RetrogeneDB ID: retro_pvam_802

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_1186:201854..202606(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPVAG00000009937
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SPR
• Ensembl ID: ENSPVAG00000016383
• Aliases: None
• Description: sepiapterin reductase (7,8-dihydrobiopterin:NADP+ oxidoreductase) [Source:HGNC Symbol;Acc:11257]

Sequence

>retro_pvam_802
GTGTGTGTGCTTACCAAGGCCTCCCACGGCTTCAGCTTGGCACTGGCCCTGCTCCTGACCCTGCCTTTCTTCCCTGGCTC
CATGCTGGTCCTAAACGCCCTCAATGATGAGGTGCTGCAGCAGCTGGAGGCTGAGCTGGGCGCGCAGATGGCCCAGCCTA
CGTGTGGTGCGGGTGCCCGCTGACCTGGGCACCAAGGCTGGCTTACAGCGGCTTCTCGGCCACCTGCGCGAGCTCCCCAG
GCCAGAGAGCCTGCAGCAAAAGCTGCTGATCAACAACGCAGGCGCTCTTGGAGATGTGTCCAGAGGCTTTGTGGACCTAG
CTGATCCAGCTGAAATGAATAGCTGCTGGGCTCTGAACTTGACCTCTGTGCTCTGCGTGACTTCCAGCATCCTGAAGGCC
TTCCCAGGCAGTCCTGGCCTCAGCAGGACAGTGGTTAACATCTCATCCCTCCATGCTCTGCATCACTTCAAGGGCTGGAC
ACTGCACTGTGCAGGGAAGGCTGCCAGTAACATGATGTTCCAAATCCTAGCCACAGAGGAACCTAGTGTGAGGGTACTGA
GCTATGCCCAGGACCCTGGACACAGACATGAAGCAGTTGGCCCAGGAGACCTCCATGGTCTCAGACATGCAAAAAAGTCC
GCAGGAGATGAAGACAAAGGGAGAACTGGTGGATTGTAAGATGTCAGCCCAGAAACTGGTAAGCCTGTTACAAAAGGACA
TGTTCAAGTCCGGAGCCCATGCTGACTTCTAT

Alignment

ORF - retro_pvam_802 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.53 %
• Parental protein coverage: 96.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VCVLTGASRGFGRALALLLAPLLSPGSMLVLNARNDESLQQLEAELGAGQ-PGLRVVRVPADLGSEAGLQ
          VCVLT.AS.GF..ALALLL.....PGSMLVLNA.NDE.LQQLEAELGA...P.LRVVRVPADLG..AGLQ
Retrocopy VCVLTKASHGFSLALALLLTLPFFPGSMLVLNALNDEVLQQLEAELGAQM>PSLRVVRVPADLGTKAGLQ

Parental  RLLGALRELPRPDGLQRVLLINNAGTL--VSKGFVDLADPDEMNSYWALNLTSMLCLTSSILKAFPDSPG
          RLLG.LRELPRP..LQ..LLINNAG.L..VS.GFVDLADP.EMNS.WALNLTS.LC.TSSILKAFP.SPG
Retrocopy RLLGHLRELPRPESLQQKLLINNAGALGDVSRGFVDLADPAEMNSCWALNLTSVLCVTSSILKAFPGSPG

Parental  LSRTVVNISSLCALQPFKGWTLYCAGKAARNMMFQVLATEEPSVRVLSYA-PGP-LDTDMQQLARETSVD
          LSRTVVNISSL.AL..FKGWTL.CAGKAA.NMMFQ.LATEEPSVRVLSYA.PGP.LDTDM.QLA.ETS..
Retrocopy LSRTVVNISSLHALHHFKGWTLHCAGKAASNMMFQILATEEPSVRVLSYA<PGP<LDTDMKQLAQETSMV

Parental  PDMRKSLQEMKTKGKLVDCKISAQKLLSLLQKDVFKSGVHVDFY
          .DM.KS.QEMKTKG.LVDCK.SAQKL.SLLQKD.FKSG.H.DFY
Retrocopy SDMQKSPQEMKTKGELVDCKMSAQKLVSLLQKDMFKSGAHADFY

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_802 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000012959	1 retrocopy	retro_ogar_2301,
Pelodiscus sinensis	ENSPSIG00000013998	1 retrocopy	retro_psin_10,
Pteropus vampyrus	ENSPVAG00000016383	1 retrocopy	retro_pvam_802 ,
Sus scrofa	ENSSSCG00000008309	1 retrocopy	retro_sscr_410,