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

...tacttgaagttatataaggctagacatatgaaaaactctgcgctgtgcatttgaatgctttgtttgctaaggcattgctctcattttctacttgcatcagATCTGCGCTCGATGGAGAATGTGGGTTCCTTGCTGCAAATCTCTATGCCAAGAGTGTGTTTGGCGAGGACGCTCTGGTGAATATCAGTGTTGAGAAGCAG

Basic information

species	Zea mays
transcript	GRMZM2G094699_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G094699_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g07280.1 (Oryza sativa), 3'ss of exon 3

tacttgaagttatataaggctagacatatgaaaaactctgcgctgtgcatttgaatgctttgtttgctaaggc-attgctctcattttctacttgcatcagATCTGCGCTCGATGGAGAATGTGGGTTCCTTGCTGCAAATCTCTATGCCAAGAGTGTGTTTGGCGAGGACGCTCTGGTGAATATCAGTGTTGAGAAGCAG
| |    |   |     || |   ||||  |       |||         |||  ||||      ||| |  | |||   ||  | |   | |  ||||||||||||||| |||||||||||||||||  | ||||| |||||||||||||||||||| ||||| ||||| ||  ||||||| ||||| ||||| ||||| 
ttccaacatcaaagctgggttcttcatagcatgtctaatgccactgctgcttggttgctaataccgctgaccctattatacttgtatatga-taacatcagATCTGCGCTTGATGGAGAATGTGGGTTTATCGCTGCTAATCTCTATGCCAAGAGTGTTTTTGGTGAGGATGCATTGGTGAACATCAGCGTTGAAAAGCAA

upper sequence: GRMZM2G094699_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G23780.1 (Glycine max), 3'ss of exon 3

--tacttgaagttatataaggctagacatatgaaaaactctgcgctgtgcattt--gaatgctttgtttgctaaggcattgctctcattttctacttgcatcagATCTGCGCTCGATGGAGAATGTGGGTTCCTTGCTGCAAATCTCTATGCCAAGAGTGTGTTTGGCGAGGACGCTCTGGTGAATATCAGTGTTGAGAAGCAG
  ||||   | | ||  | |  | ||||||  || |    |  |   ||  |||  |    |    |      |  ||||    |    || |  ||   | ||||| ||  | || || || ||||| |||||||||||||| || ||||| |||||||| ||||| || || ||| |||||||| | ||  |||| ||||| 
cgtact---aatcattaatgtgtggacata-aaacattgttatgtcatgattttatggggacccattccatataatcatttggtttgcgttgttgtttgtttagATCGGCATTGGAAGGGGATTGTGGATTCCTTGCTGCAAACCTTTATGCTAAGAGTGTTTTTGGGGAAGATGCTTTGGTGAATGTGAGCATTGAAAAGCAA

upper sequence: GRMZM2G094699_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G00610.1 (Glycine max), 3'ss of exon 3

---tacttgaa-gttatataaggctagaca--tatgaaaaactctgcgctgtgcatttgaatgctttgtttgctaaggcattgctctcattttctacttgcatcagATCTGCGCTCGATGGAGAATGTGGGTTCCTTGCTGCAAATCTCTATGCCAAGAGTGTGTTTGGCGAGGACGCTCTGGTGAATATCAGTGTTGAGAAGCAG
   || || ||  ||  ||    ||    |   || ||    |   |      ||||   ||   ||| ||  || ||  ||    |  || | |  ||     ||||| ||  | || || || ||||| |||||||||||||| || ||||| |||||||| ||||| || || ||| |||||||| | ||  |||| ||||| 
tattatttcaacatttcatgttacttactaatcattaatgtatggacataaaacattgttatatcttgatt-ttatggggttttggttgttgtttgttt-----agATCGGCATTGGAAGGGGATTGTGGATTCCTTGCTGCAAACCTTTATGCTAAGAGTGTTTTTGGGGAAGATGCTTTGGTGAATGTGAGCATTGAAAAGCAA

upper sequence: GRMZM2G094699_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT4G31490.1 (Arabidopsis thaliana), 3'ss of exon 4

