ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

...tcagcttgtgtgtgcagttcaggtttggtgttcatgagactaagcactgggaatcttatcgagtattgttctgaacttctcacgaaatgtacattgttagGCGGCATTGGCGCACACAATTGGGCACGTGGCAGCGACTGTGAGTATGTCGAAGGTTGCAGTGTCATTCACACACATCATCAAGAGCGCGGAACCCGCAT

Basic information

species	Physcomitrella patens
transcript	PP1S190_76V6.1
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: PP1S190_76V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os07g33910.2 (Oryza sativa), 3'ss of exon 1

------tcagcttgtgtgtgcagttca--ggtttggtgttcatgagactaagc-actgggaatct-tatcgagt--attg---ttctgaact---tctcacgaaatgtacattgt-tagGCGGCATTGGCGCACACAATTGGGCACGTGGCAGCGACTGTGAGTATGTCGAAGGTTGCAGTGTCATTCACACACATCATCAAGAGCGCGGAACCCGCAT
      ||   |||    || |   ||  |  |     ||| |||  ||   | | |  |||||| |  || ||   |||   ||  | | |   | |  |    |||     |   ||| |||  | |||||||| || ||||||||||| ||||| ||||| ||| ||||||| || ||||| ||||| ||||||||||||||||  || || || |
gtgagatcgcattgaccatggacaccatcgtctcctccttcttgattctgttctattctgaatctctgacgcgttcgttggatttggggattcgtttttgctcgttgtgggacgagcagGTGGCGATCGCGCACACCATCGGGCACGTGGCGGCGACGGTGAGCATGGCGAAGGTGGCGGTGTCGTTCACCCACATCATCAAGAGCGGCGAGCCGGCGT

upper sequence: PP1S190_76V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os08g08840.2 (Oryza sativa), 3'ss of exon 2

tcagcttgtgtgtgcagttcaggt-ttggtgttcatgagactaagcactgggaatcttatcgagtattgttctgaacttctcacgaaatgtacattgttagGCGGCATTGGCGCACACAATTGGGCACGTGGCAGCGACTGTGAGTATGTCGAAGGTTGCAGTGTCATTCACACACATCATCAAGAGCGCGGAACCCGCAT
       ||| ||| | |     | ||||   | ||  |  ||    ||| |   ||  | | | |    |      || |  | |  |     |||  |||  ||  |||| || ||||||||||| || || ||||| ||||||||||| || || |||||||||||||||||||| ||||| || || || || ||||
-------gtgagtggaatctttttcttggcaattatttgtatatttgctgtg--cctgcttgggcaagcatgattgattttggctattttccttttga-agGTTGCTGTGGCTCATACAATTGGGCATGTTGCTGCGACAGTGAGTATGTCAAAAGTAGCAGTGTCATTCACACACATTATCAAAAGTGCAGAGCCTGCAT

upper sequence: PP1S190_76V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G009223_T01 (Zea mays), 3'ss of exon 1

tcagcttgtgtgtgcagttcaggtttggtgttcat--gagactaagcactgggaatcttatcgagtattgttctgaacttctcacgaaatgta-cattgttagGCGGCATTGGCGCACACAATTGGGCACGTGGCAGCGACTGTGAGTATGTCGAAGGTTGCAGTGTCATTCACACACATCATCAAGAGCGCGGAACCCGCAT
   |   || |   | |  | | ||   |  ||     |||        |    ||        || | | | ||    |    ||||  ||  | || | |||  ||  | |||||||| || ||||||||||| ||||| ||||| ||| | ||||| || ||||| ||||| |||||||||||||||| ||| || ||||
---gtgagtatcatcggcgccgattaattcctccctaaagatctcttcttctagatgcggctctgtctcggtgtggtgctgatgcgaatcgtctcgttctcagGTTGCGATCGCGCACACGATCGGGCACGTGGCGGCGACGGTGAGCATGGCCAAGGTGGCCGTGTCGTTCACGCACATCATCAAGAGCGGGGAGCCGGCAT

upper sequence: PP1S190_76V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 2

