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

gtgggtgcacattttctatcttaaatgtcagatcatgtagaaacttccaacaccaaaagacgaactatttatctataatacttttgttttgcagCTGATGAGATTAAAGAGTTGTGGGAAGAATATGAGAACAATTCTTCTATTGAAGCCAATCTTGTAAAAGATTTTGATAAA

Basic information

species	Zea mays
transcript	GRMZM2G088397_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G088397_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g45390.2 (Oryza sativa), 3'ss of exon 4

gtgggtgcacattttctatcttaaatgtcagatcatgtagaa--acttccaacaccaaaagacgaactatttatctataatacttttgttttgcagCTGATGAGATTAAAGAGTTGTGGGAAGAATATGAGAACAATTCTTCTATTGAAGCCAATCTTGTAAAAGATTTTGATAAA
||  |||  |||||   || | |  |   || ||||| || |  |  |   ||| |||    |  |||| ||   ||   | || || ||||| |||||||||||| || ||| | |||||||||||||| || ||||| || ||||||||||| |||||||| ||||||||||||
gtttgtgtccatttgggatgtgacgtccgagttcatgaaggatgatgtttgacatcaatcttc--actactt--ttagtgttctgtt-ttttgtagCTGATGAGATCAAGGAGCTCTGGGAAGAATATGAAAATAATTCATCCATTGAAGCCAACCTTGTAAAGGATTTTGATAAA

upper sequence: GRMZM2G088397_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA01G23210.1 (Glycine max), 3'ss of exon 1

gtgggtgcacattttctatcttaaatgtcagatcatgtagaaacttccaacaccaaaagacgaactatttatctataatacttttgttttgcagCTGATGAGATTAAAGAGTTGTGGGAAGAATATGAGAACAATTCTTCTATTGAAGCCAATCTTGTAAAAGATTTTGATAAA
||   |||| ||| | | |||   |    |  |  |  ||| | ||||||       |    |  || ||      | |   ||| | || ||||||| ||||| |||||  | |||| ||| ||||| |||||||||||| | || || ||||||||||| |||||||| || 
gtat-tgcaaattatttttctggga----aacttttacagaga-ttccaaatttggcatcaaatttacttgaggccactttgtttttattacagCTGAAGAGATCAAAGAACTTTGGGCAGAGTATGAAAACAATTCTTCTTTAGAGGCAAATCTTGTAAAGGATTTTGACAAG

upper sequence: GRMZM2G088397_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G14300.1 (Glycine max), 3'ss of exon 4

gtgggtgcacattttctatcttaaatgtcagatcatgtagaaacttccaacac--caaaagacgaact--atttatctataatacttttgttttgcagCTGATGAGATTAAAGAGTTGTGGGAAGAATATGAGAACAATTCTTCTATTGAAGCCAATCTTGTAAAAGATTTTGATAAA
||   || | ||| | | ||||  |  |    |  |  ||| | | | ||     ||  | |   |||    | |  | |  |  |  | | || ||||||| ||||| |||||  | |||||||| ||||| |||||||||||| | || || |||||||| || |||||||| || 
gtat-tgtaaattatttttcttggaatt----ttttacagagattccaaatttggcatcaaatttacttaggtcacttttttttttcctttattacagCTGAGGAGATCAAAGAACTTTGGGAAGAGTATGAAAACAATTCTTCTGTAGAGGCAAATCTTGTTAAGGATTTTGACAAG

upper sequence: GRMZM2G088397_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT1G26160.1 (Arabidopsis thaliana), 3'ss of exon 4

gtgggtgcacattttctatcttaaatgtcagatcatgtagaaacttccaacaccaaaagacgaactatttatctataatacttttgttttgcagCTGATGAGATTAAAGAGTTGTGGGAAGAATATGAGAACAATTCTTCTATTGAAGCCAATCTTGTAAAAGATTTTGATAAA
      | | ||   |  |    | |||||  |  | | |    ||      |||||| ||    |||||||      || | |     |||||| || ||||| | |||  | |||   || |||||||||||| ||||| | ||||| ||| |||||||||| |||||||| 
------gtatatacgcctttgccactgtcatcttctattg---ttttggtttccaaaacac---ttatttataagcc-taatgtcaacgtgcagCGGAGGAGATCACAGAACTTTGGCTGGAGTATGAGAACAATGCTTCTTTAGAAGCAAATATTGTAAAAGACTTTGATAAG

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|37398538|gb|CF636584.1|CF636584

