RetrogeneDB ID: retro_pvam_1039

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_24245:58..766(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF115
• Ensembl ID: ENSPVAG00000014487
• Aliases: None
• Description: ring finger protein 115 [Source:HGNC Symbol;Acc:18154]

Sequence

>retro_pvam_1039
ACACATTTTGCAGAGTTCTGGTGCAATTCGAACCTCAGTATGATTATACAGGATTTTAGGCAATTTCTAAGTAGCAATCT
ACTGGACTAAAATAATAGAGCCAATGAGAGAGGTCACCAAACTCACACTGACTCTGGGGACCAAGTTGGCCTTCAAGTTG
CCAGTGACTGGGAGATAAAGATCAGAAGGAAGTACTCATCCCAGTAGATCTCCAGCTATTGAAAGAATAATACAACAGTT
CTTTGCTGGAGTCTTTGCAAATTCTGCAGTTCCTGGGTCCCCACACCCTTTTTCCTGGAGGAGGATGCTGCACTCCAGCC
CTGGGGACTATGCCTGGGGTTACACAGAGCTTGATGCCCTCGTAACCCAGTTTTTAAGACAACTGGAAAACACAGGGCCT
CCACAACCTGACAAGGGGAAGATCACAGCTCTTCCAACAGTGACAGTAACTCAGGAGCAAGTCGATATGTGTTTAGAGTG
TTCGGTATGCAAAGAAGATTACACAGTTGAAGAGGAAGTCGGCAGTTACCCTGCAGCCACATCTTTCAGAGCAGTTGTAT
TGTGCCATGGTTAGAACTGCATGATACATGTTCTATATGCGGGCAGAGCTGAAATGGTGAGCACACTACTTGGCAAAGCC
GGAGCTCTGAGTGTTCTGCAGGCAACAGATTTAGCAGTGACAGCCAACTACAGGAGTGATGGACTTTC

Alignment

ORF - retro_pvam_1039 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.83 %
• Parental protein coverage: 77.7 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  THFAEFWRNLDHTMIIQDFRPFLSSNPLDQDNRASERGHQTHTD-FWGPSRPP-RLPMTRRYRSQGSTRP
          THFAEFW.N....MIIQDFR.FLSSN.LD..NRA.ERGHQTHTD..WGPS.P...LP.T.R.RS.GST.P
Retrocopy THFAEFWCNSNLSMIIQDFRQFLSSNLLD*NNRANERGHQTHTD<LWGPSWPS<KLPVTGR*RSEGSTHP

Parental  DRSPAIEGIIQQFFAGFFANSAVPGSPHPLSWSGLLHSNPGDYAWGQTGLDAIVTQLLGQLENTGPPPAD
          .RSPAIE.IIQQFFAG.FANSAVPGSPHP.SW...LHS.PGDYAWG.T.LDA.VTQ.L.QLENTGPP..D
Retrocopy SRSPAIERIIQQFFAGVFANSAVPGSPHPFSWRRMLHSSPGDYAWGYTELDALVTQFLRQLENTGPPQPD

Parental  KEKITSLPTVTVTQEQVDTGLECSVCKEDYTVGEEV-RQLPCNHFFHSSCIVPWLELHDTCPICRKSLNG
          K.KIT.LPTVTVTQEQVD..LECSVCKEDYTV.EEV.RQLPC.H.F.SSCIVPWLELHDTC.IC..S.NG
Retrocopy KGKITALPTVTVTQEQVDMCLECSVCKEDYTVEEEV<RQLPCSHIFQSSCIVPWLELHDTCSICGQS*NG

Parental  EDSTWQTQSSEASASNRFSSDSQLHDRWTF
          E..TWQ..SSE.SA.NRFSSDSQL...WTF
Retrocopy EHTTWQSRSSECSAGNRFSSDSQLQE*WTF

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_1039 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000009030	1 retrocopy	retro_ecab_459,
Macropus eugenii	ENSMEUG00000002500	1 retrocopy	retro_meug_1546,
Oryctolagus cuniculus	ENSOCUG00000003055	1 retrocopy	retro_ocun_1138,
Pteropus vampyrus	ENSPVAG00000014487	13 retrocopies	retro_pvam_1039 , retro_pvam_1096, retro_pvam_1111, retro_pvam_1293, retro_pvam_1295, retro_pvam_1442, retro_pvam_730, retro_pvam_733, retro_pvam_759, retro_pvam_796, retro_pvam_806, retro_pvam_849, retro_pvam_964,
Tarsius syrichta	ENSTSYG00000004867	2 retrocopies	retro_tsyr_1734, retro_tsyr_1870,