-----tcagcttgtgtgtgcagttcaggtttggtgttcatgagactaagcactgggaatcttatcgagtattgttctgaacttctcacgaaatgtacattgttagGCGGCATTGGCGCACACAATTGGGCACGTGGCAGCGACTGTGAGTATGTCGAAGGTTGCAGTGTCATTCACACACATCATCAAGAGCGCGGAACCCGCAT
     |    |  | |||||   | |  | |  | ||      ||    |      | | | |  || | | ||  | ||||         ||| |  ||| |         ||||||| |||||||| || || || || || ||||| ||||| ||||| |||||||||||||||||||| || || ||||| ||||| ||||
gtgagttgattattttgtgccagtaacttcttttattttatttacctgcctggaaaagtgtaactgaatttggtgattaact--------gatgaagGTTGCTG--------TGGCGCATACAATTGGCCATGTTGCTGCTACAGTGAGCATGTCTAAGGTGGCAGTGTCATTCACACACATAATTAAAAGCGCAGAACCTGCAT

upper sequence: PP1S190_76V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G431314_T01 (Zea mays), 3'ss of exon 2

tcagcttgtgtgtgcagttcaggtttggtgttcatgagactaag--cactgggaatcttatcgagtattgttctgaacttctcacgaaatgtacattgttagGCGGCATTGGCGCACACAATTGGGCACGTGGCAGCGACTGTGAGTATGTCGAAGGTTGCAGTGTCATTCACACACATCATCAAGAGCGCGGAACCCGCAT
         ||| |  | | |  ||| |||    | |  ||      | |    ||    ||  | |    | | |     |   |  ||  ||      |||  ||  |||| || |||||||| || || || ||||| ||||| ||||| ||||| |||||||||||||||||||| || || || || ||||| ||||
---------gtgagttgctta--tttcgtgccagtaactcttcttttattttatataccttcctggaaaagtgtaactgaatttggtgattaactgatgaagGTTGCTGTGGCACATACAATTGGCCATGTTGCTGCGACAGTGAGCATGTCTAAGGTGGCAGTGTCATTCACACACATAATTAAAAGTGCAGAACCTGCAT

upper sequence: PP1S190_76V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA13G27680.1 (Glycine max), 3'ss of exon 1

--tcagcttgtgtgtgcagttcaggtttggtgttcatgagact-aagcactgggaatcttatcgagtattgtt--ctgaacttctcacgaaatgtacattgttagGCGGCATTGGCGCACACAATTGGGCACGTGGCAGCGACTGTGAGTATGTCGAAGGTTGCAGTGTCATTCACACACATCATCAAGAGCGCGGAACCCGCAT
    | |  || | ||  | |||  |  ||||    ||||  | ||| |  |  |   | ||  |||| |  |  || ||    |  | || | |    ||  |||  ||  |||| |||||||||||||| || || || |||||||| ||||| |||||||| || |||||||| |||||||||||||| |  || || || |
aagtaacgcgtttatggtggtcaaat--ggtgg--gtgagtttgaagtaaggaaaggttgatttagtagtactcactaaagaaatttcaaatttttttgtgc-agGTTGCGGTGGCACACACAATTGGGCATGTTGCTGCAACTGTGAGCATGTCCAAGGTTGCTGTTTCATTCACTCACATCATCAAGAGTGGAGAGCCAGCTT

upper sequence: PP1S190_76V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA15G11270.1 (Glycine max), 3'ss of exon 1

tcagcttgtgtgtgcagttcaggtttggtgttcatgagact-aagcactgggaatcttatcgagtattgtt--ctgaacttctcacgaaatgtacattgttagGCGGCATTGGCGCACACAATTGGGCACGTGGCAGCGACTGTGAGTATGTCGAAGGTTGCAGTGTCATTCACACACATCATCAAGAGCGCGGAACCCGCAT
 ||     | | ||  | |||  |  |||||   ||||  | ||| |  |  |   | || ||||| |  |  ||  |    |  | || | ||   ||  |||  ||  |||| |||||||||||||| || || || |||||||| ||||| |||||||| || |||||||| |||||||||||||| |  || || || |
gcaatgcatttatggtggtcaaat--ggtgtgagtgagtttgaagtaaggaaaggttgattgagtagtactcacttgagaaatttcaaattttattgtgc-agGTTGCGGTGGCACACACAATTGGGCATGTTGCTGCAACTGTGAGCATGTCCAAGGTTGCTGTTTCATTCACTCACATCATCAAGAGTGGAGAGCCAGCTT

upper sequence: PP1S190_76V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA07G38830.1 (Glycine max), 3'ss of exon 1

