RetrogeneDB ID: retro_pvam_418

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3020:25559..26207(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GOT1
• Ensembl ID: ENSPVAG00000008890
• Aliases: None
• Description: glutamic-oxaloacetic transaminase 1, soluble [Source:HGNC Symbol;Acc:4432]

Sequence

>retro_pvam_418
ACTGGGACTGATGCAACTCCAGAGCAGTGGAGGGAGATTGCCTCCATCATGAAGTGCCGGTTTCTGTTCCCCTTCTTTAA
CTCAGCCTATCAGGGCTTTGCTTCTGGAGACCTAGAGAAAGATGCCTGGGCCATTCACTATTTTGTGTCTGAAGGATTCG
AGCTCTTCTGTGTCCAGTCCTTCTCCAAGAACTACGGGGTCTGCAGTGAACGAGTGGGGAGTCTGATCATTGTTGCAAAA
GAACCTGATAGCATCCTGTGTGTCCTTTCCCAGATGGAGAAGATCGTGTGAATTACCTGATCCAATCTCCCTGCTCAGGG
AGCATGAATGGTGGCCAATGTGCTCTCTAACCCTGAGCTCTTTAAGGAATGGACAGGTGATGTGAAGACAATGGTTGACT
GGATTCTGACCATGAGATCTGAATTCAGGGCATGAATAGAAGCCCTCAAAATGCCTGGAACCTGGAACCACATCACTAAA
CAAATTGGAATGTTCCATTTCACTGGGTTGAACCCCAAACAGGTTGAATATCTGATCAGAGAAAAGCACATTTATCTGCT
GCCAAGTAGTCTGATCGATATGTGTGGCTTAACCACCAAAAATCTAGATTATGTGGTCACCTCCATCCATGAAGCAGTCA
CCAAAATC

Alignment

ORF - retro_pvam_418 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.48 %
• Parental protein coverage: 52.3 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TGTDPTPEQWKEIASVMKRRFLFPFFDSAYQGFASGDLEKDAWAVRYFVSEGFELFCAQSFSKNFGLYNE
          TGTD.TPEQW.EIAS.MK.RFLFPFF.SAYQGFASGDLEKDAWA..YFVSEGFELFC.QSFSKN.G...E
Retrocopy TGTDATPEQWREIASIMKCRFLFPFFNSAYQGFASGDLEKDAWAIHYFVSEGFELFCVQSFSKNYGVCSE

Parental  RVGNLTVVAKEADSILRVLSQMEKIVRITWSNPPAQGARIVASTLSNPELFKEWIGNVKTMADRILAMRS
          RVG.L..VAKE.DSIL.VLSQMEKIV.IT.SN.PAQGA..VA..LSNPELFKEW.G.VKTM.D.IL.MRS
Retrocopy RVGSLIIVAKEPDSILCVLSQMEKIV*IT*SNLPAQGA*MVANVLSNPELFKEWTGDVKTMVDWILTMRS

Parental  ELRARLEALKTPGTWNHITEQIGMFSFTGLNPKQVEYLIREKHIYLLPSGRINMCGLTTKNLEYVATSIH
          E.RA..EALK.PGTWNHIT.QIGMF.FTGLNPKQVEYLIREKHIYLLPS..I.MCGLTTKNL.YV.TSIH
Retrocopy EFRA*IEALKMPGTWNHITKQIGMFHFTGLNPKQVEYLIREKHIYLLPSSLIDMCGLTTKNLDYVVTSIH

Parental  EAVTKI
          EAVTKI
Retrocopy EAVTKI

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_418 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000007333	1 retrocopy	retro_mluc_2538,
Mustela putorius furo	ENSMPUG00000016996	1 retrocopy	retro_mputfur_861,
Pteropus vampyrus	ENSPVAG00000008890	1 retrocopy	retro_pvam_418 ,