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

gtacgtacgcacctgtcccccagcttgattggggttgtgttggtgaggaaggctaattctggaggttggttggttgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCAGCCGGGCCGGAGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTA

Basic information

species	Zea mays
transcript	GRMZM2G127453_T03
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G127453_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g56890.3 (Oryza sativa), 3'ss of exon 1

gtacgtacgcacctgtcccccagcttgattggggttgtgttggtgaggaaggctaattctggaggttggttggttgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCAGCCGGGCCGGAGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTA
    || ||  ||  |  | | | | | || || | |||  || || |  || |||||||     | || |   ||||| |||||||||||||||||| || |||||| |||| ||||||||  | | |||||| |||||||||||||||||||||||||| ||||| ||||| ||  ||||  
----gtgcgttcccttttctcggttcggtttggttggtg--ggggaaggggg-taattctaattctgggct---tgctctgcagCATCCGGATCCGATAGGGGAGGGGTTGGCCATGGAGGCTATGGTGGAGGCGGCCGGGCCGGAGTGCATCGTGCCCGGGCAGCAGGCGCCGCTGCGGCTGC

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|211045913|gb|FK963041.1|FK963041

EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATCGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA

EST: gi|31909649|gb|CD651024.1|CD651024

EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA

EST: gi|211042955|gb|FK963033.1|FK963033

EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATCGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA

EST: gi|211042961|gb|FK963039.1|FK963039

EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATCGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA

EST: gi|211042956|gb|FK963034.1|FK963034

EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATCGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA

EST: gi|211045917|gb|FK963045.1|FK963045

EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATCGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA

EST: gi|211167601|gb|FL258650.1|FL258650

EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA

EST: gi|211245830|gb|FL313150.1|FL313150

EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATCGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA

EST: gi|31353639|gb|CD437996.1|CD437996

EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATCGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA

EST: gi|211042950|gb|FK963028.1|FK963028

EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATCGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA

EST: gi|211167597|gb|FL258646.1|FL258646

EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA

EST: gi|78180798|gb|DV551171.1|DV551171

EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA

EST: gi|8665358|gb|BE186174.1|BE186174

EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA

EST: gi|211167599|gb|FL258648.1|FL258648

EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA

EST: gi|211045919|gb|FK963047.1|FK963047

EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATCAAC                         CATCCGGATCCGATCGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA

EST: gi|8401369|gb|BE057003.1|BE057003

EST:     CCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: CCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA

EST: gi|5525193|gb|AI861191.1|AI861191

EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA

EST: gi|211042953|gb|FK963031.1|FK963031

EST:     GCGTTTCCACGCAGGAAGACTCCGNCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATCGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA

EST: gi|88755570|gb|DY539711.1|DY539711

EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA

EST: gi|211115674|gb|FL110115.1|FL110115

EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA

EST: gi|31909179|gb|CD650789.1|CD650789

EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA

EST: gi|211167596|gb|FL258645.1|FL258645

EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA

EST: gi|211045915|gb|FK963043.1|FK963043

EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATCGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGARGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA

EST: gi|211115672|gb|FL110113.1|FL110113

EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGA

EST: gi|31360970|gb|CD445327.1|CD445327

EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATCGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA

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), 46 (downstream exon)
Score: 93

GGGGCAGGGGATCCGACCCGTCCCGCGCATCAACCACGCCTCCGTCCTCCGCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCAGCCGGGCCGGAGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 819

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 327

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 164

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tggggttgtgttggtgaggaaggctaattctggaggttggttggttgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCAGCCGGGCCGGAGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTA

                     ggctaat  putative branch site (score: 164)
                                            ttgctcc  putative PPT
                        taattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtacgcacctgtcccccagcttgattggggttgtgttggtgaggaaggctaattctggaggttggttggttgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCAGCCGGGCCGGAGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG