RetrogeneDB ID: retro_pvam_964

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_19689:6770..7443(+)
• 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_964
CATTTTGCAGAGCTCTGGTGCAATTTGAACCTCAGAATAATTATACAAAATTTTAGGCCATTTCTAAGTAGCAATCCACT
GGACCAAGATAATAGAGCCAATGAGGGAGGTCACCAAACTCACACTGACTCTGGGGACCAAGTCAGTCTTCAAGGTTGCC
AATGACTTGGAGATACAGATCGCAAGGAAGTACTCATCCCAGGAGATCTCCGGCTATTGAAAGAATAATACAACAGTTCT
TTGCCAACATCTTTGCAAATTCCGTAGTTCCTGGATCCCCACACCCTTTTCCTGGAGCAAGATGCTGCACTCCAACCCTG
GGAAATATGCTTGGGGTCACACAGGGCTTGATGCCATTGTAACCCAGCTTTTAAGACAACTGGAAAACACAGGGCCTCCA
CAAGCTGACAAGGGAAAAATCACATCTTCCAACAGAGACAGTAACTCAGGAGCGAGTCGATATGTGTTTAGAGTGTTCGG
TATGCAAAGAAGATTACACAGTTGAAGAGGAAGTTGGCAGTTACCCTGCAGCCACATCTTTCACAGCAGTTGTAATGTGC
CATGGTTAGAACTGCATGATACATGTTCTATATGTGGGAAGAGCTTAAATGATGAGCACGCTACTTGGCAAACCCAGAGC
TCTGAGGCCTCTGCAAGCAACGGATTTAGCAGT

Alignment

ORF - retro_pvam_964 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.7 %
• Parental protein coverage: 74.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  HFAEFWRNLDHTMIIQDFRPFLSSNPLDQDNRASERGHQTHTD-FWGPSRPPRLPMTRRYRSQGSTRPDR
          HFAE.W.NL....IIQ.FRPFLSSNPLDQDNRA.E.GHQTHTD..WGPS...RLPMT.RYRSQGST.P.R
Retrocopy HFAELWCNLNLRIIIQNFRPFLSSNPLDQDNRANEGGHQTHTD<LWGPSQSSRLPMTWRYRSQGSTHPRR

Parental  SPAIEGIIQQFFAGFFANSAVPGSPHPL-SWSGLLHSNPGDYAWGQTGLDAIVTQLLGQLENTGPPPADK
          SPAIE.IIQQFFA..FANS.VPGSPHP..SWS..LHSNPG.YAWG.TGLDAIVTQLL.QLENTGPP.ADK
Retrocopy SPAIERIIQQFFANIFANSVVPGSPHPF<SWSKMLHSNPGKYAWGHTGLDAIVTQLLRQLENTGPPQADK

Parental  -EKITSLPTVTVTQEQVDTGLECSVCKEDYTVGEEVR-QLPCNHFFHSSCIVPWLELHDTCPICRKSLNG
          .EK...LPT.TVTQE.VD..LECSVCKEDYTV.EEV..QLPC.H.FHSSC.VPWLELHDTC.IC.KSLN.
Retrocopy >EK-SHLPTETVTQERVDMCLECSVCKEDYTVEEEVG<QLPCSHIFHSSCNVPWLELHDTCSICGKSLND

Parental  EDSTWQTQSSEASASNRFSS
          E..TWQTQSSEASASN.FSS
Retrocopy EHATWQTQSSEASASNGFSS

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_964 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,