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

...atgtgtttgctttaaacagagaggaaaaatagatatgtgtaagctatatttatttaaggaatctctatgctatttttatgacaaaagcttatttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGCCATCCAGATGTGTATGAGCCATGTGATGATTCCTTTGCCCTTGTTGATG

Basic information

species	Zea mays
transcript	GRMZM2G121840_T01
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G121840_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g60920.1 (Oryza sativa), 3'ss of exon 1

atgtgtttgctttaaacagagaggaaaaatagatatgtgtaagctata-tttatttaaggaatctctat-gctatttttatg-aca----aaagcttatttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGCCATCCAGATGTGTATGAGCCATGTGATGATTCCTTTGCCCTTGTTGATG
          ||    |||  |    | || | | |  |||||  ||| ||||||| || ||| | | | ||| ||  |||   ||     |  |||  | |||||| |||  || || |||||||||||||||||||| ||||  || ||||| ||||||||||| |||||||| |||||||||||||||||||| ||||| ||||
------caagttatctcagtaaaattacat-gttttcagtaaggaataatttatttgagtaatgtatgttgcttttaatatccgcatggtgacactttctattgcagTCTTTATCAGGAAGGACATTAAACACCGCACAGATTCAACTCGTTGCAAGCCATCCAGAGGTGTATGAACCATGTGATGATTCCTTTGCACTTGTCGATG

upper sequence: GRMZM2G121840_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S78_28V6.2 (Physcomitrella patens), 3'ss of exon 2

atgtgtttgctttaaacagagaggaaaaatagatatgtgtaagctatatttatttaaggaatctct-atgctatttttatgacaaaagcttatttttgcagGCTTCTTCTGGGAGGACAT---TAAACACCGCACAA--------ATTCCGCTTGTTGCGAGCCATCCAGATGTGTATGAGCCATGTGATGATTCCTTTGCCCTTGTTGATG
 | |||| |  || ||||  | | |  | || |||   | |   |  |    ||     | |   | ||| |   | |  || ||      | || ||     | ||  ||| |||       |   | |||   ||        || | ||| || |   | |||||||||||||||||||| |||||||| ||||| || |         
ctatgttag--ttgaacactg-gaagtattaaatactggaagattccagcccttctgcaatttcttgatgttgcgtctgggagaagttacaagttgtgagtagTCCTCATGGCAGGGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACATCCAGATGTGTATGAGCCCTGTGATGACTCCTTCGCTC---------

upper sequence: GRMZM2G121840_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S78_28V6.3 (Physcomitrella patens), 3'ss of exon 2

atgtgtttgctttaaacagagaggaaaaatagatatgtgtaagctatatttatttaaggaatctct-atgctatttttatgacaaaagcttatttttgcagGCTTCTTCTGGGAGGACAT---TAAACACCGCACAA--------ATTCCGCTTGTTGCGAGCCATCCAGATGTGTATGAGCCATGTGATGATTCCTTTGCCCTTGTTGATG---
              ||||  | | |  | || |||   | |   |  |    ||     | |   | ||| |   | |  || ||      | || ||     | ||  ||| |||       |   | |||   ||        || | ||| || |   | |||||||||||||||||||| |||||||| ||||| || || |||||||   
--------------aacactg-gaagtattaaatactggaagattccagcccttctgcaatttcttgatgttgcgtctgggagaagttacaagttgtgagtagtcctcatggcagGGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACATCCAGATGTGTATGAGCCCTGTGATGACTCCTTCGCTCTGGTTGATGCGT

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|211481128|gb|FL012858.1|FL012858

EST:     TCGCGGA-STCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAG                         GCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC
genomic: TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAGgtaagcacct ... atttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC

EST: gi|76292687|gb|DV032255.1|DV032255

EST:     TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAG                         GCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC
genomic: TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAGgtaagcacct ... atttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC

EST: gi|67039937|gb|CO466192.1|CO466192

EST:     TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAG                         GCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC
genomic: TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAGgtaagcacct ... atttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC

EST: gi|149014020|gb|EE043537.2|EE043537

EST:     TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAG                         GCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC
genomic: TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAGgtaagcacct ... atttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC

EST: gi|149082133|gb|EE171313.2|EE171313

EST:     TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAG                         GCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC
genomic: TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAGgtaagcacct ... atttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC

EST: gi|78079126|gb|DV507538.1|DV507538

EST:     TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAG                         GCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC
genomic: TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAGgtaagcacct ... atttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC

EST: gi|91051911|gb|EB162329.1|EB162329

EST:     TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAG                         GCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC
genomic: TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAGgtaagcacct ... atttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC

EST: gi|148949173|gb|EC894610.2|EC894610

EST:     TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAG                         GCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC
genomic: TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAGgtaagcacct ... atttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC

EST: gi|91875347|gb|EB405304.1|EB405304

EST:     TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAG                         GCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC
genomic: TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAGgtaagcacct ... atttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC

EST: gi|91878618|gb|EB408575.1|EB408575

EST:     TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAG                         GCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC
genomic: TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAGgtaagcacct ... atttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC

EST: gi|101382449|gb|EB813280.1|EB813280

EST:     TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAG                         GCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC
genomic: TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAGgtaagcacct ... atttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC

EST: gi|93281851|gb|EB674115.1|EB674115

EST:     TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAG                         GCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC
genomic: TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAGgtaagcacct ... atttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC

EST: gi|91872433|gb|EB402390.1|EB402390

EST:     TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAG                         GCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC
genomic: TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAGgtaagcacct ... atttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC

EST: gi|211481127|gb|FL012857.1|FL012857

EST:     TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAG                         GCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC
genomic: TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAGgtaagcacct ... atttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC

EST: gi|91051957|gb|EB162375.1|EB162375

EST:     TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAG                         GCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC
genomic: TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAGgtaagcacct ... atttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC

EST: gi|50330269|gb|CO525395.1|CO525395

EST:     AAGGGGCTCCCCAGGAGGGGCAAG                         GCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC
genomic: AAGGGGCTCCCCAGGAGGGGCAAGgtaagcacct ... atttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC

EST: gi|76020633|gb|DT947803.1|DT947803

EST:     TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAG                         GCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC
genomic: TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAGgtaagcacct ... atttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC

EST: gi|91873736|gb|EB403693.1|EB403693

EST:     TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAG                         GCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC
genomic: TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAGgtaagcacct ... atttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC

EST: gi|71425558|gb|DR806750.1|DR806750

EST:     TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAG                         GCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC
genomic: TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAGgtaagcacct ... atttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC

EST: gi|71315864|gb|DR794609.1|DR794609

EST:     TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAG                         GCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC
genomic: TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAGgtaagcacct ... atttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC

EST: gi|101382765|gb|EB813438.1|EB813438

EST:     TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAG                         GCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC
genomic: TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAGgtaagcacct ... atttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC

EST: gi|148934967|gb|EC879011.2|EC879011

EST:     TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAG                         GCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC
genomic: TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAGgtaagcacct ... atttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC

EST: gi|149080207|gb|EE169229.2|EE169229

EST:     TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAG                         GCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC
genomic: TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAGgtaagcacct ... atttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC

EST: gi|71323041|gb|DR798192.1|DR798192

EST:     TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAG                         GCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC
genomic: TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAGgtaagcacct ... atttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC

EST: gi|15312727|gb|BI478338.1|BI478338

EST:     TCGCGGAGCTCCCCAGCGGCGTCGAGAAGGGGCTCCCCAGGAGGGGCAAG                         GCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC
genomic: TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAGgtaagcacct ... atttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC

EST: gi|91052265|gb|EB162683.1|EB162683

EST:     TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAG                         GCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC
genomic: TCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAGgtaagcacct ... atttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGC

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 4 RNA-Seq libraries.

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 75

CGACTGCTGTTCCATGGCGGACGGCGACGGCGCGGCGGCGACGGGGAAGCTCGCGGAGCTCCCCAGCGGCGCCGAGAAGGGGCTCCCCAGGAGGGGCAAGgtaagcacct ... atttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGCCATCCAGATGTGTATGAGCCATGTGATGATTCCTTTGCCCTTGTTGATG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 89

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 67

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

atatttatttaaggaatctctatgctatttttatgacaaaagcttatttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGCCATCCAGATGTGTATGAGCCATGTGATGATTCCTTTGCCCTTGTTGATG

                                          cttattttt  CT-rich tract
                         tatttttatgacaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtgtttgctttaaacagagaggaaaaatagatatgtgtaagctatatttatttaaggaatctctatgctatttttatgacaaaagcttatttttgcagGCTTCTTCTGGGAGGACATTAAACACCGCACAAATTCCGCTTGTTGCGAGCCATCCAGATGTGTATGAGCCATGTGATGATTCCTTTGCCCTTGTTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- -tgtttgc
- - - - - - -aaacaga
- - - - - - - - - - - - aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gacaaaa