RetrogeneDB ID: retro_pvam_620

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_4070:56870..57254(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPVAG00000004362
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SEC11C
• Ensembl ID: ENSPVAG00000002950
• Aliases: None
• Description: SEC11 homolog C (S. cerevisiae) [Source:HGNC Symbol;Acc:23400]

Sequence

>retro_pvam_620
GTATTGGCCAATACTCAGGTAGAGCCAGTGTTTCATAGAGGAGACCTGTTCCTAACAATTTCTGGGAAGACCTTACTGGA
GGTGGTGAAGTAGTTGTTTTTAAAGTTGAAGGACTAGATATTACAATAGTTCACAGAGTAATCAAACTTCATGAAAATGA
TGATGAAGACATCAAATTTCTAACTGAAAGAGACAATAATGAAGATGATGATAGAAGCTTGTACAAAGAAAGCCTGAACT
GGCTCAAAAGGAACAGAGTGGGAAGAGCCCGAAGGTTTTTACTATATGTTGGTATCAGTCACCATGATAATGACTGACTA
CTCAAAATTCAAGTATGCACTCTTGGCTGTAATGAGTGCGTATGTGTTACTTAAACATGAATCC

Alignment

ORF - retro_pvam_620 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.7 %
• Parental protein coverage: 67.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VVLSGSMEPAFHRGDLLFLT-NFREDPIRAGEIVVFKVEGRDIPIVHRVIKVHEKDNGDIKFLTKGDNNE
          V......EP.FHRGDL.FLT.NF.ED....GE.VVFKVEG.DI.IVHRVIK.HE.D..DIKFLT..DNNE
Retrocopy VLANTQVEPVFHRGDL-FLT<NFWEDLTGGGEVVVFKVEGLDITIVHRVIKLHENDDEDIKFLTERDNNE

Parental  VDDRGLYKEGQNWLEKKDVVGRARGFLPYVGM-VTIIMNDYPKFKYALLAVMGAYVLLKRES
          .DDR.LYKE..NWL.K...VGRAR.FL.YVG..VT.IM.DY.KFKYALLAVM.AYVLLK.ES
Retrocopy DDDRSLYKESLNWL-KRNRVGRARRFLLYVGI>VTMIMTDYSKFKYALLAVMSAYVLLKHES

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_620 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 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000017024	3 retrocopies	retro_ecab_1009, retro_ecab_455, retro_ecab_989,
Echinops telfairi	ENSETEG00000005115	2 retrocopies	retro_etel_1081, retro_etel_1139,
Felis catus	ENSFCAG00000006501	1 retrocopy	retro_fcat_1815,
Microcebus murinus	ENSMICG00000016052	1 retrocopy	retro_mmur_271,
Monodelphis domestica	ENSMODG00000020427	2 retrocopies	retro_mdom_1517, retro_mdom_377,
Oryctolagus cuniculus	ENSOCUG00000009204	2 retrocopies	retro_ocun_738, retro_ocun_895,
Otolemur garnettii	ENSOGAG00000002570	1 retrocopy	retro_ogar_400,
Pteropus vampyrus	ENSPVAG00000002950	2 retrocopies	retro_pvam_620 , retro_pvam_869,
Sus scrofa	ENSSSCG00000004912	1 retrocopy	retro_sscr_775,
Tupaia belangeri	ENSTBEG00000014804	1 retrocopy	retro_tbel_2357,
Tursiops truncatus	ENSTTRG00000007676	5 retrocopies	retro_ttru_1278, retro_ttru_1508, retro_ttru_1780, retro_ttru_1916, retro_ttru_490,