RetrogeneDB ID: retro_pvam_1148

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_3260:82511..83054(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF114
• Ensembl ID: ENSPVAG00000004117
• Aliases: None
• Description: ring finger protein 114 [Source:HGNC Symbol;Acc:13094]

Sequence

>retro_pvam_1148
ATGGTGGCGCAACAGCAGGACCGAGAGGGTGGTGTGCAGATGGCAGGCCTCCGGCGGAGCCCGACCCTCTGGGCTGGTGC
ATGTGTCCCATGTGCACGGAGGTGCAAGAGAGGTGGGCACAGGTGCTCTTTGGACATGCCTTTTGCTCTGCAGGCCTGCA
GAAATTCTGAAGCCGAAAAAGCCTGTCGGTGGGGTGTGTCCTAGCCCTCTGGCACCTGGCAACCAAGCTGTGGAGCTCGG
GTGGCAGTTTGAGAGCACAGAGACTTCGTGCCATGGCTGATGTAAAAATTTGTTCCGATCCAAGATCCTGATCCAAAAAG
CTACCTGTTTCAAATGCCAGAATTACATCACGGAATGTGTGAAGCCCCCACAGAGGGTGCCTCCGTTCAGCCGACGCGTG
TCCCAAACCGTAACACCTTTCCTTTCCCCTCGTCTCCTGAGAAGAACTTTGATCAAGAAGGACTTGAGGAACACTGCAAG
TTATCCCATTGCACACATACCAGATCTGTGCTTTGTCGAATATGTGCCTTGATGCCCTAGGGA

Alignment

ORF - retro_pvam_1148 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.03 %
• Parental protein coverage: 79.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAQQQDREGGAQLAGRA-AEPDPLSRFTCPVCLEVYEKPVRVLCGHVFCSACLQ-ECLKPKKPVCGVCR
          M.AQQQDREGG.Q.AG...AEPDPL....CP.C.EV.E....VL.GH.FCSA.LQ.E.LKPKKPV.GVC.
Retrocopy MVAQQQDREGGVQMAGLR<AEPDPLGWCMCPMCTEVQERWAQVLFGHAFCSAGLQ<EILKPKKPVGGVCP

Parental  SPLAPGDRAVELERQIESTETSCHGCRKNFFLSKIRAHVATCSKYQNYIMEGVK-ATTKDASLQPRNVPN
          SPLAPG..AVEL..Q.ESTETSCHG..KN.F.SKI....ATC.K.QNYI.E.VK.A.T..AS.QP..VPN
Retrocopy SPLAPGNQAVELGWQFESTETSCHG*CKNLFRSKILIQKATCFKCQNYITECVK<APTEGASVQPTRVPN

Parental  RYTFPCPYCPEKNFDQEGLVEHCKISHSTDTKSVVCPICASMPWG
          R.TFP.P..PEKNFDQEGL.EHCK.SH.T.T.SV.C.ICA.MP.G
Retrocopy RNTFPFPSSPEKNFDQEGLEEHCKLSHCTHTRSVLCRICALMP*G

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_1148 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 7 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009113	2 retrocopies	retro_dnov_1534, retro_dnov_1557,
Microcebus murinus	ENSMICG00000011155	1 retrocopy	retro_mmur_992,
Otolemur garnettii	ENSOGAG00000003953	3 retrocopies	retro_ogar_1149, retro_ogar_2158, retro_ogar_2330,
Ochotona princeps	ENSOPRG00000004732	2 retrocopies	retro_opri_368, retro_opri_709,
Pteropus vampyrus	ENSPVAG00000003778	2 retrocopies	retro_pvam_1316, retro_pvam_1379,
Pteropus vampyrus	ENSPVAG00000004117	4 retrocopies	retro_pvam_1136, retro_pvam_1148 , retro_pvam_1149, retro_pvam_1477,
Sarcophilus harrisii	ENSSHAG00000001827	1 retrocopy	retro_shar_193,