RetrogeneDB ID: retro_pvam_1439

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_87082:325..960(-)
• 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_1439
GTCTCCCACAGTCAAGTCTTAATTCGAAGCAGAGTCCTCAGGGAAAATGGAAAATACATTCCCAAACAGTCTTTCTTGAT
ACAAAAATATTACTTCAACAACCCAGAGAATGGGCTTTTCAAAAAAATTAGAAGGAAAGTAGTGCCTTCTCCTGTGACTG
ATCCCACTATGCCCACAGGCATGATGAAAGGCAGTGTAACAAATGTTCTCCCTATGATTCTTATTGGTGGATGGATCAAC
ATGATATTCTCAGGCTTTGTCACAACCAAGGTCTCATTTCCACTGACCCTCCATTTTAAGCCTGTGCTACCGCAAGGAAT
CAAACTACTCACATTAGATGCATCCTGGGTGAGTTCTCCATTCTAACACTTCCTCAATGTCTTTGAGCTTTGGAGCACTT
ACTCTTTGATTCTGGGTCAAGATAATGCCACTGACCAGTCACAGATGATACAGGAACAGATGACTGGAGCAGCCATGGCC
ATCGCCAGAGACACCAACAAAGCTTTTAAGCAGAGTGAGAAGCTTTGGAGCTGACAGATCACCAGTGAGCACTAGATGAT
GTCAAAGAGGAACTCATGGCCAAAGACCTCCACCCTGAAGGCACGTTCAAAAAGAAATTACAGACCTCTATGTTT

Alignment

ORF - retro_pvam_1439 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.31 %
• Parental protein coverage: 81.61 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VSDSQVLIRSRVLRENGKYIPKQSFLTRKYYFNNPEDGFFKKTKRKVVPPSPMTDPTMLTDMMKGNVTNV
          VS.SQVLIRSRVLRENGKYIPKQSFL..KYYFNNPE.G.FKK..RKVVP.SP.TDPTM.T.MMKG.VTNV
Retrocopy VSHSQVLIRSRVLRENGKYIPKQSFLIQKYYFNNPENGLFKKIRRKVVP-SPVTDPTMPTGMMKGSVTNV

Parental  LPMILIGGWINMTFSGFVTTKVPFPLTLRFKPMLQQGIELLTLDASWVSSASWYFLNVFGLRSIYSLILG
          LPMILIGGWINM.FSGFVTTKV.FPLTL.FKP.L.QGI.LLTLDASWVSS....FLNVF.L.S.YSLILG
Retrocopy LPMILIGGWINMIFSGFVTTKVSFPLTLHFKPVLPQGIKLLTLDASWVSSPF*HFLNVFELWSTYSLILG

Parental  QDNAADQSRMMQEQMTGAAMAMPADTNKAFK-TEWEALELTDHQWALDDVEEELMAKDLHFEGMFKKELQ
          QDNA.DQS.M.QEQMTGAAMA...DTNKAFK..E.EALELTDHQ.ALDDV.EELMAKDLH.EG.FKK.LQ
Retrocopy QDNATDQSQMIQEQMTGAAMAIARDTNKAFK<AE*EALELTDHQ*ALDDVKEELMAKDLHPEGTFKKKLQ

Parental  TSIF
          TS.F
Retrocopy TSMF

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_1439 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,