RetrogeneDB ID: retro_pvam_727

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_999:393993..394413(-)
• Located in intron of: ENSPVAG00000015208

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2L3
• Ensembl ID: ENSPVAG00000013575
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2L 3 [Source:HGNC Symbol;Acc:12488]

Sequence

>retro_pvam_727
GACATTCAAAAATGTGGAATGAAAAATTTCCATAACATCCAGGTTGATGAAGCTAATTTACTGACTTGGGAAAGGCTTAT
TGTTCCTGACAACCCTCCATATAAGAGGGACTTCAGAATTGAAATCAACTTTCCAGCAGAGTACCCACTCGAACTACTTA
AGATCACACTTAAAACAAAGATTTATCACCCAAACATCGATTAAAGGGGGCAGGTCTGTCTGCCAGTAATTAGTGCTGAA
AACTAGAAGCCAGCAACCAAAGCTGACCAAGTAATCCAGTTTTCCCTAGTACTGGTGAACAACCCCTAGGTGAGCACGCC
GTTTGGGCCAACCTAGCTGAAGAATACTTTAAGGGCCATTAAAAAATTCTGTAAGGACGCTGAAGAGCTTACAAAAAAAT
ATGGAGAAAAGTGACCTGTG

Alignment

ORF - retro_pvam_727 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.83 %
• Parental protein coverage: 97.24 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EIRKCGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINFPAEYPFKPPKITFKTKIYHPNIDEK
          .I.KCGMKNF.NIQVDEANLLTW..LIVPDNPPY.K..FRIEINFPAEYP....KIT.KTKIYHPNID..
Retrocopy DIQKCGMKNFHNIQVDEANLLTWERLIVPDNPPY-KRDFRIEINFPAEYPLELLKITLKTKIYHPNID*R

Parental  GQVCLPVISAENWKPATKTDQVIQSLIALVND-PQPEHPLRADLAEEYSKDR-KKFCKNAEEFTKKYGEK
          GQVCLPVISAEN.KPATK.DQVIQ....LVN..P..EH...A.LAEEY.K...KKFCK.AEE.TKKYGEK
Retrocopy GQVCLPVISAEN*KPATKADQVIQFSLVLVNN<PLGEHAVWANLAEEYFKGH>KKFCKDAEELTKKYGEK

Parental  RPV
          .PV
Retrocopy *PV

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_727 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 15 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000019274	1 retrocopy	retro_ecab_116,
Homo sapiens	ENSG00000185651	4 retrocopies	retro_hsap_1094, retro_hsap_1185, retro_hsap_1338, retro_hsap_1960,
Myotis lucifugus	ENSMLUG00000001547	1 retrocopy	retro_mluc_32,
Nomascus leucogenys	ENSNLEG00000000192	1 retrocopy	retro_nleu_97,
Oryctolagus cuniculus	ENSOCUG00000002610	3 retrocopies	retro_ocun_826, retro_ocun_932, retro_ocun_937,
Pongo abelii	ENSPPYG00000011602	1 retrocopy	retro_pabe_99,
Pan troglodytes	ENSPTRG00000014114	1 retrocopy	retro_ptro_123,
Pteropus vampyrus	ENSPVAG00000001773	1 retrocopy	retro_pvam_1451,
Pteropus vampyrus	ENSPVAG00000007394	2 retrocopies	retro_pvam_1139, retro_pvam_363,
Pteropus vampyrus	ENSPVAG00000013575	1 retrocopy	retro_pvam_727 ,
Pteropus vampyrus	ENSPVAG00000015438	1 retrocopy	retro_pvam_234,
Sorex araneus	ENSSARG00000005137	3 retrocopies	retro_sara_105, retro_sara_277, retro_sara_653,
Ictidomys tridecemlineatus	ENSSTOG00000016293	2 retrocopies	retro_itri_1528, retro_itri_655,
Tetraodon nigroviridis	ENSTNIG00000010600	1 retrocopy	retro_tnig_16,
Takifugu rubripes	ENSTRUG00000003392	1 retrocopy	retro_trub_39,