RetrogeneDB ID: retro_pvam_231

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2044:1163122..1163707(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPVAG00000005761
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FBL
• Ensembl ID: ENSPVAG00000010849
• Aliases: None
• Description: fibrillarin [Source:HGNC Symbol;Acc:3599]

Sequence

>retro_pvam_231
GCCGAGGGCGGCTCAAGCAAGAGATCCCGCACGTGGATCCCTTCCGCTCCCAAGCTGGCCCAGGTCATCCTTGGCCGGGG
TCGACCAGATCCACATCAAGCCCAAGTCCCAAATTGCCGTACCTTGGGTGCCCGCTTCGAGGACCTCCGTCTCCCACGTC
TCCGACATCATCGGGCCCGGACGGCCTGGTCTACGCGGTCGAGTTCTCCCACCGCGCCGGCCGCGATCTGGTCAACGTGA
GCCAAGAAGCGAACCAACATCATCCCGGTCCTGGAAGACGCCCGGCACCCGCTCAAATACCGCATGCTCATCGGGATGGT
GGACGTGATTTTCGCCGACGTGGCCCAGCCGGACCAGTCCCGCATCGTGGCCCTGAACGCCCACACCTTCCTTCGCAACG
GGGGCCACTTCCTCATTTCCATCAAGGCCAACTGCATCGACTCCACTGCGTCTGCCGAGGCCGTGTTTGCTTCTGAGGTG
AGAAAGTTGCAGCAGGAGAACTTAAAGCCTCAAGAGCAACTGACCCTTGAGCCCTATGAGAGGGACCACGCCGTGGTCGT
GGGGGTCTACCGGCCCCTTCCCAAG

Alignment

ORF - retro_pvam_231 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.68 %
• Parental protein coverage: 60.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SEGDDKIEYRAWNPFRSKLAAAILG-GVDQIHIKPGAKVLYLGA-ASGTTVSHVSDIVGP-DGLVYAVEF
          .EG......R.W.P...KLA..ILG.GVDQIHIKP..........AS.T.VSHVSDI.GP.DGLVYAVEF
Retrocopy AEGGSSKRSRTWIPSAPKLAQVILG>GVDQIHIKPKSQIAVPWVPASRTSVSHVSDIIGP>DGLVYAVEF

Parental  SHRSGRDLINL-AKKRTNIIPVIEDARHPHKYRMLIAMVDVIFADVAQPDQTRIVALNAHTFLRNGGHFM
          SHR.GRDL.N..AKKRTNIIPV.EDARHP.KYRMLI.MVDVIFADVAQPDQ.RIVALNAHTFLRNGGHF.
Retrocopy SHRAGRDLVNV>AKKRTNIIPVLEDARHPLKYRMLIGMVDVIFADVAQPDQSRIVALNAHTFLRNGGHFL

Parental  ISIKANCIDSTASAEAVFASEVKKMQQENMKPQEQLTLEPYERDHAVVVGVYRPPPK
          ISIKANCIDSTASAEAVFASEV.K.QQEN.KPQEQLTLEPYERDHAVVVGVYRP.PK
Retrocopy ISIKANCIDSTASAEAVFASEVRKLQQENLKPQEQLTLEPYERDHAVVVGVYRPLPK

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_231 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 13 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002579	1 retrocopy	retro_btau_108,
Canis familiaris	ENSCAFG00000005412	1 retrocopy	retro_cfam_1697,
Homo sapiens	ENSG00000105202	1 retrocopy	retro_hsap_99,
Macropus eugenii	ENSMEUG00000014684	1 retrocopy	retro_meug_1077,
Microcebus murinus	ENSMICG00000007686	1 retrocopy	retro_mmur_1127,
Mus musculus	ENSMUSG00000046865	4 retrocopies	retro_mmus_1141, retro_mmus_1585, retro_mmus_1609, retro_mmus_89,
Nomascus leucogenys	ENSNLEG00000014234	1 retrocopy	retro_nleu_1947,
Otolemur garnettii	ENSOGAG00000006463	2 retrocopies	retro_ogar_3102, retro_ogar_504,
Pan troglodytes	ENSPTRG00000010982	2 retrocopies	retro_ptro_2208, retro_ptro_3074,
Pteropus vampyrus	ENSPVAG00000010849	1 retrocopy	retro_pvam_231 ,
Rattus norvegicus	ENSRNOG00000019229	4 retrocopies	retro_rnor_1082, retro_rnor_1780, retro_rnor_643, retro_rnor_75,
Sus scrofa	ENSSSCG00000030510	1 retrocopy	retro_sscr_39,
Tupaia belangeri	ENSTBEG00000007755	2 retrocopies	retro_tbel_3774, retro_tbel_3974,