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

...tacagtagcttggctccaaatatcaaatcagtggactatcatgttgttcttgtattacctatttgttcagtgtttcacatttattttttctgccagccagAATGGTAGATTTAGCTATGGCTATGCAAGCTCCCCTGGTAAAAGGGCATCCATGGAAGACTTCTATGAGACAAAAATTGATTGTGTTGATGGTCAGATAG

Basic information

species	Zea mays
transcript	GRMZM2G056572_T01
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G056572_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g56450.1 (Oryza sativa), 3'ss of exon 1

------------tacagtagcttggctcca-aatatcaaatcagtggactatcatgttgttcttgtattacctatttgttcagtgtttcacatttattttttctgccagccagAATGGTAGATTTAGCTATGGCTATGCAAGCTCCCCTGGTAAAAGGGCATCCATGGAAGACTTCTATGAGACAAAAATTGATTGTGTTGATGGTCAGATAG
             |  ||||||||  |  |   | | ||  ||||         ||||| |||       |||||||| |||   |||| ||||   ||||| |||||||||||||||||  ||||||||||| ||||| |||||||||||||||||||| |||||||||||||| || ||||||| |||||| | ||||||||| |||    
aatcaacgttgtcatggtagcttgattttatggtgtaaatgcagttattaggactgttgctct-------cctatttgctcaacatttctcattc--tttttttgccagCCAGAATGGTAAGTTTAGCTATGGGTATGCGAGCTCCCCTGGTAAAAGGGCTTCCATGGAAGACTTTTACGAGACAAGAATTGACTCTGTTGATGGGCAG----

upper sequence: GRMZM2G056572_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA14G12220.1 (Glycine max), 3'ss of exon 1

-tacagtagcttggctccaaatatcaaatcagtggactatcatgttgttc-----ttgtattacctatttgttcagtgtttcacatttattttttctgccagccagAATGGTAGATTTAGCTATGGCTATGCAAGCTCCCCTGGTAAAAGGGCATCCATGGAAGACTTCTATGAGACAAAAATTGATTGTGTTGATGGTCAGATAG
  |   ||| | |  |  || |      ||  |  | |     ||| ||      ||| || |  |  || |    |||||   ||   || |  |||| || |||||||| | ||| |||||||| ||||| ||||||||||| || ||  | || |||||||| || |||||||||||||||||| ||||||||||| |     
agattatagat-gattttaattggtttttctttatatttctgggtttttagttgattgaatgatatgattttgacatgtttgttatgatttgtaactgc-agTCAGAATGGAAAATTCAGCTATGGGTATGCTAGCTCCCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAAAATTGATGGTGTTGATGGTGAA----

upper sequence: GRMZM2G056572_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA06G06310.1 (Glycine max), 3'ss of exon 1

-----tacagtagcttggctccaaatatcaaatcagtggactatcatgttgttcttgtattacctatttgttcagtgtttcacatttattttttctgccagccagAATGGTAGATTTAGCTATGGCTATGCAAGCTCCCCTGGTAAAAGGGCATCCATGGAAGACTTCTATGAGACAAAAATTGATTGTGTTGATGGTCAGATAG
       || |  |||      ||| |  |||  |    ||||  |   ||    || || |  |  ||||       ||    || | || |  |   || || ||| | | ||| |||||||| ||||| ||||| ||||| || ||  | || |||||||| || |||||||||| ||||||| ||||||||||| |     
tctctggcatttcctttaaaaaaaaaaagaaagaaaaaaactaa-acaatgaagctgcatgagatgattgtgacacagtttgttttgaattgtatttatagTCACAATAGAAAATTCAGCTATGGGTATGCTAGCTCTCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAGAATTGATGGTGTTGATGGTGAA----

upper sequence: GRMZM2G056572_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA14G12220.2 (Glycine max), 3'ss of exon 1

------------tacagtagcttggctccaaatatcaaatcagtggactatcatgt-tgttcttgtattacctatttgttcagtg-------tttcacat-----ttattttttctgcc---agccagAATGGTAGATTTAGCTATGGCTATGCAAGCTCCCCTGGTAAAAGGGCATCCATGGAAGACTTCTATGAGACAAAAATTGATTGTGTTGATGGTCAGATAG
            | ||| |          | | || |  | | | |  | |  | | | ||  ||  ||     ||  || | ||       ||| ||||     ||||  ||| |  |   || |||||||| | ||| |||||||| ||||| ||||||||||| || ||  | || |||||||| || |||||||||||||||||| ||||||||||| |     
gtgatttatgtgtgcagaattcaaagattatagatgattttaattggtttttctttatatttctgggtttttagttgattgaatgatatgattttgacatgtttgttatgatttgtaactgcagTCAGAATGGAAAATTCAGCTATGGGTATGCTAGCTCCCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAAAATTGATGGTGTTGATGGTGAA----

upper sequence: GRMZM2G056572_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA17G33690.2 (Glycine max), 3'ss of exon 2

