ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

gtttgggattcttttcattcaacccaatagtcttagtggcaagtaactacttgtgtaacttttaaaaaatttgacagtgaacgtcagttctatattcctgcttgattcagttaagtaattttacttgggccaaccactgtctctctcttgtgttttaacagGTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAAGATGAGGTGAATGTGGCGTGCTTTCATCCCCAAGTTGGTGGTGGTCTTG

Basic information

species	Physcomitrella patens
transcript	PP1S150_95V6.1
intron #	11
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: PP1S150_95V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: LOC_Os09g12550.1 (Oryza sativa), 3'ss of exon 12

gtttgggattcttttcattcaacccaatagtcttagtggcaagtaactacttgtgtaacttttaaaaaatttgacagtgaacgt-cagttctatattcctgcttgattcagttaagtaattttacttgggccaaccactgtctctctcttgtgttttaacagGTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAAGATGAGGTGAATGTGGCGTGCTTTCATCCCCAAGTTGGTGGTGGTCTTG
                                                              |      ||  ||  |  | || ||||  |   |     | | || |  | | |  ||    ||  || | |  ||| | ||| | |||   ||  | |||| || ||||||||||| ||||||||||| || ||  | ||||||||||||||||| || ||||| || || ||||||||      |||||  |||||||
------------------------------------------------------------actgtggggtt--acgatttatgtgcagtaatgactaatgacctcatactttcaggatataaggctatgggctaatactatttctttattgcacttccatagGTGTATAGAGTTTCAGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAAGATGAAGTCAATGTCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTG

upper sequence: PP1S150_95V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GRMZM2G007229_T01 (Zea mays), 3'ss of exon 12

gtttgggattcttttcattcaacccaatagtcttagtggcaagtaactacttgtgtaacttttaaaaaatttgacagtgaacgtcagtt-cta-tattcctgcttgattcagttaagtaattttacttgggccaaccactgtctctctcttgtgttttaacagGTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAAGATGAGGTGAATGTGGCGTGCTTTCATCCCCAAGTTGGTGGTGGTCTTG
                                                            |  ||| |||||     | | | ||     ||| || |  ||||         |    ||| | | |      |  || | |||   | |  |  |||   |||| || |||||||||||||||||||||||||| ||  | ||||| ||||||||||| || ||||| || |||||||||||   |   || ||||| ||||
------------------------------------------------------------tcaaaataatttacttattatcctcctcaactactaatattgctcatactttgtgtacaatgtaagtcaaatta-tcattttcttcatttattacttt--tagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGCGCTGAAGATGAAGTTAATGTTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTG

upper sequence: PP1S150_95V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GRMZM2G353548_T01 (Zea mays), 3'ss of exon 12

gtttgggattcttttcattcaacccaatagtcttagtggcaagtaactacttgtgtaacttttaaaaaatttgacagtgaacgtcagtt-cta-tattcctgcttgattcagttaagtaattttacttgggccaacca-ctgtctctctcttgtgttttaacagGTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAAGATGAGGTGAATGTGGCGTGCTTTCATCCCCAAGTTGGTGGTGGTCTTG
                                                                ||  |||||    | | | ||     ||| |  |  ||||         |    ||| | |      | | | | || | | | |  | | ||     |||| || |||||||||||||||||||||||||| ||  | |||||||| |||||||| || ||||| || |||||||||||   |   || ||||| ||||
----------------------------------------------------------------aatgatttgcttattatcctccacaactactcatattgctcatactttgtgtacaatgtaagccaaactatcaatctttttttttaatttattactttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG

upper sequence: PP1S150_95V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 11

gtttgggattcttttcattcaacccaatagtcttagtggcaagtaactacttgtgtaacttttaaaaaatttgacagtgaacgtcagttctatattcctgcttgattcagttaagtaattttacttgggccaaccactgtctctctcttgtgttttaacagGTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAAGATGAGGTGAATGTGGCGTGCTTTCATCCCCAAGTTGGTGGTGGTCTTG
                                                 |  |   || || |    | |   |   |  | | |  || | || | ||  | | || |||    | | |||| |         |  ||  | |   |||| |||||   ||| |||||||| ||||||||||| ||||| |||||  | |||||||| ||||||||||| |||||||| |||||||||||    |  || || || || |
------------------------------------------------gccggcacaaattgttgtcattcatatcatctatgccctttttgtagttctaatggttttagtc---tgaatttaat-------gtctttgaatttgctttgtctttta---gGTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGATGAGGTCAATGTGGCATGCTTTCATCCTTTTGCCGGAGGAGGACTAG

upper sequence: PP1S150_95V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA03G32620.4 (Glycine max), 3'ss of exon 11

gtttgggattcttttcattcaacccaatagtcttagtggcaagtaactacttgtgtaacttttaaaaaatttgacagtgaacgtcagttctatattcctgcttgattcagttaagtaattttacttggg--ccaaccactgtctctctcttgtgttttaacagGTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAAGATGAGGTGAATGTGGCGTGCTTTCATCCCCAAGTTGGTGGTGGTCTTG
                                                          ||   | ||| | |  |  |  |  |||  |||||   | |  |  | |   | || |  ||||| |  |     ||   || |   | |  | ||| ||   |||| |||| ||| ||||||||||| ||||| |||||  | |||||||| ||||| ||||| |||||||| |||||||||||    | ||| || || || |
---------------------------------------------------------gctggcacaaattgttgccattcatatca--tctatgccctttttgtagt---tcaaatggttttaatctgaatttaatgtctatgaatttgctttgtcttt-tagGTATACAAAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGACGAGGTCAATGTGGCATGCTTTCATCCTTTTGCTGGGGGAGGACTAG

upper sequence: PP1S150_95V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: AT5G43930.1 (Arabidopsis thaliana), 3'ss of exon 11

gtttgggattcttttcattcaacccaatagtcttagtggcaagtaactacttgtgtaacttttaaaaaatttgacagtgaacgtcagttctatattcctgcttgattca-gttaagtaattttacttgggccaaccactgtctctctcttgtgttttaacagGTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAAGATGAGGTGAATGTGGCGTGCTTTCATCCCCAAGTTGGTGGTGGTCTTG
                                                                            || ||     |   |||  | ||  |  || || ||| || | ||  |  |    ||  ||     | | | |   |      ||| | ||||||||||||||||||||||||||||| ||| | || ||| | || ||||| ||||| || ||||| ||||||||      ||| || |||||||
----------------------------------------------------------------------------gtaaa-----gccttatgctactagtacatccatgttcagaacttggagatataaca--cagaacttgtttgtgtgggccggtcagATATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTGCCAAGTTCAGAGGATGAAGTGAACGTTGCGTGTTTTCATCCTTCTCCTGGAGGAGGTCTTG

upper sequence: PP1S150_95V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 11

gtttgggattcttttcattcaacccaatagtcttagtggcaagtaactacttgtgtaacttttaaaaaatttgacagtgaacgtcagttctatattcctgcttgattcagttaagtaattttacttgggccaacca---ctgtctctctcttgtgttttaacagGTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAAGATGAGGTGAATGTGGCGTGCTTTCATCCCCAAGTTGGTGGTGGTCTTG
                 |   ||   | | | ||| | |||     |      | |     | || |  |   |  |  |  |   ||    || |      | ||    | || |  |  |  |  |  |   ||   ||  |   ||||| |  |    ||||||||| |||| ||||||||||| ||||| || ||  | || ||||||||||||||||| ||||| || |||||||||||   |  ||| || |||||||
----------------gtaacacttcaaaattttaatagcattaggcagtaaatatggtactgaagatctccaattg-aagtgctggtcaagtacttta---ttatctgttcaaatcttactgttctgatctttcaggtctcacaggctctttttgtcactcagGTTTACCGAGTCTCAGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAAGATGAGGTCAATGTAGCTTGCTTTCATCCTTTACCTGGAGGAGGTCTTG

upper sequence: PP1S150_95V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: Vv05s0077g00140.t01 (Vitis vinifera), 3'ss of exon 11

gtttgggattcttttcattcaacccaatagtcttagtggcaagtaactacttgtgtaacttttaaaaaatttgacagtgaacgtcagttctatattcctgcttgattcagttaagtaattttacttgggccaaccactgtctctctcttgtgttttaacagGTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAAGATGAGGTGAATGTGGCGTGCTTTCATCCCCAAGTTGGTGGTGGTCTTG
                                              |||||| |||     ||| |  |    | |     | |   || | ||||  |  ||   | | ||     |||||| ||   |    ||   | | | | |  ||      ||||| ||||||||||| |||||||| |||||||| ||  | |||||||| || |||||||| ||||| || |||||||||||    ||||| ||||| ||||
--------------------------------------------tgctacttatgttgtgattatagga----ataaaactcttggattttttatttattttt---ttattt---ctattttatttcaactt-tcaaaatatttttatcatg------cagGTCTACAGAGTTTCTGATATGGAACTTGTGAGAGTTCTTCCTAGTGCAGAGGATGAGGTTAATGTAGCTTGCTTTCATCCTTCTGTTGGAGGTGGCCTTG

upper sequence: PP1S150_95V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: EFJ26270 (Selaginella moellendorffii), 3'ss of exon 12

gtttgggattcttttcattcaacccaatagtcttagtggcaagtaactacttgtgtaacttttaaaaaatttgacagtgaacgtcagttctatattcctgcttgattcagttaagtaattttacttgggccaaccactgtctctctcttgtgttttaacagGTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAAGATGAGGTGAATGTGGCGTGCTTTCATCCCCAAGTTGGTGGTGGTCTTG
                                                                                                       | ||  | |   |  ||||   ||| |   ||| ||    | || | |  |||  ||| |||| ||| | |||||| || | || ||| | ||  | || |||||||||||||| || ||||| |||||||||||||| | |||||| || || ||||
-------------------------------------------------------------------------------------------------------gtttgcgctctctgttttt---tggact--ccattgaaattttccttttgtttctcagATTTATAGAATATCAGATTTGAAACTAGTGCGAGTTCTCCCAAGTGCTGAAGATGAAGTTAATGTAGCGTGCTTTCATCCTCGAGTTGGCGGAGGGCTTG

