RetrogeneDB ID: retro_pvam_43

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1115:50756..51213(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAP18
• Ensembl ID: ENSPVAG00000016315
• Aliases: None
• Description: Sin3A-associated protein, 18kDa [Source:HGNC Symbol;Acc:10530]

Sequence

>retro_pvam_43
ATAGCAGTGGAATCTCACGTAATTCAGGAGGAAATGAAAGAGATGGAGAAGCCAATTGACCGGAAGATTTTCTCACTGCT
GCAGTGTGCTTTCAACAACGACAATGGGCCACCACCACTGCAGAATGGATGAATTCTCCCACAGGAACATGCAGTCCAGC
AAATTGCAGATCTACACCTGGATGGATACAACCTTAAAATAACTGGCTAGTTTAGTGAAAGAGGTCTACACAGAAGCTAG
AAAGGAAAGCACACACTTTAATTTTGCAATTGTTTTTATGGCTATGAAAAAACCTGGCTATCGAGTAAAGGAGATTGGCA
ACACCATGTCTGAGAGAAAGGAGACTGAGGAGCCCATGACTCTGCAACCGCAGAAGTTCCATATAGGATATTATTTGGGC
ATAGTGATCATCCCTCTGCATCAAGCACCACCTCCTTCAGGGTGCATGAGGCCATAT

Alignment

ORF - retro_pvam_43 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.39 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAVESRVTQEEIKKEPEKPIDREKTCPLLLRVF-TTNNGRHH-RMDEFSRGNVPSSELQIYTWMDATLKE
          .AVES.V.QEE.K.E.EKPIDR.K...LL...F.TT..G.HH.RMDEFS..N..SS.LQIYTWMD.TLK.
Retrocopy IAVESHVIQEEMK-EMEKPIDR-KIFSLLQCAF>TTTMGHHHCRMDEFSHRNMQSSKLQIYTWMDTTLK*

Parental  LTSLVKEVYPEARKKGTHFNFAIVFTDIKRPGYRVKEIGSTMSVRKGTDDAMTLQSQKFQIGDYLDIAIT
          L.SLVKEVY.EARK..THFNFAIVF...K.PGYRVKEIG.TMS.RK.T...MTLQ.QKF.IG.YL.I.I.
Retrocopy LASLVKEVYTEARKESTHFNFAIVFMAMKKPGYRVKEIGNTMSERKETEEPMTLQPQKFHIGYYLGIVII

Parental  PPNRAPPPSGRMRPY
          P...APPPSG.MRPY
Retrocopy PLHQAPPPSGCMRPY

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_43 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 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000006309	1 retrocopy	retro_eeur_674,
Mustela putorius furo	ENSMPUG00000000607	1 retrocopy	retro_mputfur_35,
Mus musculus	ENSMUSG00000021963	1 retrocopy	retro_mmus_82,
Pteropus vampyrus	ENSPVAG00000016315	2 retrocopies	retro_pvam_1246, retro_pvam_43 ,
Rattus norvegicus	ENSRNOG00000010732	1 retrocopy	retro_rnor_163,
Tarsius syrichta	ENSTSYG00000005454	22 retrocopies	retro_tsyr_1018, retro_tsyr_1117, retro_tsyr_1225, retro_tsyr_1342, retro_tsyr_1439, retro_tsyr_1490, retro_tsyr_1578, retro_tsyr_1708, retro_tsyr_1767, retro_tsyr_1851, retro_tsyr_1938, retro_tsyr_2118, retro_tsyr_2179, retro_tsyr_398, retro_tsyr_451, retro_tsyr_563, retro_tsyr_826, retro_tsyr_837, retro_tsyr_886, retro_tsyr_892, retro_tsyr_901, retro_tsyr_967,