RetrogeneDB ID: retro_pvam_719

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_95:85713..86185(+)
• Located in intron of: ENSPVAG00000004614

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A36
• Ensembl ID: ENSPVAG00000007958
• Aliases: None
• Description: solute carrier family 25 (pyrimidine nucleotide carrier ), member 36 [Source:HGNC Symbol;Acc:25554]

Sequence

>retro_pvam_719
TGCAAGGAAAAGCTGAATGGTGTATTTGATCCTGATGACACCTGGTACAAGATTTCAGCTGTGGTGACCTGTTTCACTGC
AATCACAGCAACCAACTTCTCTGGCTAATAAAGAATCAGTTAAAGTTTGATGCAAGGAACTACAGAACAAAACAAATGGG
TGCTCTTGAAAGTGGTCATAAAGTATATCAGACAGATGGCTCAACAGGACTTTACACAAGCGTGCCTGCTTCATGTGGTG
GCACATCAGAGGCTGAGATTCATCTGTTATTTGTGACAGTATTCAGCAGACACCACTGGAAGATGAGATTACGTCTGCAA
TGGGAGATGATGGAGAACATGAGAAAGTATCAGATTTTGTGGGAACGATGCTGCTGTCACTCCAAAAACTTGGGCCACAT
ATAGAATTTCTGTATGAAGTAATAAGAACAAGACCATGTAAAGAGGGCACAATGTACAGAAATTTTTTCAGA

Alignment

ORF - retro_pvam_719 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.53 %
• Parental protein coverage: 51.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CKETLNGVFDPDSTQVHMIAAMAGFTAITATN-PIWLVKTRLQLDARNRGEKRMGAFECVRKVYQTDGLR
          CKE.LNGVFDPD.T.....A....FTAITATN...WL.K..L..DARN...K.MGA.E...KVYQTDG..
Retrocopy CKEKLNGVFDPDDTWYKISAVVTCFTAITATN<LLWLIKNQLKFDARNYRTKQMGALESGHKVYQTDGST

Parental  GFYRGMSASYAGISETVIHF-VIYESIKQKLLEYKIASTMENDEESVKEASDFVGMMLAAATSKTCATSI
          G.Y....AS..G.SE..IH..VI..SI.Q..LE..I.S.M..D.E..K..SDFVG.ML...........I
Retrocopy GLYTSVPASCGGTSEAEIHL<VICDSIQQTPLEDEITSAMGDDGEHEK-VSDFVGTMLLSL--QKLGPHI

Parental  AYPHEVIRTRLREEGTKYRSFFQ
          ....EVIRTR...EGT.YR.FF.
Retrocopy EFLYEVIRTRPCKEGTMYRNFFR

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_719 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000010094	1 retrocopy	retro_ecab_234,
Felis catus	ENSFCAG00000027489	1 retrocopy	retro_fcat_1680,
Macaca mulatta	ENSMMUG00000022153	1 retrocopy	retro_mmul_2243,
Mus musculus	ENSMUSG00000032449	1 retrocopy	retro_mmus_2007,
Oryctolagus cuniculus	ENSOCUG00000002085	1 retrocopy	retro_ocun_361,
Pteropus vampyrus	ENSPVAG00000007958	1 retrocopy	retro_pvam_719 ,
Sus scrofa	ENSSSCG00000011669	1 retrocopy	retro_sscr_871,
Tupaia belangeri	ENSTBEG00000001759	1 retrocopy	retro_tbel_3349,
Tursiops truncatus	ENSTTRG00000003288	2 retrocopies	retro_ttru_1146, retro_ttru_947,
Vicugna pacos	ENSVPAG00000008292	1 retrocopy	retro_vpac_603,