----tacagtagcttggctccaaatatcaaatcagtggactatcatgttgttcttgtattacctatttgttcagtgtttcacatttattttttctgccagccagAATGGTAGATTTAGCTATGGCTATGCAAGCTCCCCTGGTAAAAGGGCATCCATGGAAGACTTCTATGAGACAAAAATTGATTGTGTTGATGGTCAGATAG
    || ||  | ||         | |    | |     || || | ||  |    |      ||||  || |   | |    || | || |     ||| |||||||| | ||| |||||||| ||||| ||||||||||| || ||  | || |||||||| || |||||||||||||||||| ||||||||||| |     
agattatagatgattttaattggtttttcttttatatttctgtctttttagttgattgaatgatattattttaacatgttgttttgaattgtaactgcagTCAGAATGGAAAATTCAGCTATGGGTATGCTAGCTCCCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAAAATTGATGGTGTTGATGGTGAA----

upper sequence: GRMZM2G056572_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT5G24940.1 (Arabidopsis thaliana), 3'ss of exon 1

-------tacagtagcttggctccaaatatcaaatcagt--ggactatcatgttgttcttgtattacctatttgttcagtgtttcacatttattttttctgccagccagAATGGTAGATTTAGCTATGGCTATGCAAGCTCCCCTGGTAAAAGGGCATCCATGGAAGACTTCTATGAGACAAAAATTGATTGTGTTGATGGTCAGATAG
        |   | | || |   |||| || | ||   |  | ||| || | ||    |   || | ||  |    || ||||| |      |||   |||| || |||||||| | |||||||||||| |||||||||||  |||| |||||| |||| ||||||||||| | ||||||||  || ||  || | |||||  |     
ctagctacatgtttgtttcgtctcaaagattatattgattcgaactttcgt-tttccttaacatgaactcatca--caatgttt-atgaacttttgaactgc-agTCAGAATGGAAAATTTAGCTATGGATATGCAAGCTCAGCTGGAAAAAGGTCATCTATGGAAGACTTTTTTGAGACAAGGATCGACGGTATCGATGGAGAA----

upper sequence: GRMZM2G056572_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT5G10740.1 (Arabidopsis thaliana), 3'ss of exon 2

--tacagtagcttggctccaaatatcaaatcagtggactatcatgttgttcttgtattacctatttgttcagtgtttcacatttattttttctgc--cagccagAATGGTAGATTTAGCTATGGCTATGCAAGCTCCCCTGGTAAAAGGGCATCCATGGAAGACTTCTATGAGACAAAAATTGATTGTGTTGATGGTCAGATAG
  |  |      ||| ||    | |      |    |   |    || ||  ||| |||  | ||| ||  |  ||  ||||    |  ||||    |||||||||||| | |||||||||||| |||||||||||| |||| || ||  |||| ||||||||||| | ||| || |  || ||  || |  ||||  |     
gatttatctcactggttcattctgttttcctatcataaagtgtgatttttggtgtgttaaatgtttattgtgctttgtacatgatatgattctattgcagCCAGAATGGAAAATTTAGCTATGGATATGCAAGCTCCGCTGGCAAGAGATCATCTATGGAAGACTTTTTTGAAACTAGGATCGACGGTATCAATGGAGAA----

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|87156931|gb|DY401720.1|DY401720

EST:     GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCTCAGCCAG                      
genomic: GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCT----CAGgtggtgaatc ... tgccagc

EST: gi|149111016|gb|EE294515.2|EE294515

EST:     GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCTCAGCCAG                      
genomic: GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCT----CAGgtggtgaatc ... tgccagc

EST: gi|76931265|gb|DV172687.1|DV172687

EST:     GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCTCAGCCAG                      
genomic: GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCT----CAGgtggtgaatc ... tgccagc

EST: gi|60394530|gb|DN227400.1|DN227400

EST:     GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCTCAGCCAG                      
genomic: GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCT----CAGgtggtgaatc ... tgccagc

EST: gi|76917080|gb|DV166669.1|DV166669

EST:     GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCTCAGCCAG                      
genomic: GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCT----CAGgtggtgaatc ... tgccagc

