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

...ttgcatgtatattatgttggttcagagttcaggggactcaattgaactcttgtgcatatgcaatgcgaaaacatgtataaataacaatttctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCACCTTCATTCGAGGATATTTCTCAAGCCATAGATTTCATCCATC

Basic information

species	Zea mays
transcript	GRMZM2G051288_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G051288_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g53710.1 (Oryza sativa), 3'ss of exon 2

ttgcatgtatattatgttggttcagag---ttcaggggactcaattgaactcttgtgcatatgcaatgcgaaaacatgt--ataaataacaatttct--cttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCACCTTCATTCGAGGATATTTCTCAAGCCATAGATTTCATCCATC
       |  |||   ||  ||||| |   ||      |||  |||      |||   ||   |||||| | | | |    |  | |||||| | ||   ||  |||||  ||| |||||| |||||  | ||||| |||||||| ||||| ||||||||  |  || ||||||||| ||||||||||||||| ||||| |
------attcatttgattcattcaggggattttcaatcactttattttgtgtttgca-atcaacaatgcaagatcctcctgacgagtaacaagtcctacttttgcagGCCCATGGGATTGACCACCTTATTATTCCCACAAGAGACTACCTGTTTGCACCAGCCCTCCAGGATATTTGTCAAGCCATAGATTTTATCCACC

upper sequence: GRMZM2G051288_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv11s0016g02890.t01 (Vitis vinifera), 3'ss of exon 3

ttgcatgtatattatgttggttcagagttcaggggactcaattgaactcttgtgcatatgcaatgcgaaaacatgtataaataacaatttctc--ttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCACCTTCATTCGAGGATATTTCTCAAGCCATAGATTTCATCCATC
 | | |   ||||||     || ||  || |      |   ||||||  |  |   | ||  ||     | |      |    |   |||     ||  |||||| ||||||| || |||||||||||||| |||||||||||||| ||||| |||||||| | |||||||   |  ||  |||||||||| ||| 
-tcctttgctattattccctttaagtatttaaaattttggcttgaacattcttttttgtg-gatttatgacctctcccattccattgtttgatggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA

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|50332926|gb|CO528052.1|CO528052

EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA

EST: gi|149104022|gb|EE289453.2|EE289453

EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA

EST: gi|148932664|gb|EC876596.2|EC876596

EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA

EST: gi|93014040|gb|EB639560.1|EB639560

EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCCACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA

EST: gi|67018199|gb|CO446948.1|CO446948

EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCTACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA

EST: gi|76928986|gb|DV171845.1|DV171845

EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA

EST: gi|149009261|gb|EE041354.2|EE041354

EST:     AACCGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTC
genomic: AAC-GTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTC

EST: gi|50327588|gb|CO522714.1|CO522714

EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA

EST: gi|71444037|gb|DR825087.1|DR825087

EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA

EST: gi|149080697|gb|EE169757.2|EE169757

EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGAATACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA

EST: gi|148985353|gb|EE029663.2|EE029663

EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA

EST: gi|71310365|gb|DR791488.1|DR791488

EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACA-GAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA

EST: gi|101385912|gb|EB815004.1|EB815004

EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA

EST: gi|50338986|gb|CO534112.1|CO534112

EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA

EST: gi|71766290|gb|DR964227.1|DR964227

EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA

EST: gi|91055876|gb|EB166294.1|EB166294

EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA

EST: gi|78119952|gb|DV538336.1|DV538336

EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA

EST: gi|148952076|gb|EC897867.2|EC897867

EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAGCAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA

EST: gi|88756074|gb|DY540215.1|DY540215

EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACA-GAGATTACCTCTTTG
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTG

EST: gi|89250671|gb|DY622457.1|DY622457

EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA

EST: gi|50328153|gb|CO523279.1|CO523279

EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA

EST: gi|71331076|gb|DR802368.1|DR802368

EST:     TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAG                         GCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA
genomic: TAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCA

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: 73

TTTCCCAAGTGATGTTCCACGGTTGAAGCAGCTTGGAGTTCAAGGGGTTGTAACGTTGAATGAACCTTATGAAACTCTTGTCCCAACATCTTTATACCAGgtactattcc ... ctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCACCTTCATTCGAGGATATTTCTCAAGCCATAGATTTCATCCATC

Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 85

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 99

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 78

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

actcttgtgcatatgcaatgcgaaaacatgtataaataacaatttctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCACCTTCATTCGAGGATATTTCTCAAGCCATAGATTTCATCCATC

                                 aaataac  putative branch site (score: 78)
                                          tttctcttacc  putative PPT
                      aaaacatgtataaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgcatgtatattatgttggttcagagttcaggggactcaattgaactcttgtgcatatgcaatgcgaaaacatgtataaataacaatttctcttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCACCTTCATTCGAGGATATTTCTCAAGCCATAGATTTCATCCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
-tgcatgt
- -catgtat
- - - - - - - tgttggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aataaca