RetrogeneDB ID: retro_pvam_670

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_643:58532..59208(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUCLG1
• Ensembl ID: ENSPVAG00000003656
• Aliases: None
• Description: succinate-CoA ligase, alpha subunit [Source:HGNC Symbol;Acc:11449]

Sequence

>retro_pvam_670
GTCTTTGATACTATAAAGGAGGCCAAAGAACAGATAGGAGTGCCAGTTTTACTCATTTATATCTCTCCTCCTTTTGCTGC
TGCTGTCATTAAACTATTGAGGCAGAAGTGCCCTTGGTCAGGGGCATTGCTGAAGGTATCCCCACAACAGGACACAGTAT
GAGCCAAGCACACACTGCTGTTCAAGGGAAAGACAAGGCTGATCAGGCCAAAATGCCCTGGAGTCATCAATCGTGGAAAA
CGCAAAATTGGCATGCCTGGCCATATTCACACACAAAAAAATTGATATTGTGTCCAGATCTGGCACCCTGACTTATGAAG
CAGTTCACTAAAAAGCACAAGTCCGATGCGGGCAGTCTTTCTGCATTGGCATTGGAGGTGATCCTTTTAATGGAACAAAT
TTTATTGACTGCCTTGAAGTCTTTGTAAATGATCCAGCCATACAAGGCATCATATTGATTTGTGGAATTGGTGGTAATGC
AGAAGAAAATGCTGCAGAATTTTTGAAGCAACATAATTCAGGTCCCAAAGCCAAGCCTGTGGTGTCTTTTGTTGCTGGTC
TAATGGCCCCTTCATGTAGGAGAATGGGTCATGCAGGGGCAATTAGTGCTGGAGGAAAAGGTGGAGCTAAAGAAGTCTCT
GCCCTTCAGAGTGCAGAAGTGTTGTTACAAGTCTCC

Alignment

ORF - retro_pvam_670 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.12 %
• Parental protein coverage: 66.38 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VFNTVKEAKEQTGATASVIYVPPPFAAAAIDE-AVEAEVPLVVCITEGIP-QQDMVRVKHRLLRQGKTRL
          VF.T.KEAKEQ.G.....IY..PPFA.AA......EAEVPLV..I.EGIP.QQD.V..KH.LL..GKTRL
Retrocopy VFDTIKEAKEQIGVPVLLIYISPPFA-AAVIK<TIEAEVPLVRGIAEGIP>QQDTV*AKHTLLFKGKTRL

Parental  IGPNCPGVINPGECKIGI-MPGHIHKKGRIGIVSRSGTLTYEAVHQTTQVGLGQSLCIGIGGDPFNGTDF
          I.P.CPGVIN.G..KIG.......HKK..I.IVSRSGTLTYEAVH...QV..GQS.CIGIGGDPFNGT.F
Retrocopy IRPKCPGVINRGKRKIGM>LAIFTHKK--IDIVSRSGTLTYEAVH*KAQVRCGQSFCIGIGGDPFNGTNF

Parental  IDCLEVFLNDPATEGIILIGEIGGNAEENAAEFLKQHNSGPKAKPVVSFIAGLTAPPGRRMGHAGAIIAG
          IDCLEVF.NDPA..GIILI..IGGNAEENAAEFLKQHNSGPKAKPVVSF.AGL.AP..RRMGHAGAI.AG
Retrocopy IDCLEVFVNDPAIQGIILICGIGGNAEENAAEFLKQHNSGPKAKPVVSFVAGLMAPSCRRMGHAGAISAG

Parental  GKGGAKEKISALQNAGVVVSMS
          GKGGAKE..SALQ.A.V....S
Retrocopy GKGGAKE-VSALQSAEVLLQVS

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_670 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003017	1 retrocopy	retro_cpor_1170,
Myotis lucifugus	ENSMLUG00000012370	1 retrocopy	retro_mluc_1231,
Procavia capensis	ENSPCAG00000013405	1 retrocopy	retro_pcap_356,
Pteropus vampyrus	ENSPVAG00000003656	2 retrocopies	retro_pvam_1160, retro_pvam_670 ,
Drosophila melanogaster	FBgn0004888	1 retrocopy	retro_dmel_47,