-tcagcttgtgtgtgcagttcaggtttggtgttcatgagactaagcactgggaatct-tatcgagtattgttctgaacttctcacgaaatgtacattgt-tagGCGGCATTGGCGCACACAATTGGGCACGTGGCAGCGACTGTGAGTATGTCGAAGGTTGCAGTGTCATTCACACACATCATCAAGAGCGCGGAACCCGCAT
  ||   |  ||    || | |||   |||       |   ||| |     | ||   | || | || |  ||            ||||  |     ||  |||  ||  ||   || ||||||||||| || ||||| || ||||||||||| || |||||||| ||||| || |||||||||||||| || ||||| ||||
ggcaaaata-gtaaagagattaggg--ggtaaaagaaatcataatcgtcaagcattaatgtcaattagtactcaatggggaatttgaaactttgggagtgcagGTCGCGGTGTTACATACAATTGGGCATGTTGCAGCTACGGTGAGTATGTCCAAAGTTGCAGTTTCATTTACCCACATCATCAAGAGTGCAGAACCTGCAT

upper sequence: PP1S190_76V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA17G01890.1 (Glycine max), 3'ss of exon 1

--tcagcttgtgtgtgcagttcaggtttggtgttcatgagactaagcac-tgggaatcttatcgagtattgttctgaacttctcacgaaatgtacattgt-tagGCGGCATTGGCGCACACAATTGGGCACGTGGCAGCGACTGTGAGTATGTCGAAGGTTGCAGTGTCATTCACACACATCATCAAGAGCGCGGAACCCGCAT
    |  | |||   |   ||  ||  |       || | | ||  ||      ||||| |   | || |  |  | |  | |   ||||| |     ||  |||  ||  ||   || ||||||||||| || ||||| || ||||||||||| || |||||||| ||||| || |||||||||||||| || || || ||||
tacaaaatagtgaa-gagattagggggtaaaagaaattataatagtcaaacattaatctcaattaatacttattgggaaattt---gaaattttgggagtgcagGTTGCGGTGTTACATACAATTGGGCATGTTGCAGCTACCGTGAGTATGTCCAAAGTTGCAGTTTCATTTACCCACATCATCAAGAGTGCAGAGCCTGCAT

upper sequence: PP1S190_76V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G54800.1 (Arabidopsis thaliana), 3'ss of exon 1

tcagcttgtg--tgtgcag-ttcaggtttggtgttcatgagactaagcactgggaatctt-atcgagtattgttctgaacttctcacgaaatgtacattgt-tagGCGGCATTGGCGCACACAATTGGGCACGTGGCAGCGACTGTGAGTATGTCGAAGGTTGCAGTGTCATTCACACACATCATCAAGAGCGCGGAACCCGCAT
    |||||   | |  || |||  || |    ||| |      ||| | ||    | || ||    | |||| |||||  |         || |     | ||||  ||  |||| ||||||||||| || ||||| || || ||||||||||| |||||||| || || ||||| |||||||||||||| |  ||||| || |
----cttgtcattatatagcttctagtatttcattc-tagtttaaagtattgaactttttgatattttgttgtactgaaagtggtttatgttgaattgcatatagGTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCAAAGGTTGCTGTTTCTTTCACTCACATCATCAAGAGTGGTGAACCTGCGT

upper sequence: PP1S190_76V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv19s0177g00300.t01 (Vitis vinifera), 3'ss of exon 1

tcagcttgtgtgtgcagttcaggtttggtgttcatgagactaagcactgggaatcttatcgagtattgttctgaacttctcacgaaatgtacattgt------tagGCGGCATTGGCGCACACAATTGGGCACGTGGCAGCGACTGTGAGTATGTCGAAGGTTGCAGTGTCATTCACACACATCATCAAGAGCGCGGAACCCGCAT
  |  |||    |||  || |  |  ||  | | | ||  |       || |  |  |  |||     || |||| || | |  ||    |  || |      ||||  ||  |||| || ||||||||||| ||||| || || ||||||||||| |||||||| ||||| || || ||||| |||||||| |  || || ||||
-taaattggagttgcttttaaaat--ggattcccttagttt---tctcggcagccaaacagagctggattgtgaatttataatcaatctgattttatgttttgtagGTTGCTGTGGCTCATACAATTGGGCATGTGGCTGCAACAGTGAGTATGTCCAAGGTTGCGGTGTCTTTTACTCACATAATCAAGAGTGGTGAGCCTGCAT

upper sequence: PP1S190_76V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv10s0116g00760.t01 (Vitis vinifera), 3'ss of exon 1