EST: gi|149106821|gb|EE188718.2|EE188718

EST:     GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCTCAG                         AATGGTAGATTTAGCTATGGCTATGCAAGCTCCCCTGGTAAAAGGGCATCC
genomic: GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCTCAGgtggtgaatc ... tgccagccagAATGGTAGATTTAGCTATGGCTATGCAAGCTCCCCTGGTAAAAGGGCATCC

EST: gi|31406344|gb|CD485076.1|CD485076

EST:     GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCTCAGCCAG                      
genomic: GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCT----CAGgtggtgaatc ... tgccagc

EST: gi|74237808|gb|DT645722.1|DT645722

EST:     GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCTCAGCCAG                      
genomic: GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCT----CAGgtggtgaatc ... tgccagc

EST: gi|26558429|gb|CA830664.1|CA830664

EST:     GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCTCAGCCAG                      
genomic: GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCT----CAGgtggtgaatc ... tgccagc

EST: gi|94472146|gb|EB701104.1|EB701104

EST:     GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCTCAGCCAG                      
genomic: GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCT----CAGgtggtgaatc ... tgccagc

EST: gi|60351289|gb|DN218262.1|DN218262

EST:     GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCTCAGCCAG                      
genomic: GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCT----CAGgtggtgaatc ... tgccagc

EST: gi|91051774|gb|EB162192.1|EB162192

EST:     GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCTCAGCCAG                      
genomic: GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCT----CAGgtggtgaatc ... tgccagc

EST: gi|76290021|gb|DV029589.1|DV029589

EST:     GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCTCAGCCAG                      
genomic: GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCT----CAGgtggtgaatc ... tgccagc

EST: gi|76288715|gb|DV028283.1|DV028283

EST:     GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCTCAGCCAG                      
genomic: GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCT----CAGgtggtgaatc ... tgccagc

EST: gi|22133680|gb|BQ833845.1|BQ833845

EST:     CGTCAGCGGCGGCGGCCTCAGCCAG                      
genomic: CGTCAGCGGCGGCGGCCT----CAGgtggtgaatc ... tgccagc

EST: gi|37425087|gb|CF650279.1|CF650279

EST:     GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCTCAGCCAG                      
genomic: GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCT----CAGgtggtgaatc ... tgccagc

EST: gi|50323711|gb|CO518837.1|CO518837

EST:     GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCTCAGCCAG                      
genomic: GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCT----CAGgtggtgaatc ... tgccagc

EST: gi|211209068|gb|FL368391.1|FL368391

EST:     GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCTCAGCCAG                      
genomic: GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCT----CAGgtggtgaatc ... tgccagc

EST: gi|60359261|gb|DN226234.1|DN226234

EST:     GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCTCAGCCAG                      
genomic: GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCT----CAGgtggtgaatc ... tgccagc

EST: gi|71448387|gb|DR829437.1|DR829437

EST:     GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCTCAGCCAG                      
genomic: GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCT----CAGgtggtgaatc ... tgccagc

EST: gi|101386844|gb|EB815439.1|EB815439

EST:     GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCTCAGCCAG                      
genomic: GTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCT----CAGgtggtgaatc ... tgccagc

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: 41 (upstream exon), 49 (downstream exon)
Score: 155

GTCTACTCGGCCCAGCCGGGGATCCAAGCGGGATGGGGTACTTGAGCTCCGTGATCGGCCACCCCACCGATGGATCCTCCGTCAGCGGCGGCGGCCTCAGgtggtgaatc ... tgccagccagAATGGTAGATTTAGCTATGGCTATGCAAGCTCCCCTGGTAAAAGGGCATCCATGGAAGACTTCTATGAGACAAAAATTGATTGTGTTGATGGTCAGATAG

Block sizes: 25 (upstream exon), 49 (downstream exon)
Score: 186

Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 142

Block sizes: 21 (upstream exon), 49 (downstream exon)
Score: 143

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gttcttgtattacctatttgttcagtgtttcacatttattttttctgccagccagAATGGTAGATTTAGCTATGGCTATGCAAGCTCCCCTGGTAAAAGGGCATCCATGGAAGACTTCTATGAGACAAAAATTGATTGTGTTGATGGTCAGATAG

                                  tttattttttctgcc  CT-rich tract
                           tttcacatttattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacagtagcttggctccaaatatcaaatcagtggactatcatgttgttcttgtattacctatttgttcagtgtttcacatttattttttctgccagccagAATGGTAGATTTAGCTATGGCTATGCAAGCTCCCCTGGTAAAAGGGCATCCATGGAAGACTTCTATGAGACAAAAATTGATTGTGTTGATGGTCAGATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- cagtagc
- - - - - - gctccaa
- - - - - - - - - - - - - - - - - - - - -tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - - cttgtat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttca