ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

...gcgttttgtatgattactgtgttcttctggttcatgtgcaaataattaaatgaacaatcgcagcggtccataataagcactgacgatgatcgctattcagGGTTCTCCGTCTGCGTTGGTGGTCAAATGGGCTGACACTGAGAAAGAAAGGCAGGCGCGTAAAGTGCAGAAGGCTCAGTCGGTTTCTTCTCCCCCCATTC

Basic information

species	Physcomitrella patens
transcript	PP1S175_12V6.1
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: PP1S175_12V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G177001_T01 (Zea mays), 3'ss of exon 5

---------gcgttttgtatgattactgtgttcttctggttcatgtgcaaataattaaatgaacaatcgcagcggtccataataagcactgacgatgatcgctattcagGGTTCTCCGTCTGCGTTGGTGGTCAAATGGGCTGACACTGAGAAAGAAAGGCAGGCGCGTAAAGTGCAGAAGGCTCAGTCGGTTTCTTCTCCCCCCATTC
              |||      ||   | ||  ||   ||||  |   ||  |||  |||| || |  ||    ||  ||| | || |||   ||  | | ||    ||||||      | | ||||| |||||||||||||||||||| || ||||||||||| || ||||  || || ||||| |     ||||||  |    |  
atatcattgataccttggtcttgtatgatattgatc-acttcagttctgaa--atttcatgaccagttacacaaatc--taacatgccctggtcatttttgtta----gGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAGGCTCGAAAAGCACAAAAAGCTCAATTCCAGTCTTCTAACATGTTGA

upper sequence: PP1S175_12V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G128809_T01 (Zea mays), 3'ss of exon 6

gcgttttgtatgattactgtgttcttctggttcatgtgcaaataattaaatgaa-caatcgcagcggtccataataagcactgacgatgatcgctat--tcagGGTTCTCCGTCTGCGTTGGTGGTCAAATGGGCTGACACTGAGAAAGAAAGGCAGGCGCGTAAAGTGCAGAAGGCTCAGTCGGTTTCTTCTCCCCCCATTC
   |  |  || |||  |   ||   || ||  |  || |    ||  | |    || |          ||| |     ||      || ||  | |  | |||||||      | | ||||| |||||||||||||||||||| || |||||||| || || |||| ||| ||  |||  |     ||||||  |    |  
---taatagatcattgataccttggccttgtatagttgtatgatatagattacttcagttctgaaatctcatgaatctaacatggcttggtcattttggttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAAGCTCGAAAAGCGCAAAAATCTCCATTCCAGTCTTCTAACATGTTGA

upper sequence: PP1S175_12V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ23463 (Selaginella moellendorffii), 3'ss of exon 5

gcgttttgtatgattactgtgttcttctggttcatgtgcaaataattaaatgaacaatcgcagcggtccataataagcactgacgatgatcgctattcagGGTTCTCCGTCTGCGTTGGTGGTCAAATGGGCTGACACTGAGAAAGAAAGGCAGGCGCGTAAAGTGCAGAAGGCTCAGTCGGTTTCTTCTCCCCCCATTC
                                          ||  |  |  |    |||    |||  || |||           | | |||| |||||||| |  | ||||| |||||||| |||||||| ||||| |||||||||||||| || || ||  |||| ||| ||||  || | ||| || |  | |   
-----------------------------------------gtagcttgagaagttgtcgtgatggtatattatat----------tcagcgct-ttcagGGTGCGTCTTCTGCCTTGGTGGTGAAATGGGCCGACACGGAGAAAGAAAGGCAAGCTCGAAAGATGCAAAAGTCTCAAACGCTATCTCCTGCAACGAACG

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|100372155|gb|BY967732.1|BY967732

EST:     AACAAGCCGTTGCTGCTATTGAAGCTTTGAATGGAGTACACAAAATGGAG                         GGTTCTCCGTCTGCGTTGGTGGTCAAATGGGCTGACACTGAGAAAGAAAGG
genomic: AACAAGCCGTTGCTGCTATTGAAGCTTTGAATGGAGTACACAAAATGGAGgtatacattt ... cgctattcagGGTTCTCCGTCTGCGTTGGTGGTCAAATGGGCTGACACTGAGAAAGAAAGG

EST: gi|100420134|gb|BY975953.1|BY975953

EST:     AACAAGCCGTTGCTGCTATTGAAGCTTTGAATGGAGTACACAAAATGGAG                         GGTTCTCCGTCTGCGTTGGTGGTCAAATGGGCTGACACTGAGAAAGAAAGG
genomic: AACAAGCCGTTGCTGCTATTGAAGCTTTGAATGGAGTACACAAAATGGAGgtatacattt ... cgctattcagGGTTCTCCGTCTGCGTTGGTGGTCAAATGGGCTGACACTGAGAAAGAAAGG

EST: gi|162176555|gb|FC353024.1|FC353024

EST:     AACAAGCCGTTGCTGCTATTGAAGCTTTGAATGGAGTACACAAAATGGAG                         GGGTTCTCCGTCTG
genomic: AACAAGCCGTTGCTGCTATTGAAGCTTTGAATGGAGTACACAAAATGGAGgtatacattt ... cgctattcagGG-TTCTCCGTCTG

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: 33 (upstream exon), 18 (downstream exon)
Score: 4

GATGCGCTTTTTTAAAATATGAAACTAAAGAACAAGCCGTTGCTGCTATTGAAGCTTTGAATGGAGTACACAAAATGGAGgtatacattt ... cgctattcagGGTTCTCCGTCTGCGTTGGTGGTCAAATGGGCTGACACTGAGAAAGAAAGGCAGGCGCGTAAAGTGCAGAAGGCTCAGTCGGTTTCTTCTCCCCCCATTC

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttaaatgaacaatcgcagcggtccataataagcactgacgatgatcgctattcagGGTTCTCCGTCTGCGTTGGTGGTCAAATGGGCTGACACTGAGAAAGAAAGGCAGGCGCGTAAAGTGCAGAAGGCTCAGTCGGTTTCTTCTCCCCCCATTC