EST:     ACAAGCAGCACTAGATGAAATGTGCCAAGTTCTTGGTGGTGGGCCAGCTG                         CTGATGAGATTAAAGAGTTGTGGGAAGAATATGAGAACAATTCTTCTATTG
genomic: ACAAGCAGCACTAGATGAAATGTGCCAAGTTCTTGGTGGTGGGCCAGCTGgtgggtgcac ... tgttttgcagCTGATGAGATTAAAGAGTTGTGGGAAGAATATGAGAACAATTCTTCTATTG

EST: gi|211216465|gb|FL469136.1|FL469136

EST:     GTGGTGGGCCAGCTG                         CTGATGAGATTAAAGAGTTGTGGGAAGAATATGAGAACAAATTCTTCTATT
genomic: GTGGTGGGCCAGCTGgtgggtgcac ... tgttttgcagCTGATGAGATTAAAGAGTTGTGGGAAGAATATGAGAAC-AATTCTTCTATT

EST: gi|37383541|gb|CF628790.1|CF628790

EST:     ACAAGCAGCACTATATGAAATGTGCCAAGTTCTTGGTGGTGGGCCAGCTG                         CTGATGAGATTAAAGAGTTGTGGGAAGAATATGAGAACAATTCTTCTATTG
genomic: ACAAGCAGCACTAGATGAAATGTGCCAAGTTCTTGGTGGTGGGCCAGCTGgtgggtgcac ... tgttttgcagCTGATGAGATTAAAGAGTTGTGGGAAGAATATGAGAACAATTCTTCTATTG

EST: gi|32840843|gb|CD980524.1|CD980524

EST:     ACAAGCAGCACTAGATGAAATGTGCCAAGTTCTTGGTGGTGGGCCAGCTG                         CTGATGAGATTAAAGAGTTGTGGGAAGAATATGAGAACAATTCTTCTATTG
genomic: ACAAGCAGCACTAGATGAAATGTGCCAAGTTCTTGGTGGTGGGCCAGCTGgtgggtgcac ... tgttttgcagCTGATGAGATTAAAGAGTTGTGGGAAGAATATGAGAACAATTCTTCTATTG

EST: gi|194717181|gb|FK934334.1|FK934334

EST:     ACAAGCAGCACTAGATGAAATGTGCCAAGTTCTTGGTGGTGGNCCAGCTG                         CTGATGAGATTAAAGAGTTGTGGGAAGAATATGAGAACAATTCTTCTATTG
genomic: ACAAGCAGCACTAGATGAAATGTGCCAAGTTCTTGGTGGTGGGCCAGCTGgtgggtgcac ... tgttttgcagCTGATGAGATTAAAGAGTTGTGGGAAGAATATGAGAACAATTCTTCTATTG

EST: gi|32945555|gb|CF050374.1|CF050374

EST:     ACAAGCAGCACTAGATGAAATGTGCCAAGTTCTTGGTGGTGGGCCAGCTG                         CTGATGAGATTAAAGAGTTGTGGGAAGAATATGAGAACAATTCTTCTATTG
genomic: ACAAGCAGCACTAGATGAAATGTGCCAAGTTCTTGGTGGTGGGCCAGCTGgtgggtgcac ... tgttttgcagCTGATGAGATTAAAGAGTTGTGGGAAGAATATGAGAACAATTCTTCTATTG

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: 156

GACATTACCCCATCGGATGGTATACCTAAGGCTGAAAAAAGCCGGCGCGAACAAGCAGCACTAGATGAAATGTGCCAAGTTCTTGGTGGTGGGCCAGCTGgtgggtgcac ... tgttttgcagCTGATGAGATTAAAGAGTTGTGGGAAGAATATGAGAACAATTCTTCTATTGAAGCCAATCTTGTAAAAGATTTTGATAAA

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 107

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 99

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 132

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gaaacttccaacaccaaaagacgaactatttatctataatacttttgttttgcagCTGATGAGATTAAAGAGTTGTGGGAAGAATATGAGAACAATTCTTCTATTGAAGCCAATCTTGTAAAAGATTTTGATAAA

                                         cttttgtttt  CT-rich tract
                       aactatttatctataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtgcacattttctatcttaaatgtcagatcatgtagaaacttccaacaccaaaagacgaactatttatctataatacttttgttttgcagCTGATGAGATTAAAGAGTTGTGGGAAGAATATGAGAACAATTCTTCTATTGAAGCCAATCTTGTAAAAGATTTTGATAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC