGCTAAAAGATGACAGAGTTGGACAAC
ATGTTCCAACATTACATCTCACTTCAAAACTAACCATTGCTAGGGTGAACTTTACAACTTTTGATCTGGATGGACATGTT
TGAGCTTGAGGAGTGTGGAAAAACTACCGTCCTGCTATCAATGGAATTGTGTTTCTGGTGTATTGTGCAGACCATGAAAG
GCTGTTAGAATCAAAAGAACCTGATACACTAATGACAGATGAAACCATTGCTAACATGCCTGTACTGATTGTCGGGAATA
GGATCAACAGATCTGAAGCCATAAGAGAGGTTAGG

Alignment

ORF - retro_pvam_725 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.51 %
• Parental protein coverage: 73.74 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSFIFDWIYSGFSSVLQFLGLYKKT-GKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGM
          ..F.FDWIYSGFS.VLQFLG.Y....GKLVFLGLDN.GK..LLHMLKDDR.GQHVPTLH.TS..LTIA..
Retrocopy VTFTFDWIYSGFSNVLQFLGSYXXXXGKLVFLGLDNTGKRILLHMLKDDRVGQHVPTLHLTSK-LTIARV

Parental  TFTTFDLGGHVQARRVWKNYLPAINGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDRP
          .FTTFDL.GHV.A..VWKNY.PAINGIVFLV.CADHERLLESKE..D.LMTDETIAN.P.LI.GN.I.R.
Retrocopy NFTTFDLDGHV*A*GVWKNYRPAINGIVFLVYCADHERLLESKEP-DTLMTDETIANMPVLIVGNRINRS

Parental  EAISEER
          EAI.E.R
Retrocopy EAIREVR

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_725 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 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017849	1 retrocopy	retro_amel_1075,
Dasypus novemcinctus	ENSDNOG00000013784	3 retrocopies	retro_dnov_1584, retro_dnov_1804, retro_dnov_919,
Loxodonta africana	ENSLAFG00000001021	1 retrocopy	retro_lafr_1043,
Oryctolagus cuniculus	ENSOCUG00000008250	1 retrocopy	retro_ocun_1004,
Pteropus vampyrus	ENSPVAG00000012433	2 retrocopies	retro_pvam_1219, retro_pvam_725 ,
Tursiops truncatus	ENSTTRG00000016864	2 retrocopies	retro_ttru_1225, retro_ttru_857,