RetrogeneDB ID: retro_pvam_710

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_912:98626..99257(+)
• Located in intron of: ENSPVAG00000017188

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC35E3
• Ensembl ID: ENSPVAG00000002545
• Aliases: None
• Description: solute carrier family 35, member E3 [Source:HGNC Symbol;Acc:20864]

Sequence

>retro_pvam_710
TTGTACATCTCTGCCCCCCAAAGTCTGCCTCTTACCACGCTCCTCCTCTTGCTCCTGAGCTTCTGTGGCTTTGGTGGTCT
TCACCAACCTCTCTCTCTGTAGAACAGTGCCATAGGCACCTATCAGCTGGCCAAGGCCATGACCACCCCAGAGATTATAG
TCATCTAGACCCTCTGCTACAAGAAAGTCTTCTCTACCAAAATATAGTTCACGCTGATTCCTATAACTTTAGGTGTAATC
CTAAATTCTTATTACAATATGAAGCTTAATTTCCTTGGAATGGTGTTTGCTGCTCTTGGTGTTTTATTTTACACCCCTTT
ATCGAGTGTGGGTAAGAGCAAAACAGCTCTTAAATTACAAGTAAACTCAGTGCAGCTGCTGTGCTACCAGGCTCTGATGT
CATCTGCCATGTTGCTGGTCCCCGGTGCCCTTCATTGAGCCAGTTTTTGGAGAAGGAGGACTATTTGGTCCCTGGTCAGT
TTTTGCTTTGCTTATGGTTCTGCTATCTGGAGTAGTAGCTTTCATGGTGAATTTATCAATTTATTGGATCGTTGGAAACA
CTTCACCAGTCACCTATAACATGTTTGGACACTTCGAGTTCTGGATTATTTTATTTGGAATATATTTCATT

Alignment

ORF - retro_pvam_710 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.93 %
• Parental protein coverage: 59.43 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LDIFAPKSLPPSKLLLLALSFCGFV-VFTNLSLQNNTIGTYQLAKAMTTPVIIVIQTLCYKKTFSTKIQL
          L.I.AP.SLP...LLLL.LSFCGF......LSL.N..IGTYQLAKAMTTP.IIVI.TLCYKK.FSTKI..
Retrocopy LYISAPQSLPLTTLLLLLLSFCGFGGLHQPLSL*NSAIGTYQLAKAMTTPEIIVI*TLCYKKVFSTKI*F

Parental  TLIPITLGVILNSYYDVKFNFPGMVFAALGVLVTSPYQ-VWVGAKQHELQVNSMQLLYYQAPMSSAMLLV
          TLIPITLGVILNSYY..K.NF.GMVFAALGVL...P...V........LQVNS.QLL.YQA.MSSAMLLV
Retrocopy TLIPITLGVILNSYYNMKLNFLGMVFAALGVLFYTPLSSVGKSKTALKLQVNSVQLLCYQALMSSAMLLV

Parental  A-VPFFEPVFGEGGLFGPWSISALLMVLLSGVIAFMVNLSIYWIIGNTSPVTYNMFGHFKFCITLFGGYV
          ..VPF.EPVFGEGGLFGPWS..ALLMVLLSGV.AFMVNLSIYWI.GNTSPVTYNMFGHF.F.I.LFG.Y.
Retrocopy P>VPFIEPVFGEGGLFGPWSVFALLMVLLSGVVAFMVNLSIYWIVGNTSPVTYNMFGHFEFWIILFGIYF

Parental  L
          .
Retrocopy I

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_710 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031919	1 retrocopy	retro_btau_642,
Choloepus hoffmanni	ENSCHOG00000013347	1 retrocopy	retro_chof_2348,
Cavia porcellus	ENSCPOG00000004322	3 retrocopies	retro_cpor_1404, retro_cpor_1487, retro_cpor_339,
Homo sapiens	ENSG00000175782	1 retrocopy	retro_hsap_513,
Gorilla gorilla	ENSGGOG00000012605	1 retrocopy	retro_ggor_473,
Mus musculus	ENSMUSG00000060181	1 retrocopy	retro_mmus_287,
Pan troglodytes	ENSPTRG00000005201	1 retrocopy	retro_ptro_383,
Pteropus vampyrus	ENSPVAG00000002545	1 retrocopy	retro_pvam_710 ,