tacttgaagttatataaggctagacatatgaaaaactctgcgctgtgcatttgaatgctttgtttgctaaggcattgctctcattttctacttgcatcagATCTGCGCTCGATGGAGAATGTGGGTTCCTTGCTGCAAATCTCTATGCCAAGAGTGTGTTTGGCGAGGACGCTCTGGTGAATATCAGTGTTGAGAAGCAG
              ||||  || |    |       |     ||||  |   |||    | || |    |   | | ||     | | ||||||||   |||||||  | |  || |||||||| |||||||| |||||  | ||||| || ||||||||||| ||||| ||||| |||||| | ||| |||||||||| 
-------------gtaagtgtaaattcttc-----tttcatcctgtagaaacgaaaaactcgtcttactaattaatact-----tctttacttgca---gATCTGCAATAGCAGGTGAATGTGGATTCCTTGCAGCAAACTTATATGCAAAAAGTGTGTTTGGTGAGGATGCTCTTGTGAATTTGAGTATTGAGAAGCAA

upper sequence: GRMZM2G094699_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S309_15V6.2 (Physcomitrella patens), 3'ss of exon 4

---tacttga-agttatataaggctagacatatgaaaaactctgcgctgtgcatttgaa-tgctttgtttgctaaggcattgctctcattttctacttgcatcagATCTGCGCTCGATGGAGAATGTGGGTTCCTTGCTGCAAATCTCTATGCCAAGAGTGTGTTTGGCGAGGACGCTCTGGTGAATATCAGTGTTGAGAAGCAG
    || ||| || | |  | |  |      || |||   |   | | ||  |  |||| || |  |  |  |    ||   ||   || || ||| ||||   |||||||  | || || || ||||| ||  | || |||||||| ||||| ||||| |||||||| ||||| ||  |||||||| |||||||||||||||| 
tgtaacgtgatagcttttgatgattttttcaatcaaacttttgccacagtttaagtgaaatgatccgagt-ttgtaacac-acttgaatcttgtacatgca---gATCTGCTTTGGAAGGTGATTGTGGCTTTTTGGCGGCAAATCTTTATGCGAAGAGCGTGTTTGGAGAGGATGCGTTGGTGAATGTCAGTGTTGAGAAGCAA

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|16377392|gb|BI991902.1|BI991902

EST:     TTCTTGAATCATATTATTAAGTCCACAAACATGAAGTGTCTAACACCACC                         ATCTGCGCTCGATGGAGAATGTGGGTTCCTTGCTGCAAATCTCTATGCCAA
genomic: TTCTTGAATCATATTATTAAGTCCACAAACATGAAGTGTCTAACACCACCgtaagttcca ... cttgcatcagATCTGCGCTCGATGGAGAATGTGGGTTCCTTGCTGCAAATCTCTATGCCAA

EST: gi|148934854|gb|EC878899.2|EC878899

EST:     TTCTTGAATCATATTATTAAGTCCACAAACATGAAGTGTCTAACACCACC                         ATCTGCGCTCGATGGAGAATGTGGGTTCCTTGCTGCAAATCTCTATGCCAA
genomic: TTCTTGAATCATATTATTAAGTCCACAAACATGAAGTGTCTAACACCACCgtaagttcca ... cttgcatcagATCTGCGCTCGATGGAGAATGTGGGTTCCTTGCTGCAAATCTCTATGCCAA

EST: gi|6012725|gb|AW062162.1|AW062162

EST:     TTCTTGAATCATATTATTAAGTCCACAAACATGAATTGTCTAACACCACC                         ATCTGCGCTCGATGGAGAATGTGGGTTCCTTGCTGCAAATCTCTATGCCAA
genomic: TTCTTGAATCATATTATTAAGTCCACAAACATGAAGTGTCTAACACCACCgtaagttcca ... cttgcatcagATCTGCGCTCGATGGAGAATGTGGGTTCCTTGCTGCAAATCTCTATGCCAA

