RetrogeneDB ID: retro_pvam_1420

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_82500:341..777(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2N
• Ensembl ID: ENSPVAG00000013734
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2N [Source:HGNC Symbol;Acc:12492]

Sequence

>retro_pvam_1420
AGGATTATCAAGGAAACCCAGTGTTTGCTGGCAGAACCAGTTCCCAGAATTCAAGCAGAACCAGACGAGAACAACGCACA
TTATTTTCCTGTGGTCATTGCTGGTCCCCATGATTCCCCCTTTGAGGGAGAGACTTTTAAACTTGAACTATTCCTTTGAG
AAGAATACCTGATGACAACCCCTAAAGTACATTTCATGACCAAAATCTTTCATCCTAATGTAGGCAAGCTGGGAAGACTA
TGTTTAGATATTTTGAAAGATCAGTGGTCCCCAGCACTGCAGATCCGCACAGTTCTGCTTTGATCCAGGTTTTGTTAAGT
GCTCCCAATCCAGATGATCCATTAGCAAATGATGTAGCTGAGCAGTGGAAGACCTACAAAGTCCAAGTCAAAGAAACAGC
TACAACATGGACTAGGCTCATGCCATGAATAATATT

Alignment

ORF - retro_pvam_1420 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.41 %
• Parental protein coverage: 96.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIY
          RIIKETQ.LLAEPVP.I.AEPDE.NA.YF.VVIAGP.DSPFEG.TFKLELFL.EEY.M..PKV.FMTKI.
Retrocopy RIIKETQCLLAEPVPRIQAEPDENNAHYFPVVIAGPHDSPFEGETFKLELFL*EEYLMTTPKVHFMTKIF

Parental  HPNVDKLGRICLDILKDKWSPALQIRTVLL-SIQALLSAPNPDDPLANDVAEQWKTNEAQAIETARAWTR
          HPNV.KLGR.CLDILKD.WSPALQIRTVLL..IQ.LLSAPNPDDPLANDVAEQWKT...Q..ETA..WTR
Retrocopy HPNVGKLGRLCLDILKDQWSPALQIRTVLL<LIQVLLSAPNPDDPLANDVAEQWKTYKVQVKETATTWTR

Parental  L-YAMNNI
          L..AMNNI
Retrocopy L<HAMNNI

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_1420 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 11 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006177	1 retrocopy	retro_cfam_196,
Cavia porcellus	ENSCPOG00000008581	5 retrocopies	retro_cpor_1548, retro_cpor_230, retro_cpor_24, retro_cpor_655, retro_cpor_750,
Gorilla gorilla	ENSGGOG00000024332	4 retrocopies	retro_ggor_1079, retro_ggor_2140, retro_ggor_2720, retro_ggor_2969,
Loxodonta africana	ENSLAFG00000028985	1 retrocopy	retro_lafr_57,
Macropus eugenii	ENSMEUG00000002944	7 retrocopies	retro_meug_1236, retro_meug_1287, retro_meug_1453, retro_meug_1473, retro_meug_162, retro_meug_2009, retro_meug_31,
Macaca mulatta	ENSMMUG00000020634	3 retrocopies	retro_mmul_1587, retro_mmul_234, retro_mmul_72,
Monodelphis domestica	ENSMODG00000009451	2 retrocopies	retro_mdom_133, retro_mdom_1485,
Oryctolagus cuniculus	ENSOCUG00000011287	1 retrocopy	retro_ocun_100,
Pteropus vampyrus	ENSPVAG00000013734	2 retrocopies	retro_pvam_1420 , retro_pvam_358,
Sarcophilus harrisii	ENSSHAG00000007776	1 retrocopy	retro_shar_105,
Tarsius syrichta	ENSTSYG00000008800	5 retrocopies	retro_tsyr_1476, retro_tsyr_1754, retro_tsyr_207, retro_tsyr_348, retro_tsyr_5,