RetrogeneDB ID: retro_pvam_184

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1767:13563..14207(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MEMO1
• Ensembl ID: ENSPVAG00000011427
• Aliases: None
• Description: mediator of cell motility 1 [Source:HGNC Symbol;Acc:14014]

Sequence

>retro_pvam_184
CTTGGGCCTTCTCATCATGTGCACCTCTCTCCATGTGCGCTTTCCAGAGTGGATATATATAGGACACCTCTGTATGACCT
TGGTTTTGACCAAGAGATTTACAGAGAACTATGGAAGACAGGGATGTTTGAATGCATGTCTCTGCAGACAGATGAAGATC
AGCACAGTATTGAAATGCATTTGCCTTATACAGCTAAAGCCATGGAAAGCCATAAGGATGAGTTTACCATTATTCTTATA
TTGGGTGGAGCTCTGAATGAGTCAAAAGAACAAGAATTCAGAAAACTCTTCAGTAAATATTTAGCGGATCCTAGTAATCT
CTTTGTGGTTTCTTCTGATTTCTGGCATTAGGGCCAAAGGTTCTATTACAGTTACTATGATGAATCTCAGGGGGAGATTT
ATAGATCCATTGAACATCTAGATAAAATAGGCATGAATATTATAGAACAATTAGACCCTGTATCTTTCAGCAATTACTTG
AAGAAATACCATAATGCTATATGTGGAAGACATCCCATTGAGTATTATTAAATGCTATCACAGAGCTCCAGAAGAATGGA
ATGAATATGAGCTTTTCTTTTTTGAATTATTCCCAGTTGAGGCAGTGTAGAAACTGGCAAGACAGTTCAGTGAGTTATGC
AGCT

Alignment

ORF - retro_pvam_184 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.43 %
• Parental protein coverage: 88.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LGPSHHVPLSRCALSSVDIYRTPLYDLRIDQKIYGELWKTGMFERMSLQTDEDEHSIEMHLPYTAKAMES
          LGPSHHV.LS.CALS.VDIYRTPLYDL..DQ.IY.ELWKTGMFE.MSLQTDED.HSIEMHLPYTAKAMES
Retrocopy LGPSHHVHLSPCALSRVDIYRTPLYDLGFDQEIYRELWKTGMFECMSLQTDEDQHSIEMHLPYTAKAMES

Parental  HKDEFTIIPVLVGALSESKEQEFGKLFSKYLADPSNLFVVSSDFCHWGQRFRYSYYDESQGEIYRSIEHL
          HKDEFTII..L.GAL.ESKEQEF.KLFSKYLADPSNLFVVSSDF.H.GQRF.YSYYDESQGEIYRSIEHL
Retrocopy HKDEFTIILILGGALNESKEQEFRKLFSKYLADPSNLFVVSSDFWH*GQRFYYSYYDESQGEIYRSIEHL

Parental  DKMGMSIIEQLDPVSFSNYLKKYHNTICGRHPIG-VLLNAITELQKNGMNMSFSFLNYAQSSQCRNWQDS
          DK.GM.IIEQLDPVSFSNYLKKYHN.ICGRHPI..VLLNAITELQKNGMNMSFSFLNY.Q..QCRNWQDS
Retrocopy DKIGMNIIEQLDPVSFSNYLKKYHNAICGRHPIE<VLLNAITELQKNGMNMSFSFLNYSQLRQCRNWQDS

Parental  SVSYAA
          SVSYAA
Retrocopy SVSYAA

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_184 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012339	2 retrocopies	retro_chof_2257, retro_chof_2552,
Cavia porcellus	ENSCPOG00000012278	1 retrocopy	retro_cpor_1159,
Dasypus novemcinctus	ENSDNOG00000001254	1 retrocopy	retro_dnov_253,
Oryctolagus cuniculus	ENSOCUG00000005878	3 retrocopies	retro_ocun_1441, retro_ocun_1663, retro_ocun_928,
Pteropus vampyrus	ENSPVAG00000011427	1 retrocopy	retro_pvam_184 ,