ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

...ctatgtagcacaggtcgggcttctctttgttgagtattggttatgtacgataattcttgcgtaaaggctattcaactgagattaggcattctgggtacagACAAGGACACTGAAAGGACACACCAATGAAAAGAACTTTGTTGGATTGACTGTCAACAGCGAATACATCGCCTGTGGCAGTGAAACGAACGAGGTGTTTG

Basic information

species	Physcomitrella patens
transcript	PP1S135_17V6.1
intron #	11
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: LOC_Os02g53140.1 (Oryza sativa), 3'ss of exon 11

ctatgtagcacaggt-cgggcttctctttgttgagtattggttatgtacgataattcttgcgtaa-aggctattcaactgagatt----aggcattctgggtacagACAAGGACACTGAAAGGACACACCAATGAAAAGAACTTTGTTGGATTGACTGTCAACAGCGAATACATCGCCTGTGGCAGTGAAACGAACGAGGTGTTTG
      ||| ||  |    |  |  ||| ||| |||| |       | | |   ||||     || ||  | || | ||    ||    | |  | |    | |||  ||||||| | | ||| ||||  ||||||||||||||||||||  || |||| || | ||| ||||| ||||| || ||||||||||| ||||| ||||
------agctcatctattagtctggcttggtttagtagttacgtcatgctaggcttctcagaaaacagattgttgaccttttgtttaaaatggttacctttttcagGTAAGGACATTCAGAGGGCACAAGAATGAAAAGAACTTTGTTGGGCTGTCTGTAAATAACGAGTACATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTG

upper sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 9

--ctatgtagcacaggtcgggcttctctttgttgagtattg--gttatgtacgataattcttgcgtaaaggctattcaactgagattaggcattctgggtacagACAAGGACACTGAAAGGACACACCAATGAAAAGAACTTTGTTGGATTGACTGTCAACAGCGAATACATCGCCTGTGGCAGTGAAACGAACGAGGTGTTTG
    || | |  ||        | | |  | |  | || ||  | || | || |||||| |||  | |   | |||    |   |  |     | |   | |||  | ||||| | | ||||||||  |||||||||||||||||||| ||| |||| ||||  ||||| || || ||||| ||||| || || ||||| ||||
tctgatttggttcaacattacatgcccaatttgaaatagtgcagctacgaac-ataatttttggatga---ccattttgttataacaacattgtgttttttcagGTACGGACATTCAGAGGACACAAAAATGAAAAGAACTTTGTTGGCTTGTCTGTGAACAATGAATATATTGCTTGTGGAAGTGAGACAAATGAGGTTTTTG

upper sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: Vv10s0523g00030.t01 (Vitis vinifera), 3'ss of exon 11

------------------------------------------------------------------------------ctatgtagcacaggtcgggcttctctttgttgagtattggttatgtacgataattcttgcgtaaaggctattcaactgagattaggcattctgggtac----agACAAGGACACTGAAAGGACACACCAATGAAAAGAACTTTGTTGGATTGACTGTCAACAGCGAATACATCGCCTGTGGCAGTGAAACGAACGAGGTGTTTG
                                                                               | | ||| ||  || |  | ||  ||| |  |  ||    |    |  | |  |  | || | |    ||||| || |  |      |  |   |      ||    | ||| | | ||| ||  | ||||| ||||| ||||| ||  | || || |||||||||||||| ||||||||||||||||| ||||| ||||| |
gtaagttattatgtttttattgtttattttgttctatccccgcattataaatccctctgtatggtgatacctgccaatttttttagtac--gttgaccatccatttttgcaaaatcttgtggaaattacatatggtacgaacaactaattcatctcaattcctttttcataatttttcttagGTTCGCACATTTAGAGGGCATTCAAATGAGAAGAATTTTGTGGGTCTCACAGTAAACAGCGAATACATTGCCTGTGGCAGTGAAACAAACGAAGTGTTCG

upper sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: EFJ28584 (Selaginella moellendorffii), 3'ss of exon 11

ctatgtagcacaggtcgggcttctctttgttgagtattggttatgtacgataattcttgcgtaaaggctattcaactgagattaggcattctgggtacagACAAGGACACTGAAAGGACACACCAATGAAAAGAACTTTGTTGGATTGACTGTCAACAGCGAATACATCGCCTGTGGCAGTGAAACGAACGAGGTGTTTG
                  || | ||| |   |    || | |     |||   ||      |  |    ||  |||    |    || || |   | |||| | | |  || | ||| ||  | || || ||||||||||| || ||||| || |||||||| ||||| || || || |||||||||||||| ||  | |
--------------gtatgcatatctctacagctctttagct-----cgaaggtttcctgatcgatcaaatcaaac----accgtgctttgtctatgcagATACGCAGCCTCACAGGCCATGCTAACGAGAAGAACTTTGTAGGCTTGACAGTTAACAGCGAGTACATTGCGTGCGGTAGTGAAACGAACGAAGTCGTGG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments

ATGC    EST sequence
ATGC    genomic sequence (exon)
ATGC    genomic sequence (truncated intron)

EST: gi|100393347|gb|BY989832.1|BY989832

EST:     CATCCACCGACAGCACTTTACGTCTTTGGGATGTTAAAGATAACTGCCCG                         ACAAGGACACTGAAAGGACACACCAATGAAAAGAACTTTTGT-GGATTGAC
genomic: CATCCACCGACAGCACTTTACGTCTTTGGGATGTTAAAGATAACTGCCCGgtacgctaca ... ctgggtacagACAAGGACACTGAAAGGACACACCAATGAAAAGAACTTT-GTTGGATTGAC

EST: gi|100353725|gb|BY983279.1|BY983279

EST:     CATCCACCGACAGCACTTTACGTCTTTGGGATGT-AAAGATAACTGCCCG                         ACAAGGACACTGAAAGGACA
genomic: CATCCACCGACAGCACTTTACGTCTTTGGGATGTTAAAGATAACTGCCCGgtacgctaca ... ctgggtacagACAAGGACACTGAAAGGACA

EST: gi|162157156|gb|FC333726.1|FC333726

EST:     CATCCACCGACAGCACTTTACGTCTTTGGGATGTTAAAGATAACTGCCCG                         ACAAGGACACTGAAAGGACACACCAATGAAAAGAACTTTGTTGGATTGACT
genomic: CATCCACCGACAGCACTTTACGTCTTTGGGATGTTAAAGATAACTGCCCGgtacgctaca ... ctgggtacagACAAGGACACTGAAAGGACACACCAATGAAAAGAACTTTGTTGGATTGACT

RNA-Seq data

ATGC Supported by RNA-Seq exonic block that spans over the splice site

atgs Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.

Found data for 1 RNA-Seqlibrary.

Block sizes: 14 (upstream exon), 34 (downstream exon)
Score: 3

AAAAGCTGTTTCGTATGTTAAGTTCTTATCTCCAACAGAGTTGGCTTCTGCATCCACCGACAGCACTTTACGTCTTTGGGATGTTAAAGATAACTGCCCGgtacgctaca ... ctgggtacagACAAGGACACTGAAAGGACACACCAATGAAAAGAACTTTGTTGGATTGACTGTCAACAGCGAATACATCGCCTGTGGCAGTGAAACGAACGAGGTGTTTG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tacgataattcttgcgtaaaggctattcaactgagattaggcattctgggtacagACAAGGACACTGAAAGGACACACCAATGAAAAGAACTTTGTTGGATTGACTGTCAACAGCGAATACATCGCCTGTGGCAGTGAAACGAACGAGGTGTTTG