EST: gi|67015126|gb|CO443875.1|CO443875

EST:     TTCTTGAATCATATTATTAAGTCCACAAACATGAAGTGTCTAACACCACC                         ATCTGCGCTCGATGGAGAATGTGGGTTCCTTGCTGCAAATCTCTATGCCAA
genomic: TTCTTGAATCATATTATTAAGTCCACAAACATGAAGTGTCTAACACCACCgtaagttcca ... cttgcatcagATCTGCGCTCGATGGAGAATGTGGGTTCCTTGCTGCAAATCTCTATGCCAA

EST: gi|71764263|gb|DR962200.1|DR962200

EST:     TTCTTGAATCATATTATTAAGTCCACAAACATGAAGTGTCTAACACCACC                         ATCTGCGCTCGATGGAGAATGTGGGTTCCTTGCTGCAAATCTCTATGCCAA
genomic: TTCTTGAATCATATTATTAAGTCCACAAACATGAAGTGTCTAACACCACCgtaagttcca ... cttgcatcagATCTGCGCTCGATGGAGAATGTGGGTTCCTTGCTGCAAATCTCTATGCCAA

EST: gi|12967981|gb|BG264928.1|BG264928

EST:     TTCTTGAATCATATTATTAAGTCCACAAACATGAAGTGTCTAACACCACC                         ATCTGCGCTCGATGGAGAATGTGGGTTCCTTGCTGCAAATCTCTATGCCAA
genomic: TTCTTGAATCATATTATTAAGTCCACAAACATGAAGTGTCTAACACCACCgtaagttcca ... cttgcatcagATCTGCGCTCGATGGAGAATGTGGGTTCCTTGCTGCAAATCTCTATGCCAA

EST: gi|67011141|gb|CO439890.1|CO439890

EST:     TTCTTGAATCATATTATTAAGTCCACAAACATGAAGTGTCTAACACCACC                         ATCTGCGCTCGATGGAGAATGTGGGTTCCTTGCTGCAAATCTCTATGCCAA
genomic: TTCTTGAATCATATTATTAAGTCCACAAACATGAAGTGTCTAACACCACCgtaagttcca ... cttgcatcagATCTGCGCTCGATGGAGAATGTGGGTTCCTTGCTGCAAATCTCTATGCCAA

EST: gi|18176946|gb|BM378156.1|BM378156

EST:     AAACATGAAGTGTCTAACACCACC                         ATCTGCGCTCGATGGAGAATGTGGGTTCCTTGCTGCAAATCTCTATGCCAA
genomic: AAACATGAAGTGTCTAACACCACCgtaagttcca ... cttgcatcagATCTGCGCTCGATGGAGAATGTGGGTTCCTTGCTGCAAATCTCTATGCCAA

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: 48 (upstream exon), 46 (downstream exon)
Score: 115

GTGGCGGTGAATACTGTGATCCAGGATGAGAAGGAATTCTTGAATCATATTATTAAGTCCACAAACATGAAGTGTCTAACACCACCgtaagttcca ... cttgcatcagATCTGCGCTCGATGGAGAATGTGGGTTCCTTGCTGCAAATCTCTATGCCAAGAGTGTGTTTGGCGAGGACGCTCTGGTGAATATCAGTGTTGAGAAGCAG

Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 63

Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 105

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 125

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgcatttgaatgctttgtttgctaaggcattgctctcattttctacttgcatcagATCTGCGCTCGATGGAGAATGTGGGTTCCTTGCTGCAAATCTCTATGCCAAGAGTGTGTTTGGCGAGGACGCTCTGGTGAATATCAGTGTTGAGAAGCAG

                                ctctcattttctactt  CT-rich tract
                                     attttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacttgaagttatataaggctagacatatgaaaaactctgcgctgtgcatttgaatgctttgtttgctaaggcattgctctcattttctacttgcatcagATCTGCGCTCGATGGAGAATGTGGGTTCCTTGCTGCAAATCTCTATGCCAAGAGTGTGTTTGGCGAGGACGCTCTGGTGAATATCAGTGTTGAGAAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC