RetrogeneDB ID: retro_pvam_1136

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_3177:69960..70581(+)
• 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_1136
CCCGAACCATTGGGCTGCTGCATGTGTCCTGTGGTCTCAGAGGTGCGCGAGAGGCCAGCGCGGGCTCTCTGCGGACACAC
CTTTTGCTGTGCAGGCCTGCAGGAAAGTCTGAAGCCGAAGAAGCCTGTCGGTGGAGTCTGTCCTAGGCCGCTGGAACCTG
GCGATTGAGCTATGGAACTCGGGTGGCAGTTTGAGAGCACAGCGACTTCGTTCCATGGCTGCCGTAAAAATTTGTCCCTA
TCCAAGATCTTGGCCCACGTAGCTACCTGTTCCAAATGCCAGAATTACATCACGGAATGTGTGAAGTCCCCACGGAGGGT
GCCTCTGTTCAGCCGACGAATATCTCATACCATTACACCTTTCCTTACCCCTCATGTCCCGAGAAGTACTTTGTTCAAAA
AGGACTTGGGGAACACTCCAAGTTAACCTGTAGCACGCACACCAGATCTGTGCTTTGTCCAATATGTGCCTCGATGCCCT
GGGGACATCCGACCGGTCTATGCTCCAACTTCATAGAGCATTTCCAAGGCCGGCAAGCAGGTTTCTTATGACACTTTTGT
GGCCTCCAATGTCGGCAAAGAGGACGGAACGAATCGGGTGTGGCAACGCTTCATCAGCGAT

Alignment

ORF - retro_pvam_1136 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.2 %
• Parental protein coverage: 90.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PDPLSRFTCPVCLEVYEKPVRVLCGHVFCSACLQECLKPKKPVCGVCRSPLAPGDRAVELERQIESTETS
          P.PL....CPV..EV.E.P.R.LCGH.FC.A.LQE.LKPKKPV.GVC..PL.PGD.A.EL..Q.EST.TS
Retrocopy PEPLGCCMCPVVSEVRERPARALCGHTFCCAGLQESLKPKKPVGGVCPRPLEPGD*AMELGWQFESTATS

Parental  CHGCRKNFFLSKIRAHVATCSKYQNYIMEGVKA-TTKDASLQPRNVPNRYTFPCPYCPEKNFDQEGLVEH
          .HGCRKN..LSKI.AHVATCSK.QNYI.E.VK...T..AS.QP.N....YTFP.P.CPEK.F.Q.GL.EH
Retrocopy FHGCRKNLSLSKILAHVATCSKCQNYITECVKS<PTEGASVQPTNISYHYTFPYPSCPEKYFVQKGLGEH

Parental  CKISHSTDTKSVVCPICASMPWGDPNYRSANFMEHVQRRH-QFSYDTFVDYDVDEEDMMNQVLQRSIID
          .K...ST.T.SV.CPICASMPWG.P.....NF.EH.Q.R..Q.SYDTFV...V..ED..N.V.QR.I.D
Retrocopy SKLTCSTHTRSVLCPICASMPWGHPTGLCSNFIEHFQGRQ>QVSYDTFVASNVGKEDGTNRVWQRFISD

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_1136 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,