RetrogeneDB ID: retro_pvam_1219

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_43516:1680..2038(-)
• 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_1219
GGTAAATTGGTATTTCCTGGCTTGGATAATACAGGGAAAAGAATATTGCTACACATGCTAAAAGATGACAGAGTTGGACA
ACATGTTCCCAACATTACATCTCACTTCAAAACTAACCATTGCTAGGGTGAACTTTACAACTTTTGATCTGGAGGGACAT
GTTTGAGCTTGAGGAGTGTGGAAAAACTACCGTCCTGCTATCAATGGAATTGTGTTTCTGGTGTATTGTGCAGACCATGA
AAGGCTGTTAGAATCAAAAGAACCTGATACACTAATGACAGATGAAACCATTGCTAACATGCCTGTACTGATTGTCGGGA
ATAGGATCAACAGATCTGAAGCCATAAGAGAGGTTAGG

Alignment

ORF - retro_pvam_1219 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.23 %
• Parental protein coverage: 61.11 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GKLVFLGLDNAGKTTLLHMLKDDRLGQHVP-TLHPTSEELTIAGMTFTTFDLGGHVQARRVWKNYLPAIN
          GKLVF.GLDN.GK..LLHMLKDDR.GQHVP.TLH.TS..LTIA...FTTFDL.GHV.A..VWKNY.PAIN
Retrocopy GKLVFPGLDNTGKRILLHMLKDDRVGQHVP>TLHLTSK-LTIARVNFTTFDLEGHV*A*GVWKNYRPAIN

Parental  GIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDRPEAISEER
          GIVFLV.CADHERLLESKE..D.LMTDETIAN.P.LI.GN.I.R.EAI.E.R
Retrocopy GIVFLVYCADHERLLESKEP-DTLMTDETIANMPVLIVGNRINRSEAIREVR

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_1219 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,