--tcagcttgtgtgtgcagttcaggtttggtgttcatgagactaagcactg--ggaatcttatcgagtattgttctgaacttctcacgaaatgtacattgttagGCGGCATTGGCGCACACAATTGGGCACGTGGCAGCGACTGTGAGTATGTCGAAGGTTGCAGTGTCATTCACACACATCATCAAGAGCGCGGAACCCGCAT
  || | || ||  |  | || |   ||  |||   |      |||   |   | |  |  |   ||  ||  | | |  ||   | |   | |    ||| |||  ||| | || || |||||||| || || ||||| ||||| || ||||| || |||||||| || ||||| |||||||||||||| |  || || || |
gttctggttttgccta-aatttaaaattcttgtctttttcctgaagtttttccgcagacaaacaaagctttagtttaa--tttgaatggcttttgttgtgt-agGTTGCAGTAGCTCATACAATTGGTCATGTAGCAGCAACTGTTAGCATGTCAAAAGTTGCAGTTTCCTTCACCCACATCATCAAGAGTGGTGAGCCTGCTT

upper sequence: PP1S190_76V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ15095 (Selaginella moellendorffii), 3'ss of exon 1

tcagcttgtgtgtgcagttcaggtttggtgttcatgagactaagcactgggaatcttatcgagtattgttctgaacttctcacgaaatgtacattgttagGCGGCATTGGCGCACACAATTGGGCACGTGGCAGCGACTGTGAGTATGTCGAAGGTTGCAGTGTCATTCACACACATCATCAAGAGCGCGGAACCCGCAT
                                                |  | || |          | |||  ||||  | | |||   ||      ||| |||  |||| || || ||||||||||| || || || ||||| ||||| |||||||| || || ||||| || ||||||||||||||||| || || |
------------------------------------------------gtaagtcctccacctgcgagctcttgactttccgctaaaaccacg--aacagGTGGCGCTGGCTCATACCATTGGGCACGTTGCCGCCACGGTGAGCATGTCCAAGGTTGCCGTCTCCTTCACTCATATCATCAAGAGCGCGGAGCCAGCCT

upper sequence: PP1S190_76V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ37594 (Selaginella moellendorffii), 3'ss of exon 1

tcagcttgtgtgtgcagttcaggtttggtgttcatgagactaagcactgggaatcttatcgagtattgttctgaacttctcacgaaatgtacattgttagGCGGCATTGGCGCACACAATTGGGCACGTGGCAGCGACTGTGAGTATGTCGAAGGTTGCAGTGTCATTCACACACATCATCAAGAGCGCGGAACCCGCAT
                                                |  | || |          | |||  ||||  | | |||   ||      |||  ||  |||| || || ||||| ||||| || || || ||||| ||||| |||||||| || || ||||| |||||||||||||||||||| || || |
------------------------------------------------gtaagtcctccacctgcgagctcttgactttccgctaaaaccacg--aacagGTTGCGCTGGCTCATACCATTGGTCACGTTGCCGCCACGGTGAGCATGTCCAAGGTTGCCGTCTCCTTCACTCACATCATCAAGAGCGCGGAGCCAGCCT

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|162156936|gb|FC333090.1|FC333090

EST:     TTGTTCCTGCACCGGACGTGGACGTCGAGTTTTGGAAAGGCCTTGCTCCG                         GCGGCATTGGCGCACACAATTGGGCACGTGGCAGCGACTGTGAGTATGTCG
genomic: TTGTTCCTGCACCGGACGTGGACGTCGAGTTTTGGAAAGGCCTTGCTCCGgtatgtcact ... acattgttagGCGGCATTGGCGCACACAATTGGGCACGTGGCAGCGACTGTGAGTATGTCG

EST: gi|162277254|gb|FC453684.1|FC453684

EST:     TTGTTCCTGCACCGGACGTGGACGTCGAGTTTTGGAAAGGCCTTGCTCCG                         GCGGCATTGGCGCACACAATTGGGCACGTGGCAGCGACTGTGAGTATGTCG
genomic: TTGTTCCTGCACCGGACGTGGACGTCGAGTTTTGGAAAGGCCTTGCTCCGgtatgtcact ... acattgttagGCGGCATTGGCGCACACAATTGGGCACGTGGCAGCGACTGTGAGTATGTCG

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: 27 (upstream exon), 35 (downstream exon)
Score: 15

GTCCCTCGCAGCCGGTTCAGCTATCATGCTGATTTCATGGGCCCTGCGGATTGTTCCTGCACCGGACGTGGACGTCGAGTTTTGGAAAGGCCTTGCTCCGgtatgtcact ... acattgttagGCGGCATTGGCGCACACAATTGGGCACGTGGCAGCGACTGTGAGTATGTCGAAGGTTGCAGTGTCATTCACACACATCATCAAGAGCGCGGAACCCGCAT

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

actgggaatcttatcgagtattgttctgaacttctcacgaaatgtacattgttagGCGGCATTGGCGCACACAATTGGGCACGTGGCAGCGACTGTGAGTATGTCGAAGGTTGCAGTGTCATTCACACACATCATCAAGAGCGCGGAACCCGCAT