upper sequence: PP1S150_95V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: EFJ14567 (Selaginella moellendorffii), 3'ss of exon 11

gtttgggattcttttcattcaacccaatagtcttagtggcaagtaactacttgtgtaacttttaaaaaatttgacagtgaacgtcagttctatattcctgcttgattcagttaagtaattttacttgggccaaccactgtctctctcttgtgttttaacagGTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAAGATGAGGTGAATGTGGCGTGCTTTCATCCCCAAGTTGGTGGTGGTCTTG
                                                                                                       | ||  | |   || ||||   ||| |   ||| ||    | || | |  |||  ||| |||| ||| | |||||| || | || ||| | ||  | || |||||||||||||| || ||||| |||||||||||||| | |||||| || || ||||
-------------------------------------------------------------------------------------------------------gtttgcgctctctattttt---tggact--ccattgaaattttccttttgtttctcagATTTATAGAATATCAGATTTGAAACTAGTGCGAGTTCTCCCAAGTGCTGAAGATGAAGTTAATGTAGCGTGCTTTCATCCTCGAGTTGGCGGAGGGCTTG

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|37846878|gb|BJ604886.1|BJ604886

EST:     TTGTAGACGGCTCAGCAACCATTCCGATTCGAGTCTATACTATTCTCGAG                         GTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAA
genomic: TTGTAGACGGCTCAGCAACCATTCCGATTCGAGTCTATACTATTCTCGAGgtttgggatt ... gttttaacagGTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAA

EST: gi|162194031|gb|FC370206.1|FC370206

EST:     TTGTAGACGGCTCAGCAACCATTCCGATTCGAGTCTATACTATTCTCGAG                         GTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAA
genomic: TTGTAGACGGCTCAGCAACCATTCCGATTCGAGTCTATACTATTCTCGAGgtttgggatt ... gttttaacagGTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAA

EST: gi|162150990|gb|FC327886.1|FC327886

EST:     TTGTAGACGGCTCAGCAACCATTCCGATTCGAGTCTATACTATTCTCGAG                         GTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAA
genomic: TTGTAGACGGCTCAGCAACCATTCCGATTCGAGTCTATACTATTCTCGAGgtttgggatt ... gttttaacagGTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAA

EST: gi|162227631|gb|FC402624.1|FC402624

EST:     TTGTAGACGGCTCAGCAACCATTCCGATTCGAGTCTATACTATTCTCGAG                         GTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAA
genomic: TTGTAGACGGCTCAGCAACCATTCCGATTCGAGTCTATACTATTCTCGAGgtttgggatt ... gttttaacagGTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAA

EST: gi|162195510|gb|FC370901.1|FC370901

EST:     TTGTAGACGGCTCAGCAACCATTCCGATTCGAGTCTATACTATTCTCGAG                         GTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAA
genomic: TTGTAGACGGCTCAGCAACCATTCCGATTCGAGTCTATACTATTCTCGAGgtttgggatt ... gttttaacagGTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAA

EST: gi|162178843|gb|FC354775.1|FC354775

EST:     TTGTAGACGGCTCAGCAACCATTCCGATTCGAGTCTATACTATTCTCGAG                         GTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAA
genomic: TTGTAGACGGCTCAGCAACCATTCCGATTCGAGTCTATACTATTCTCGAGgtttgggatt ... gttttaacagGTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAA

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: 35 (upstream exon), 25 (downstream exon)
Score: 2

CATATTGCTAGCGTATGGTAGACGTCATAATTCACTTCTGAGAAGTCTTGTTGTAGACGGCTCAGCAACCATTCCGATTCGAGTCTATACTATTCTCGAGgtttgggatt ... gttttaacagGTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAAGATGAGGTGAATGTGGCGTGCTTTCATCCCCAAGTTGGTGGTGGTCTTG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tcagttaagtaattttacttgggccaaccactgtctctctcttgtgttttaacagGTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAAGATGAGGTGAATGTGGCGTGCTTTCATCCCCAAGTTGGTGGTGGTCTTG

                                 tctctctcttgtgttt  CT-rich tract
     taagtaattttactt  TA-rich tract

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgggattcttttcattcaacccaatagtcttagtggcaagtaactacttgtgtaacttttaaaaaatttgacagtgaacgtcagttctatattcctgcttgattcagttaagtaattttacttgggccaaccactgtctctctcttgtgttttaacagGTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAAGATGAGGTGAATGTGGCGTGCTTTCATCCCCAAGTTGGTGGTGGTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG