RetrogeneDB ID: retro_pvam_1022

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_2305:120932..121378(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NOL12
• Ensembl ID: ENSPVAG00000010097
• Aliases: None
• Description: nucleolar protein 12 [Source:HGNC Symbol;Acc:28585]

Sequence

>retro_pvam_1022
TACTCAGCACACCTGAAGATGCTGGCAGAGAGAGAGGAGGTGCTGGAGGCGCAGATGAGCTGGACTGGCTGGTGACAGGA
CAGACTGAGTGGGTGCAATATGACCACTCCAGCCTCACAGTCACAACGTCACCAGCAGCAGCCTGGAGCTCTCGGGGGCC
TGGCTACTGGGACTGCCACTACCTGAAAAAGCGGTTGGGCACTTGTCCAGGAGGTGTCACCCAGAGAGGCCGAGAAAAGT
CTTGCCTAGGAAGTCCAGAGATTCCTGCTATCCTAATGGATATTTTTCTTTACTGCATAAGCATCGCCACCCACGCAGTC
GCAAAAAAGTCAAGAAGAAACATCCCGAAAGGTCTCGGGACTTCACCAAGAAGCCCTTAAGTGTCATTCGTAACCAACAA
GATCCAGTGCTGCCGGATGACAGCCAAAGCCCGGCACAGAAGACAG

Alignment

ORF - retro_pvam_1022 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.6 %
• Parental protein coverage: 70.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  HQEYLKMLAEREEALEE-ADELDRLVTAKTESVQYDHPNHTVTVT-TISDLDLSGARLLGLLPPEQEAGY
          ....LKMLAEREE.LE..ADELD.LVT..TE.VQYDH...TVT...T.S.L.LSGA.LLGL..PE...G.
Retrocopy YSAHLKMLAEREEVLEA<ADELDWLVTGQTEWVQYDHSSLTVTTS<TSSSLELSGAWLLGLPLPEKAVGH

Parental  GSEEEASSMEKPTKALPRKSRDPLLSQRISSLTAS-LHAHSRKKVKRKHPRHAQDSTKKPPSATR-TSKT
          .S.......E.P.K.LPRKSRD........SL.....H..SRKKVK.KHP....D.TKKP.S..R.T.K.
Retrocopy LSRR--CHPERPRKVLPRKSRDSCYPNGYFSLLHKHRHPRSRKKVKKKHPERSRDFTKKPLSVIR>TNKI

Parental  QRRRLTGKSQHNRE
          Q..R.T.K..H.R.
Retrocopy QCCRMTAKARHRRQ

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_1022 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010139	1 retrocopy	retro_amel_672,
Callithrix jacchus	ENSCJAG00000012487	1 retrocopy	retro_cjac_538,
Equus caballus	ENSECAG00000011050	1 retrocopy	retro_ecab_126,
Felis catus	ENSFCAG00000004273	1 retrocopy	retro_fcat_757,
Oryctolagus cuniculus	ENSOCUG00000017013	1 retrocopy	retro_ocun_1698,
Otolemur garnettii	ENSOGAG00000008255	1 retrocopy	retro_ogar_2914,
Pteropus vampyrus	ENSPVAG00000010097	1 retrocopy	retro_pvam_1022 ,
Tupaia belangeri	ENSTBEG00000009745	1 retrocopy	retro_tbel_3215,
Tursiops truncatus	ENSTTRG00000004799	1 retrocopy	retro_ttru_1165,