RetrogeneDB ID: retro_pvam_941

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_18027:6142..6585(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLBP
• Ensembl ID: ENSPVAG00000002807
• Aliases: None
• Description: stem-loop binding protein [Source:HGNC Symbol;Acc:10904]

Sequence

>retro_pvam_941
GACAGCTTTCCCATAGCTGAAGGCCCAAAGTCCCGTTCTCGATATATGGCCTGGGAAACTGCAACTGAAGAAGATGAAGT
AAGGACTAGAATTTACAAAGAAATTGCAAGATATAAAAGAAAATTCCTCATAACTGACTTTAGAATAAAGAGGAAATCAT
CATCAGGAAGCTTAGATTCAAGGAATCTACGTCTGCAGTGTCTGCTGACTTGGAGACAGATGAAAGTGGCCTGATGAGAA
GACAGAAGCAAAACAACAGTGGAAAGAACACCATTGCCTATGATAGCTGTGTTAAAGAAGTCCCAAGACACCTTCAAAAA
ATTGGCATTCATTCCAAGACCCTCAACAAAATCAAGAAGTATGGTCAACGATCGTGGGACCAGCACACCAAATTCTGGAA
GGTGGCTCTGCATTTTGGGGATCCTTCAGCCTAAGAAGGATGT

Alignment

ORF - retro_pvam_941 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.79 %
• Parental protein coverage: 56.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DTFTTPEGPKPRSRCADWASAVEEDEMRSRVNKEIARYKRKLLINDFGRERKSSSGSSDS-KESASAVPA
          D.F...EGPK.RSR...W..A.EEDE.R.R..KEIARYKRK.LI.DF...RKSSSGS.DS.KES.SAV.A
Retrocopy DSFPIAEGPKSRSRYMAWETATEEDEVRTRIYKEIARYKRKFLITDFRIKRKSSSGSLDS<KESTSAVSA

Parental  DLETDEGVLMRRQKQISYGKNTLAYDRYIKAVPRHLRQPGIHPKTPNKFKKYSRRSWDQQIKLWKVALHF
          DLETDE..LMRRQKQ...GKNT.AYD...K.VPRHL...GIH.KT.NK.KKY..RSWDQ..K.WKVALHF
Retrocopy DLETDESGLMRRQKQNNSGKNTIAYDSCVKEVPRHLQKIGIHSKTLNKIKKYGQRSWDQHTKFWKVALHF

Parental  WDPPAEEGC
          .DP.A.EGC
Retrocopy GDPSA*EGC

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_941 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001328	1 retrocopy	retro_btau_1456,
Cavia porcellus	ENSCPOG00000000031	1 retrocopy	retro_cpor_364,
Mus musculus	ENSMUSG00000004642	1 retrocopy	retro_mmus_1169,
Otolemur garnettii	ENSOGAG00000009750	1 retrocopy	retro_ogar_1463,
Pteropus vampyrus	ENSPVAG00000002807	2 retrocopies	retro_pvam_490, retro_pvam_941 ,
Rattus norvegicus	ENSRNOG00000037162	2 retrocopies	retro_rnor_1864, retro_rnor_2016,
Tarsius syrichta	ENSTSYG00000000376	2 retrocopies	retro_tsyr_1595, retro_tsyr_482,
Tursiops truncatus	ENSTTRG00000010901	1 retrocopy	retro_ttru_10,