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

...ttgtgacgaatggataaactgaatatcaggattccaagctaaccacgttccacttgtattcgatattttttgttatgttttccccatctcggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG

Basic information

species	Zea mays
transcript	GRMZM5G829894_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G829894_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g05630.1 (Oryza sativa), 3'ss of exon 4

---ttgtgacgaat-ggataaactgaatatcaggattccaagctaaccacgttccacttgtattcgatattttttgttatgttttccccatctcggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG
      || |   |   || | ||||||| ||||||| ||   ||      ||  ||   | ||    ||   |  | || |||  ||  || |     |||||| ||||| |||||||||||||||||||| || ||| |||||||||||||||||||||||||||| |||||||| || ||||||||||
ggtacatggcagttcaaattatctgaataacaggatttcatattagtattatttaacacatgtta---atcaatcataatatttctcctgtc-cacccttgcagCAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAAGAATTGAGGACGCTGGGGGCTTCGTGATGTGGGCTG

upper sequence: GRMZM5G829894_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 5

--ttgtgacgaatggataaactgaatatcaggattccaagctaaccacgttccacttgtattcgatattttttg--ttatgttttccccatctcggagctgc--agCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG
   ||  | |      |  |   | ||| |||         |||||   ||||   | | ||  ||||||  ||  |  | || | || ||   ||     |  ||| ||||| |||||  | ||||||||||| || || || |||||||| ||||| ||||| || ||||| ||||||||||||||||| |
gcatggcatgttcttgtgcatctactatgaggtagttgttttaacc---ttcc---tatgtttaatatttactgaatattattcttccaattgtggtttcccctagCCATTGCTGTTTCTCGAGATCACAAACCAGACCAAACTGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCAG

upper sequence: GRMZM5G829894_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G06310.1 (Glycine max), 3'ss of exon 4

ttgtgacgaatggataaactgaatatcaggattccaagctaaccacgtt---ccacttgtattcgatattttttg--ttatgttttccccatctcggag--ctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG
       | ||||          |      | |   || ||      ||   |    | | ||  ||||||  ||  |  | || | || ||   ||    ||  ||| ||||| |||||  | |||||||| ||||| || || |||||||| ||||| ||||| || ||||| |||||||||||||||||||
-------gtatggcatgttcttgtgcatctactgtgagatagttgttttaacctttctatgttgaatatttgctgaatattattcttccaattgtggtttcctctagCCATTGCTGTTTCTCGAGATCACAAGCCTGACCAAACTGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCTG

upper sequence: GRMZM5G829894_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA14G12220.1 (Glycine max), 3'ss of exon 4

ttgtgacgaatggataaactgaatatcaggattccaagcta-accacgttccacttgtattcgatattttttgttatgttttccccatctcggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG
|  |      |   |    ||  | |   |||     |||  | |    |  ||||| ||      ||   | || |  |||||   |||      |  ||| ||||| |||||  |||||||||| || ||||| || |||||||| | ||| ||||| || ||||| |||||||||||||||||||
tcatagtttgtacttcttgtgcttctgttgataaattgcttcagccttctgaacttgaatggtgacttaaatatttttctttccttttctttcc-ttctagCCATTGCTGTTTCTCGGGATCACAAGCCAGATCAAACTGATGAGAGGCGAAGGATTGAAGATGCAGGTGGCTTTGTTATGTGGGCTG

upper sequence: GRMZM5G829894_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 5

------ttgtgacgaatggataaactgaatatcaggattccaagctaaccacgttccacttgtattcgatattt-tttgttatgttttccccatctcggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG
      || | |  |   ||||  |    |    | | |      |||   || ||   || | |  | || |  |||| ||| ||||     | |    |    ||| ||||| || ||  | |||||||| |||||||| |  || ||| | |||||||||||||| ||||| || ||||| ||||||||||
acatacttataatcacatgatagcccttgttcatgaaatttgcaataagt-cgctctgttt-tgtatggtactaatttgatat-ttttttttgttt----gtcaaagCTATTGCTGTATCCCGAGATCACAAGCCTGATCAAAGTGACGAGCGCCAAAGAATTGAGGATGCAGGAGGATTTGTCATGTGGGCTG

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|60341056|gb|DN208029.1|DN208029

EST:     TGTTGCAAATGTTGGAGATTCTAGAGCCGTTATTTCTAAAGGAGGACAAG                         CGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAA
genomic: TGTTGCAAATGTTGGAGATTCTAGAGCCGTTATTTCTAAAGGAGGACAAGgtaagtttct ... ggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAA

EST: gi|149099178|gb|EE185204.2|EE185204

EST:     TGTTGCAAATGTTGGAGATTCTAGAGCCGTTATTTCTAAAGGAGGACAAG                         CGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAA
genomic: TGTTGCAAATGTTGGAGATTCTAGAGCCGTTATTTCTAAAGGAGGACAAGgtaagtttct ... ggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAA

EST: gi|166461242|gb|EG146934.1|EG146934

EST:     TGTTGCAAATGTTGGAGATTCTAGAGCCGTTATTTCTAAAGGAGGACAGG                         CGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGA
genomic: TGTTGCAAATGTTGGAGATTCTAGAGCCGTTATTTCTAAAGGAGGACAAGgtaagtttct ... ggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGA

EST: gi|21481348|gb|BQ578031.1|BQ578031

EST:     TGTTGCAAATGTTGGAGATTCTAGAGCCGTTATTTCTAAAGGAGGACAAG                         CGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAA
genomic: TGTTGCAAATGTTGGAGATTCTAGAGCCGTTATTTCTAAAGGAGGACAAGgtaagtttct ... ggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAA

EST: gi|33096324|gb|CF056318.1|CF056318

EST:     TGTTGCAAATGTTGGAGATTCTAGAGCCGTTATTTCTAAAGGAGGACAAG                         CGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAA
genomic: TGTTGCAAATGTTGGAGATTCTAGAGCCGTTATTTCTAAAGGAGGACAAGgtaagtttct ... ggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAA

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), 49 (downstream exon)
Score: 722

GATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGACCGTTTGCTTGTTGCAAATGTTGGAGATTCTAGAGCCGTTATTTCTAAAGGAGGACAAGgtaagtttct ... ggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 562

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 715

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 436

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cgttccacttgtattcgatattttttgttatgttttccccatctcggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG

                                ttttccccatctcg  CT-rich tract
                 atattttttgttatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtgacgaatggataaactgaatatcaggattccaagctaaccacgttccacttgtattcgatattttttgttatgttttccccatctcggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - aactgaa
- - - - - - - - - - - - - - - - -ccaagct
- - - - - - - - - - - - - - - - - - - - - - - - - - cttgtat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttgtt