RetrogeneDB ID: retro_pvam_1260

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_51363:152..931(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EMC3
• Ensembl ID: ENSPVAG00000012615
• Aliases: None
• Description: ER membrane protein complex subunit 3 [Source:HGNC Symbol;Acc:23999]

Sequence

>retro_pvam_1260
GTGGCAGGTCCCGAGCTGCTGCCTGACTCCAAAATATGCCTCTGGGTGGTCCTGCCCATCGTCATCATCACTTTCTCCTT
GAGTGTGATCTGCCACCACATGTCCATCCTGCTGCAGAGTGACAAGAAGCTTACCCAGGAGCAAGTCTCCCACAGTCAAG
TCTTAATTCGAAGCAGAGTCCTCAGGGAAAATGGAAAATACATTCCCAAACAGTCTTTCTTGATACAAAAATATTACTTC
AACAACCCAGAGAATGGGCTTTTCAAAAAAATTAGAAGGAAAGTAGTGCCTTCTCCTGTGACTGATCCCACTATGCCCAC
AGGCATGATGAAAGGCAGTGTAACAAATGTTCTCCCTATGATTCTTATTGGTGGATGGATCAACATGATATTCTCAGGCT
TTGTCACAACCAAGGTCTCATTTCCACTGACCCTCCATTTTAAGCCTGTGCTACCGCAAGGAATCAAACTACTCACATTA
GATGCATCCTGGGTGAGTTCTCCATTCTAACACTTCCTCAATGTCTTTGAGCTTTGGAGCACTTACTCTTTGATTCTGGG
TCAAGATAATGCCACTGACCAGTCACAGATGATACAGGAACAGATGACTGGAGCAGCCATGGCCATCGCCAGAGACACCA
ACAAAGCTTTTAAGCAGAGTGAGAAGCTTTGGAGCTGACAGATCACCAGTGAGCACTAGATGATGTCAAAGAGGAACTCA
TGGCCAAAGACCTCCACCCTGAAGGCACGTTCAAAAAGAAATTACAGACCTCTATGTTT

Alignment

ORF - retro_pvam_1260 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.53 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGPELLLDSNIRLWVVLPIVIITFFVGMIRHYVSILLQSDKKLTQEQVSDSQVLIRSRVLRENGKYIPK
          .AGPELL.DS.I.LWVVLPIVIITF....I.H..SILLQSDKKLTQEQVS.SQVLIRSRVLRENGKYIPK
Retrocopy VAGPELLPDSKICLWVVLPIVIITFSLSVICHHMSILLQSDKKLTQEQVSHSQVLIRSRVLRENGKYIPK

Parental  QSFLTRKYYFNNPEDGFFKKTKRKVVPPSPMTDPTMLTDMMKGNVTNVLPMILIGGWINMTFSGFVTTKV
          QSFL..KYYFNNPE.G.FKK..RKVVP.SP.TDPTM.T.MMKG.VTNVLPMILIGGWINM.FSGFVTTKV
Retrocopy QSFLIQKYYFNNPENGLFKKIRRKVVP-SPVTDPTMPTGMMKGSVTNVLPMILIGGWINMIFSGFVTTKV

Parental  PFPLTLRFKPMLQQGIELLTLDASWVSSASWYFLNVFGLRSIYSLILGQDNAADQSRMMQEQMTGAAMAM
          .FPLTL.FKP.L.QGI.LLTLDASWVSS....FLNVF.L.S.YSLILGQDNA.DQS.M.QEQMTGAAMA.
Retrocopy SFPLTLHFKPVLPQGIKLLTLDASWVSSPF*HFLNVFELWSTYSLILGQDNATDQSQMIQEQMTGAAMAI

Parental  PADTNKAFK-TEWEALELTDHQWALDDVEEELMAKDLHFEGMFKKELQTSIF
          ..DTNKAFK..E.EALELTDHQ.ALDDV.EELMAKDLH.EG.FKK.LQTS.F
Retrocopy ARDTNKAFK<AE*EALELTDHQ*ALDDVKEELMAKDLHPEGTFKKKLQTSMF

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_1260 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005202	1 retrocopy	retro_cfam_730,
Callithrix jacchus	ENSCJAG00000037305	1 retrocopy	retro_cjac_3209,
Equus caballus	ENSECAG00000024410	1 retrocopy	retro_ecab_737,
Felis catus	ENSFCAG00000024898	2 retrocopies	retro_fcat_1932, retro_fcat_2002,
Microcebus murinus	ENSMICG00000002333	2 retrocopies	retro_mmur_439, retro_mmur_707,
Mustela putorius furo	ENSMPUG00000017149	1 retrocopy	retro_mputfur_456,
Pteropus vampyrus	ENSPVAG00000012615	3 retrocopies	retro_pvam_1260 , retro_pvam_1278, retro_pvam_1439,
Tursiops truncatus	ENSTTRG00000007554	2 retrocopies	retro_ttru_1311, retro_ttru_285,
Vicugna pacos	ENSVPAG00000003247	2 retrocopies	retro_vpac_308, retro_vpac_461,