RetrogeneDB ID: retro_pvam_1455

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_91108:40..318(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP4S1
• Ensembl ID: ENSPVAG00000017161
• Aliases: None
• Description: adaptor-related protein complex 4, sigma 1 subunit [Source:HGNC Symbol;Acc:575]

Sequence

>retro_pvam_1455
AAAGTCATGAAGAGCAATCTCCCTTGATCCAATGATCGACGCTCTTTCACTGAATGTAGGGACTTTAAGCTGATGTGTCG
GAAATACGCCAGCTCCCTTCACTGTGGCCGGAGTTGATGACACTGAGAATGAGATGGTGATTTATGAATTCGTCCATAAC
TCTTGTCAAGTTGTAGACAACAACTTCAGCCAGGTGAGTGAATTAAATGGTTAATTTAGGTAAAGTACACATATTTTGGA
TGAGATGGTGTTATATGGCTGCACTGTGGCAACGACCT

Alignment

ORF - retro_pvam_1455 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.58 %
• Parental protein coverage: 58.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EVIKSCLSRSNEQCSFIEYKDFKLVYRQYA-ALFIVVGVNDTENEMAIYEFIHNFVEVLDEYFSRVSELD
          .V.KS.L..SN...SF.E..DFKL..R.YA.A.F.V.GV.DTENEM.IYEF.HN...V.D..FS.VSEL.
Retrocopy KVMKSNLP*SNDRRSFTECRDFKLMCRKYA>APFTVAGVDDTENEMVIYEFVHNSCQVVDNNFSQVSELN

Parental  -VSFNAVSQVFRSTWQTQASLDQEP
          .V....V...F...W...A.L.Q.P
Retrocopy >VNLGKV-HIFWMRWCYMAALWQRP

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_1455 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 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013301	4 retrocopies	retro_chof_2345, retro_chof_2677, retro_chof_393, retro_chof_820,
Dipodomys ordii	ENSDORG00000009468	1 retrocopy	retro_dord_595,
Erinaceus europaeus	ENSEEUG00000013009	1 retrocopy	retro_eeur_301,
Homo sapiens	ENSG00000100478	1 retrocopy	retro_hsap_3496,
Gorilla gorilla	ENSGGOG00000003198	1 retrocopy	retro_ggor_2363,
Macaca mulatta	ENSMMUG00000003123	1 retrocopy	retro_mmul_17,
Monodelphis domestica	ENSMODG00000017579	1 retrocopy	retro_mdom_1774,
Nomascus leucogenys	ENSNLEG00000015901	1 retrocopy	retro_nleu_788,
Ornithorhynchus anatinus	ENSOANG00000014031	1 retrocopy	retro_oana_60,
Pongo abelii	ENSPPYG00000005723	1 retrocopy	retro_pabe_2889,
Pan troglodytes	ENSPTRG00000006239	1 retrocopy	retro_ptro_2368,
Pteropus vampyrus	ENSPVAG00000010218	1 retrocopy	retro_pvam_783,
Pteropus vampyrus	ENSPVAG00000017161	1 retrocopy	retro_pvam_1455 ,
Ictidomys tridecemlineatus	ENSSTOG00000010759	1 retrocopy	retro_itri_1050,