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

...gcaccaaatccctgagttctgataattttcaaaccagaaattccacttgtttatcattatgatgtccagaagcatgaacatctacctttcatctctccagATACCCGAACCTGAAGAGTGTTAGGGAATTGATCTACAAAAGAGGTTATGGGAAGCTGAACAAGCAGAGGATTCCGCTTAGCAACAACAATGTCATCGAG

Basic information

species	Zea mays
transcript	GRMZM2G178807_T03
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G178807_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G23750.2 (Glycine max), 3'ss of exon 5

gcaccaaatccctgagttctgataattttcaaaccagaaattccacttgtttatcattat-gatgtccagaagcatgaacatctacctttcatct-ctccagATACCCGAACCTGAAGAGTGTTAGGGAATTGATCTACAAAAGAGGTTATGGGAAGCTGAACAAGCAGAGGATTCCGCTTAGCAACAACAATGTCATCGAG
                 | || | | || |   ||| |      | ||  |||| ||||| | | |  | ||     ||         | | | |  |  |||||||| || || |||||||| || ||| | || ||||| ||||| ||||| ||||| ||||||||||||| | | || |   |||||    |||| |||
----------------gtatgtttacttccctgccata---cttatttaattatgattataggtttttataactgctaatgagacttctgcttttgttttagATACCCAAATCTTAAGAGTGTGAGAGAACTTATTTACAAGAGAGGGTATGGAAAGCTAAACAAGCAGAGGACTGCTCTAACTGACAACTCCATCATTGAG

upper sequence: GRMZM2G178807_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA15G18170.2 (Glycine max), 3'ss of exon 5

gcaccaaatccctgagttctgataattttcaaaccagaaattccacttgtttatcattatgatgtccagaagcatgaacatctacctttcatctctccagATACCCGAACCTGAAGAGTGTTAGGGAATTGATCTACAAAAGAGGTTATGGGAAGCTGAACAAGCAGAGGATTCCGCTTAGCAACAACAATGTCATCGAG
               ||      || ||  |   ||   ||||   | ||| || |     |   |||      | || || | |   ||  | || ||| ||||| ||  ||||||||||||| |||||||||||||| || || ||||| ||  | ||||||||||| ||| |  | |   |||||  | | || || 
---------------gtaagtgaaagttcaactacattgattctcatggttcattacctgca---ccatggttcttaatatttgcaaatc--cacttcagGTACCCTAATTTGAAGAGTGTTAGAGAATTGATCTACAAGAGGGGCTATGGAAAAGTTAACAAGCAGAGAATTGCTTTGACAGACAACTCTATTATTGAA

upper sequence: GRMZM2G178807_T03 (Zea mays), 3'ss of exon 4
lower sequence: AT2G01250.1 (Arabidopsis thaliana), 3'ss of exon 5

gcaccaaatccctgagttctgataattttcaaaccagaaattccacttgtttatcattatgat-gtccagaagcatgaacatctacctttcatctctccagATACCCGAACCTGAAGAGTGTTAGGGAATTGATCTACAAAAGAGGTTATGGGAAGCTGAACAAGCAGAGGATTCCGCTTAGCAACAACAATGTCATCGAG
     |  |   |    ||| ||       |||||    | ||   |  | |   || |  |  |||  ||||  ||    | | |  |||   | | ||||| ||| ||| |||||||||| | ||||||||||||||| |||||||| || ||||| ||| | ||||||||  |  | |   |||||  | |  | |||
---gtatgtatatacactctcat----cctaaaccctttaatctgatgctatgagataacaagagtcttgaagagtgtgacttttctcttctgtttttcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGGAAAGCTTAACCACCAGAGGATAGCTTTGACTGACAACTCTATTGTAGAG

upper sequence: GRMZM2G178807_T03 (Zea mays), 3'ss of exon 4
lower sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 5

