RetrogeneDB ID: retro_pvam_1111

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_29776:3229..3940(-)
• 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_1111
ACACATTTTGCAGAGTTCTGGTGCAATTCGAACCTCAGTATGATTATACAGGATTTTAGGCAATTTCTAAGTAGCAATCT
ACTGGACTAAAATAATAGAGCCAATGAGAGAGGTCACCAAACTCACACTGACTCTGGGGACCAAGTCGGCCTTCAAGGTT
GCCAATGATTGGGAGATATAGATTGCAAAGAAGTACTCATCCCGGTAGATCTCCAGCTATGAAAAGAATAATACAACAGT
TCTTTGCTGGAGTCTTTGCAAATTCTGCAGTTCCTGGGTCCCCACACCCTTTTTCCTGGAGGAGGATGCTGCACTCCAGC
CCTGGGGACTATGCCTGGGAGTTCACACAGGGCTTGATGCCATCATAAGCTAGCTTTTAAGACAACTGAAAAACAAAGGG
CCTCCACGAGCTGCCAAGGAGAAGATCACATCTCTTCCAACAGTGACAGTAACTCAGGAGCAAGTCGATATGTGTTTAGA
GTGTTCGGTATGCAAGGAAGAATACACAGCTGAAGAGGAAGTCGGCAGTTACCCTGCAGCCACATCTTTCAGAGCAGTTG
TATTGTGCCATGGTTAGAACTGCATGATACATGTTCTATATGCGGGCAGAGCTTAAATGGTGAGCATGCTACTTGGCAAA
CCCAGAGTTCTGAGGCCTCTGCAAGCAACAGATTTAGCAGTGACTGCCAACTACAGGACTGATGGACTTTC

Alignment

ORF - retro_pvam_1111 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.35 %
• Parental protein coverage: 77.7 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  THFAEFWRNLDHTMIIQDFRPFLSSNPLDQDNRASERGHQTHTD-FWGPSRPPRLPMTRRYRSQGSTRPD
          THFAEFW.N....MIIQDFR.FLSSN.LD..NRA.ERGHQTHTD..WGPSRP.RLPM..RYR.Q.ST.P.
Retrocopy THFAEFWCNSNLSMIIQDFRQFLSSNLLD*NNRANERGHQTHTD<LWGPSRPSRLPMIGRYRLQRSTHPG

Parental  RSPAIEGIIQQFFAGFFANSAVPGSPHPLSWSGLLHSNPGDYAWGQT-GL-DAIVTQLLGQLENTGPPPA
          RSPA...IIQQFFAG.FANSAVPGSPHP.SW...LHS.PGDYAW..T.GL.DAI...LL.QL.N.GPP.A
Retrocopy RSPAMKRIIQQFFAGVFANSAVPGSPHPFSWRRMLHSSPGDYAWEFTQGL<DAIIS*LLRQLKNKGPPRA

Parental  DKEKITSLPTVTVTQEQVDTGLECSVCKEDYTVGEEV-RQLPCNHFFHSSCIVPWLELHDTCPICRKSLN
          .KEKITSLPTVTVTQEQVD..LECSVCKE.YT..EEV.RQLPC.H.F.SSCIVPWLELHDTC.IC..SLN
Retrocopy AKEKITSLPTVTVTQEQVDMCLECSVCKEEYTAEEEV<RQLPCSHIFQSSCIVPWLELHDTCSICGQSLN

Parental  GEDSTWQTQSSEASASNRFSSDSQLHDRWTF
          GE..TWQTQSSEASASNRFSSD.QL.D.WTF
Retrocopy GEHATWQTQSSEASASNRFSSDCQLQD*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_1111 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,