ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

...ttctaacagaggcgtggacacgcgtgatgatatggcatgttctttgtatggaccactgttgcattttccttggctgaaaaatggaactttcgtctcacagGATTACGTCCCTACTGTATTCGACAACTTCAGCGCGAATGTCGTGGTCGATGGGAATACCGTCAACCTGGGACTATGGGATACAGCAG

Basic information

species	Physcomitrella patens
transcript	PP1S257_74V6.1
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: PP1S257_74V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 1

--ttctaacagaggcgtggacacgcgtgatgatatggcatgttctttgtatggaccactgttgcattttccttggctgaaaaatggaac-tttcgtctcacagGATTACGTCCCTACTGTATTCGACAACTTCAGCGCGAATGTCGTGGTCGATGGGAATACCGTCAACCTGGGACTATGGGATACAGCAG
  ||||   | ||  |  ||  | | | ||  | |  | | |   | |  ||  ||  ||   |  | |               |   | || | | | ||||||||| || || || || || ||||||||||| || || |||||||| ||||| || ||||||||||| || |||||||| || ||||
agttctgtaacagtag--gattcacctcattttgtatcttatgaatcggttgtgcc-ttgagacgatatgtgcactcattgttcgcgtcattgcttttgacagGATTATGTTCCGACGGTGTTTGACAACTTCAGTGCCAACGTCGTGGTTGATGGTAACACCGTCAACCTCGGGCTATGGGACACTGCAG

upper sequence: PP1S257_74V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G375002_T03 (Zea mays), 3'ss of exon 1

ttctaacagaggcgtggacacgcgtgatgatatgg-catgttctttgtatggaccactgt----tgcattttccttggctgaaaaatggaactttcgtctcacagGATTACGTCCCTACTGTATTCGACAACTTCAGCGCGAATGTCGTGGTCGATGGGAATACCGTCAACCTGGGACTATGGGATACAGCAG
      || || |    |   |   || | | ||  | | |   |||| | | | ||  |    |||| || | |  |     ||   | |  |   |    ||||| || || || ||||| |||||||||||||| || ||||| ||||| || ||||  || |||||| |||| || |||||||||||||
-----ccacagacaactaacgggacgagggtttgttcgtttgagttgtcttggctacaatattatgcagttgcttatgtctgcaaggcgcatctcaatgctgcagGACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG

upper sequence: PP1S257_74V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ09765 (Selaginella moellendorffii), 3'ss of exon 1

ttctaacagaggcgtggacacgcgtgatgatatggcatgttctttgtatggaccactgttgcattttccttggctgaaaaatggaactttcgtctcacagGATTACGTCCCTACTGTATTCGACAACTTCAGCGCGAATGTCGTGGTCGATGGGAATACCGTCAACCTGGGACTATGGGATACAGCAG
                       ||||   |  |   ||||||||           | |   | | || | |||||      ||| | ||| ||  |||||||||||| || ||||| || || ||||||||||| ||||| || |||||||| || || |||||||| || || ||||| || || |
-----------------------gtgagatttcgttttgttctttcc-----tttttctctaactctcttgggctg------ggatcgttcatca-acagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG

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|208390035|gb|DC938090.1|DC938090

EST:     TGGGGAAGACGTGCATGCTTATTTCATATACCAGCAATACATTTCCTACT                         GATTACGTCCCTACTGTATTCGACAACTTCAGCGCGAATGTCNCGGTCGAT
genomic: TGGGGAAGACGTGCATGCTTATTTCATATACCAGCAATACATTTCCTACTgtaagctgcg ... cgtctcacagGATTACGTCCCTACTGTATTCGACAACTTCAGCGCGAATGTCGTGGTCGAT

EST: gi|208390034|gb|DC938089.1|DC938089

EST:     TGGGGAAGACGTGCATGCTTATTTCATATACCANCAATACATTTCCTACT                         GATTACGTCCCTACTGTATTCGACAACTTCAGCGCGAATGTCNCGGTCGAT
genomic: TGGGGAAGACGTGCATGCTTATTTCATATACCAGCAATACATTTCCTACTgtaagctgcg ... cgtctcacagGATTACGTCCCTACTGTATTCGACAACTTCAGCGCGAATGTCGTGGTCGAT

EST: gi|100403655|gb|BY955035.1|BY955035

EST:     TGGGGAAGACGTGCATGCTTATTTCATATACCAGCAATACATTTCCTACT                         GATTACGTCCCTACTGTATTCGACAACTTCAGCGCGAATGTCGTGGTCGAT
genomic: TGGGGAAGACGTGCATGCTTATTTCATATACCAGCAATACATTTCCTACTgtaagctgcg ... cgtctcacagGATTACGTCCCTACTGTATTCGACAACTTCAGCGCGAATGTCGTGGTCGAT

EST: gi|162169156|gb|FC345123.1|FC345123

EST:     TGGGGAAGACGTGCATGCTTATTTCATATACCAGCAATACATTTCCTACT                         GATTACGTCCCTACTGTATTCGACAACTTCAGCGCGAATGTCGTGGTCGAT
genomic: TGGGGAAGACGTGCATGCTTATTTCATATACCAGCAATACATTTCCTACTgtaagctgcg ... cgtctcacagGATTACGTCCCTACTGTATTCGACAACTTCAGCGCGAATGTCGTGGTCGAT

EST: gi|208380984|gb|DC902986.1|DC902986

EST:     TGGGGAAGACGTGCATGCTTATTTCATATACCANCAATACATTTCCTACT                         GATTACGTCCCTACTGTATTCNACANCTTCANCGCGAA
genomic: TGGGGAAGACGTGCATGCTTATTTCATATACCAGCAATACATTTCCTACTgtaagctgcg ... cgtctcacagGATTACGTCCCTACTGTATTCGACAACTTCAGCGCGAA

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: 26 (upstream exon), 23 (downstream exon)
Score: 2

CATGAGCACTTCTCGCTTTATCAAGTGCGTTACTGTAGGAGATGGAGCTGTGGGGAAGACGTGCATGCTTATTTCATATACCAGCAATACATTTCCTACTgtaagctgcg ... cgtctcacagGATTACGTCCCTACTGTATTCGACAACTTCAGCGCGAATGTCGTGGTCGATGGGAATACCGTCAACCTGGGACTATGGGATACAGCAG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gtatggaccactgttgcattttccttggctgaaaaatggaactttcgtctcacagGATTACGTCCCTACTGTATTCGACAACTTCAGCGCGAATGTCGTGGTCGATGGGAATACCGTCAACCTGGGACTATGGGATACAGCAG