ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtacttcacgttgtggcttccctgacttggaactcattttacgtgttttattattaataatcctgggtatcttatgcactgattccaattcatgccctgtcagGTCAGGGGTGGCCGCGACAGGAGACCTATAGGAGCATATGAGCTTGCCAAAGCAGTTCAAGATCTTGGTGCTGGGGAAATTCTCTTGAACTGCATCAATT

Basic information

species	Physcomitrella patens
transcript	PP1S43_232V6.1
intron #	15
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: PP1S43_232V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: LOC_Os03g15120.1 (Oryza sativa), 3'ss of exon 14

gtacttcacgttgtggcttccctgacttggaactcattttacgtgttttattattaataatcctgggtatcttatgcactgattccaattcatgccctgtc-agGTCAGGGGTGGCCGCGACAGGAGACCTATAGGAGCATATGAGCTTGCCAAAGCAGTTCAAGATCTTGGTGCTGGGGAAATTCTCTTGAACTGCATCAATT
  || | |  |      |   ||| | |  | ||  | |  | || | |  | |||||||   ||    | |  | ||   | |    || ||| | | || |||| || ||||| || |||||  | ||||||||||||||||| || |||||||||||| ||||  | |||||||| ||||| ||  | || |||||  |||
-aacattaaatgact-ttatgctggcata-atctactgtggcatgctgtcct-ttaataagattgctcttttgttccaacaagtgttgtttatgtcttttccagGTAAGTGGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAAGCAGTTGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATT

upper sequence: PP1S43_232V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: AT4G26900.1 (Arabidopsis thaliana), 3'ss of exon 16

gtacttcacgttgtggcttccctgacttggaactcattttacgtgttttattattaataatcctgggtatcttatgcactgattccaattcatgccctgtcagGTCAGGGGTGGCCGCGACAGGAGACCTATAGGAGCATATGAGCTTGCCAAAGCAGTTCAAGATCTTGGTGCTGGGGAAATTCTCTTGAACTGCATCAATT
                           |  || |      ||   ||| ||| |||| |    |  ||||| | | |     |     ||  |   ||   ||||||| || || || ||  |  ||||||| ||||||| ||||||||| ||||| ||| ||||  | ||||| || ||||| || |||||||||||  | |
--------------------------gtaaaatttcggccacccttttcatt-ttaagatcgatttgtatcattt-cttaactattggtttctcaactaaaagGTCAGTGGAGGACGAGAAGGTCGACCTATTGGAGCATTTGAGCTTGCGAAAGCGGTTGAAGAATTAGGTGCCGGTGAAATACTATTGAACTGCATAGACT

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|37841897|gb|BJ599905.1|BJ599905

EST:     TCCAGGAGCCCGGACNTAATGGAGAGAAGTTCGCTTGGTATCAGTGCACG                         GTCAGGGGTGGCCGCGACAGGAGACCTATAGGAGCATATGAGCTTGCCAAA
genomic: TCCAGGAGCCCGGACCTAATGGAGAGAAGTTCGCTTGGTATCAGTGCACGgtacttcacg ... gccctgtcagGTCAGGGGTGGCCGCGACAGGAGACCTATAGGAGCATATGAGCTTGCCAAA

EST: gi|162260812|gb|FC438168.1|FC438168

EST:     TCCAGGAGCCCGGACCTAATGGAGAGAAGTTCGCTTGGTATCAGTGCACG                         GTCAGGGGTGGCCGCGACAGGAGACCTATAGGAGCATATGAGCTTGCCAAA
genomic: TCCAGGAGCCCGGACCTAATGGAGAGAAGTTCGCTTGGTATCAGTGCACGgtacttcacg ... gccctgtcagGTCAGGGGTGGCCGCGACAGGAGACCTATAGGAGCATATGAGCTTGCCAAA

EST: gi|37850978|gb|BJ608986.1|BJ608986

EST:     TCCAGGAGCCCGGACNTAATGGAGAGAAGTTCGCTTGGTATCAGTGCACG                         GTCAGGGGTGGCCGCGACAGGAGACCTATAGGAGCATATGAGCTTGCCAAA
genomic: TCCAGGAGCCCGGACCTAATGGAGAGAAGTTCGCTTGGTATCAGTGCACGgtacttcacg ... gccctgtcagGTCAGGGGTGGCCGCGACAGGAGACCTATAGGAGCATATGAGCTTGCCAAA

EST: gi|162240841|gb|FC417512.1|FC417512

EST:     TCCAGGAGCCCGGACNTAATGGAGAGAAGTTCGCTTGGTATCAGTGCACG                         GTCAGGGGTGGCCGCGACAGGAGACCTATAGGAGCATATGAGCTTGCCAAA
genomic: TCCAGGAGCCCGGACCTAATGGAGAGAAGTTCGCTTGGTATCAGTGCACGgtacttcacg ... gccctgtcagGTCAGGGGTGGCCGCGACAGGAGACCTATAGGAGCATATGAGCTTGCCAAA

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: 32 (upstream exon), 19 (downstream exon)
Score: 2

AAGAGTGTACGTTAAAGATCCTTCAGAAGTACCTTATAAGACTATTGAAGTCCAGGAGCCCGGACCTAATGGAGAGAAGTTCGCTTGGTATCAGTGCACGgtacttcacg ... gccctgtcagGTCAGGGGTGGCCGCGACAGGAGACCTATAGGAGCATATGAGCTTGCCAAAGCAGTTCAAGATCTTGGTGCTGGGGAAATTCTCTTGAACTGCATCAATT

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tattattaataatcctgggtatcttatgcactgattccaattcatgccctgtcagGTCAGGGGTGGCCGCGACAGGAGACCTATAGGAGCATATGAGCTTGCCAAAGCAGTTCAAGATCTTGGTGCTGGGGAAATTCTCTTGAACTGCATCAATT