RetrogeneDB ID: retro_pvam_415

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3013:166597..167481(+)
• Located in intron of: ENSPVAG00000013236

Retrocopy information

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

Parental gene information

• Parental gene symbol: FBLIM1
• Ensembl ID: ENSPVAG00000009000
• Aliases: None
• Description: filamin binding LIM protein 1 [Source:HGNC Symbol;Acc:24686]

Sequence

>retro_pvam_415
GGGGGATGCTCTCTTCCTCCTACCCTGGATGGTGAGGACCCGCTCCCGGACCTGGACCTCCTTCCACCTCCGCCGGCAAC
CCCACCAGCGTACCTGCCGCCGCCTTCTGATGACGAGCCCCCTGCCTCAATGGGGGCGCAATTCATTTCGGACTTGGAGC
AGCTGCGTCTGCGCTCACCCCCGCCCCCACCACAGCCCCTGGTGGAGGGCCCTCAATTCAAGCCTCAGCTGAATAGTCAG
GGACCTGCAAAGGAGGAGCTGCTGCCTGCCCCAGAAGAGCCTGTTGGCTTCCCTAAGAAAGAGGCATCCACAGACGTTGG
TGTCTTCTGCCGCAAGACTGTGCCCCTCCGAGCGCTGGCCATGGAAGCCGTGAATAGACAGTACCACGCCTAGTGCTTCA
CGTGCTGCAACTGCTGCCGCCAGCCGGTGGGGCAGAGCTTCTACCAGAAGGATGGGTGGCCCCTCTGCGAACCCTACTAC
CGCGACACCCTGGAGAAGTGTGGCAAGTGTGGTGAGGTGGTCCGGGAACACATCATCAGGGCCCTGGGCGGAGCTTTCAC
CCAGCCTGTTTCATGAGTGTGATCTGTTCCCATTGCATCAGGAAGGAGAACCTTGCCCTGGACAGCCAGAATGAGGTGTA
CTACCTAGAGGACTTCTGTAGGAAATTTGTTGCTCCTATGTGCCATATATGTGAGAGTCCCATCATCCCCCAAGATGGGA
CGGATGCCTTCATAATTAAGTGCATGCGAAGAAACTTGCATAAAAATTGTTATAGGTGCGAGGACTGTAGGATCCTCCTC
TCTGTGAAGCCTGCGGACCAAGGCTGCTACCTCCTGAACAAACATCTCTTCTGCAAGCCAAGCCACATGAAGCGGAGTGC
CTCT

Alignment

ORF - retro_pvam_415 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.71 %
• Parental protein coverage: 77.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GGCSLPPPALDGEDALPDLDLLPPPPPPPPAYLPP-CDDQPPASMGASLISDLEQLHL--PPPPPQSLAE
          GGCSLPP..LDGED.LPDLDLLPPPP..PPAYLPP..DD.PPASMGA..ISDLEQL.L..PPPPPQ.L.E
Retrocopy GGCSLPP-TLDGEDPLPDLDLLPPPPATPPAYLPPPSDDEPPASMGAQFISDLEQLRLRSPPPPPQPLVE

Parental  GAPFQPQPGHLRPAEEKLPPPPAEPVGLPEREASTDICAFCHKTVSPRELAVEAMKRQYHAQCFTCRTCR
          G..F.PQ.....PA.E.L.P.P.EPVG.P..EASTD...FC.KTV..R.LA.EA..RQYHA.CFTC..C.
Retrocopy GPQFKPQLNSQGPAKEELLPAPEEPVGFPKKEASTDVGVFCRKTVPLRALAMEAVNRQYHA*CFTCCNCC

Parental  RQLAGQSFYQKDGRPLCEPCYQDTLEKCGKCGGVVQEHIIRAL-GRAFHPACFTCVTCARCIGDESFALD
          RQ..GQSFYQKDG.PLCEP.Y.DTLEKCGKCG.VV.EHIIRAL.GR.FHPACF..V.C..CI..E..ALD
Retrocopy RQPVGQSFYQKDGWPLCEPYYRDTLEKCGKCGEVVREHIIRAL<GRSFHPACFMSVICSHCIRKENLALD

Parental  NQNEVYCLDDFYRKF-APVCSICENPIIPRDGKDAFKIECMGRNFHENCYRCEDCRILLSVEPTDQGCYP
          .QNEVY.L.DF.RKF.AP.C.ICE.PIIP.DG.DAF.I.CM.RN.H.NCYRCEDCRILLSV.P.DQGCY.
Retrocopy SQNEVYYLEDFCRKFVAPMCHICESPIIPQDGTDAFIIKCMRRNLHKNCYRCEDCRILLSVKPADQGCYL

Parental  LDNRLFCKPCHVKRSAA
          L...LFCKP.H.KRSA.
Retrocopy LNKHLFCKPSHMKRSAS

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_415 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 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018725	1 retrocopy	retro_btau_1013,
Homo sapiens	ENSG00000162458	2 retrocopies	retro_hsap_4898, retro_hsap_778,
Gorilla gorilla	ENSGGOG00000015190	2 retrocopies	retro_ggor_3058, retro_ggor_645,
Macaca mulatta	ENSMMUG00000032243	2 retrocopies	retro_mmul_1095, retro_mmul_2635,
Nomascus leucogenys	ENSNLEG00000007650	2 retrocopies	retro_nleu_1265, retro_nleu_2840,
Pongo abelii	ENSPPYG00000001837	2 retrocopies	retro_pabe_3809, retro_pabe_751,
Pan troglodytes	ENSPTRG00000000208	2 retrocopies	retro_ptro_3266, retro_ptro_544,
Pteropus vampyrus	ENSPVAG00000009000	1 retrocopy	retro_pvam_415 ,