gcaccaaatccctgagttctgataattttcaaaccagaaattccacttgtttatcattatga-tgtccagaagcatgaacat---ctacctttcatctctccagATACCCGAACCTGAAGAGTGTTAGGGAATTGATCTACAAAAGAGGTTATGGGAAGCTGAACAAGCAGAGGATTCCGCTTAGCAACAACAATGTCATCGAG
| |||    | ||  || || | | |||  ||||       |   ||| |||| | | || | |     | ||  | | |||   | ||  ||  | ||  ||||||||||||| | || ||||| | ||||||||| |||||| |||||| ||| ||||| ||| | ||||||| | |  | |   ||||   | |  | || 
gtacc---cctcttcgtgcttaca-tttcaaaacttt---cttttcttatttaacctcattagtaagtggtagtcttaccatggacgactcttgttttcctcagATACCCGAACTTAAAAAGTGTGAAGGAATTGATTTACAAACGAGGTTTTGGAAAGCTTAACCACCAGAGGACTGCCTTAACAGACAATTCTATTGTAGAT

upper sequence: GRMZM2G178807_T03 (Zea mays), 3'ss of exon 4
lower sequence: AT2G44120.1 (Arabidopsis thaliana), 3'ss of exon 5

gcaccaaatccctgagttctgataattttcaaaccagaaattccacttgtttatcattatgatgtccagaagcatgaacatctacctttcatctctccagATACCCGAACCTGAAGAGTGTTAGGGAATTGATCTACAAAAGAGGTTATGGGAAGCTGAACAAGCAGAGGATTCCGCTTAGCAACAACAATGTCATCGAG
| |   ||||  ||| |     |   ||||||       |||        | | |  |||| ||  |  || |   |  || || ||        | ||||||||| ||| ||||||| |||| |||| |||||||||||||||||||||| ||||||||| | ||||||||  | ||||   |||||    |  | || 
gtatgcaatc--tgattctctct--ctttcaat---aggattatgtaaactaaactatatgctgctctaaaccg-aatgatatatct------ggtgcagATACCCAAACTTGAAGAGCGTTAAGGAACTGATCTACAAAAGAGGTTATGGAAAGCTGAACCACCAGAGGATAGCACTTACTGACAACTCCATTGTGGAT

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|211270703|gb|FL364931.1|FL364931

EST:     AAGGCAACTATTAACATGCTACGGAGGGTGGAGCCATATGTTGCGTATGG                         ATACCCGAACCTGAAGAGTGTTAGGGAATTGATCTACMAAAGAGGTTATGG
genomic: AAGGCAACTATTAACATGCTACGGAGGGTGGAGCCATATGTTGCGTATGGgtaagtttgt ... atctctccagATACCCGAACCTGAAGAGTGTTAGGGAATTGATCTACAAAAGAGGTTATGG

EST: gi|211320069|gb|FL327290.1|FL327290

EST:     AAGGCAACTATTAACATGCTACGGARGGTGGAGCCATATGTTGCGTATGG                         ATACCCGAACCTGAAGAGTGT
genomic: AAGGCAACTATTAACATGCTACGGAGGGTGGAGCCATATGTTGCGTATGGgtaagtttgt ... atctctccagATACCCGAACCTGAAGAGTGT

EST: gi|21809687|gb|BQ668005.1|BQ668005

EST:     AGGCCAACTATTAACATGCTACGGAGGGTGGAGCCATATGTTGCGTATGG                         ATACCCGAACCTGAAGAGTGCTTAGGGCAATTGATCTACAAAAGAGGTTAT
genomic: AGGC-AACTATTAACATGCTACGGAGGGTGGAGCCATATGTTGCGTATGGgtaagtttgt ... atctctccagATACCCGAACCTGAAGAGTG-TTAGGG-AATTGATCTACAAAAGAGGTTAT

EST: gi|211375660|gb|FL343002.1|FL343002

EST:     AAGGCAACTATTAACATGCTACGGAGGGTGGAGCCATATGTTGCGTATGG                         ATACCCGAACCTGAAGAGTGTTAGGGAATTGATCTACAAAAGAGGTTATGG
genomic: AAGGCAACTATTAACATGCTACGGAGGGTGGAGCCATATGTTGCGTATGGgtaagtttgt ... atctctccagATACCCGAACCTGAAGAGTGTTAGGGAATTGATCTACAAAAGAGGTTATGG

EST: gi|50328295|gb|CO523421.1|CO523421

EST:     AAGGCAACTATTAACATGCTACGGAGGGTGGAGCCATATGTTGCGTATGG                         ATACCCGAACCTGAAGAGTGTTAGGGAATTGATCTACAAAAGAGGTTATGG
genomic: AAGGCAACTATTAACATGCTACGGAGGGTGGAGCCATATGTTGCGTATGGgtaagtttgt ... atctctccagATACCCGAACCTGAAGAGTGTTAGGGAATTGATCTACAAAAGAGGTTATGG

EST: gi|211438494|gb|FL357614.1|FL357614

EST:     AGGCAACTATCTAACATGCTACGGAGGGTGGAGCCATATGTTGCGTATGG                         ATACCCGAACCTGAAGAGTGTTANGGGAATTGATCTACAAAAGAGGTTTAT
genomic: AGGCAACTAT-TAACATGCTACGGAGGGTGGAGCCATATGTTGCGTATGGgtaagtttgt ... atctctccagATACCCGAACCTGAAGAGTGTTA-GGGAATTGATCTACAAAAGAGGTT-AT

EST: gi|211231342|gb|FL356545.1|FL356545

EST:     AAGGCAACTATTAACATGCTACGGAGGGTGGAGCCATATGTTGCGTATGG                         ATACCCGAACCTGAAGAGTGTTAGGGAATTGATCTACAAAAGAGGTTATGT
genomic: AAGGCAACTATTAACATGCTACGGAGGGTGGAGCCATATGTTGCGTATGGgtaagtttgt ... atctctccagATACCCGAACCTGAAGAGTGTTAGGGAATTGATCTACAAAAGAGGTTATGG

EST: gi|211103246|gb|FL316732.1|FL316732

EST:     AAGGCAACTATTAACATGCTACGGAGGGTGGAGCCATATGTTGCGTATGG                         ATACCCGAACCTGAAGAGTGTTAGGGAATTGATCTACAAAAGAGGTTATGG
genomic: AAGGCAACTATTAACATGCTACGGAGGGTGGAGCCATATGTTGCGTATGGgtaagtttgt ... atctctccagATACCCGAACCTGAAGAGTGTTAGGGAATTGATCTACAAAAGAGGTTATGG

EST: gi|60359483|gb|DN226456.1|DN226456

EST:     AAGGCAACTATTAACATGCTACGGAGGGTGGAGCCATATGTTGCGTATGG                         ATACCCGAACCTGAAGAGTGTTAGGGAATTGATCTACAAAAGAGGTTATGG
genomic: AAGGCAACTATTAACATGCTACGGAGGGTGGAGCCATATGTTGCGTATGGgtaagtttgt ... atctctccagATACCCGAACCTGAAGAGTGTTAGGGAATTGATCTACAAAAGAGGTTATGG

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: 198

AGCTCCTGCGTTTGAGGCAGATCTTCAATGGTGTCTTTCTCAAGGTTAACAAGGCAACTATTAACATGCTACGGAGGGTGGAGCCATATGTTGCGTATGGgtaagtttgt ... atctctccagATACCCGAACCTGAAGAGTGTTAGGGAATTGATCTACAAAAGAGGTTATGGGAAGCTGAACAAGCAGAGGATTCCGCTTAGCAACAACAATGTCATCGAG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 86

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 125

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 73

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cttgtttatcattatgatgtccagaagcatgaacatctacctttcatctctccagATACCCGAACCTGAAGAGTGTTAGGGAATTGATCTACAAAAGAGGTTATGGGAAGCTGAACAAGCAGAGGATTCCGCTTAGCAACAACAATGTCATCGAG

                                   tctacctttcatctct  CT-rich tract
     ttatcattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaccaaatccctgagttctgataattttcaaaccagaaattccacttgtttatcattatgatgtccagaagcatgaacatctacctttcatctctccagATACCCGAACCTGAAGAGTGTTAGGGAATTGATCTACAAAAGAGGTTATGGGAAGCTGAACAAGCAGAGGATTCCGCTTAGCAACAACAATGTCATCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
-caccaaa
- - - - - - - - ttctgat
- - - - - - - - - - - - - - -caaacca
- - - - - - - - - - - - - - - - - - - - - - -cttgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgaa