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

...tattcattgtgactaacatgccttacaacaactcaaaaatcttgtacatatgtcctctgtcattagttataggtttaaattcctctttctcttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTCGAGGCAATGTCTGCGATGAGGGAATCCTTTTCTACTCTTCAGAAACTAC

Basic information

species	Zea mays
transcript	GRMZM2G151580_T01
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G151580_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os08g10410.1 (Oryza sativa), 3'ss of exon 5

tattcattgtgactaacatgccttacaa-caactcaaaaatc---ttgtacatatgtcctctgt---cattagttataggtttaa-attcctctttctcttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTCGAGGCAATGTCTGCGATGAGGGAATCCTTTTCTACTCTTCAGAAACTAC
          ||||     | | || ||    |||| |  |    ||||| || |||    |||    ||| |  || |||||||   |    ||| |||| |||||||||||||| |||||||| |||||||| |||||||| ||||| || ||||| ||||| |||||||| |||||||||||||| ||||| ||||||||| |||
--------acgactgcttggtcctataaatggctcagatttgtaattgtaaatctgttacttgttgttattggagattggtttaatggttacttttatcttgatgaagGAAATGCTTCGACCGATACCTGCTGCGCTTGCTTCTTGCACGCGCTTCTTTGAGGCCATGTCTGCAATGAGGGAATCCTTCTCTACACTTCAGAAATTAC

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|8383242|gb|BE056185.1|BE056185

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC

EST: gi|58029918|gb|CX725345.1|CX725345

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC

EST: gi|211033211|gb|FK982752.1|FK982752

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC

EST: gi|18168949|gb|BM338789.1|BM338789

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC

EST: gi|76934754|gb|DV174014.1|DV174014

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC

EST: gi|86470304|gb|DY236674.1|DY236674

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC

EST: gi|101383901|gb|EB814005.1|EB814005

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC

EST: gi|21625975|gb|BQ620896.1|BQ620896

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC

EST: gi|44901235|gb|CK827780.1|CK827780

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCTGTTCTTC
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC

EST: gi|74245692|gb|DT653606.1|DT653606

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC

EST: gi|113701683|gb|EE679187.1|EE679187

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC

EST: gi|149079676|gb|EE168672.2|EE168672

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC

EST: gi|148965294|gb|EE016099.2|EE016099

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC

EST: gi|211033210|gb|FK982751.1|FK982751

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC

EST: gi|211529717|gb|FL481424.1|FL481424

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC

EST: gi|101394443|gb|EB819156.1|EB819156

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC

EST: gi|31350966|gb|CD435323.1|CD435323

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCAC
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCAC

EST: gi|78110456|gb|DV528866.1|DV528866

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTG
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC

EST: gi|60341829|gb|DN208802.1|DN208802

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC

EST: gi|28986849|gb|CB351340.1|CB351340

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC

EST: gi|211033209|gb|FK982750.1|FK982750

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC

EST: gi|31352195|gb|CD436552.1|CD436552

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC

EST: gi|149059488|gb|EE156973.2|EE156973

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC

EST: gi|78110457|gb|DV528867.1|DV528867

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC

EST: gi|74245691|gb|DT653605.1|DT653605

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC

EST: gi|211259909|gb|FL431082.1|FL431082

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC

EST: gi|86467153|gb|DY233523.1|DY233523

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCATCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC

EST: gi|22473167|gb|BU037647.1|BU037647

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGC
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGC

EST: gi|18174900|gb|BM350288.1|BM350288

EST:     GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGG                         GAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC
genomic: GCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTC

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), 48 (downstream exon)
Score: 102

GCTACTTCTGAAAGCAGCAAGTGACTATGGGGCATTGACAGCATCAGTCGGCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCACCAGCTGTCTGGGGGgtaagttaat ... cttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTCGAGGCAATGTCTGCGATGAGGGAATCCTTTTCTACTCTTCAGAAACTAC

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 51

Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 36

Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 108

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

acatatgtcctctgtcattagttataggtttaaattcctctttctcttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTCGAGGCAATGTCTGCGATGAGGGAATCCTTTTCTACTCTTCAGAAACTAC

                                            tcttaat  putative branch site (score: 108)
                                  ttcctctttctcttaa  CT-rich tract
                     ttataggtttaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattcattgtgactaacatgccttacaacaactcaaaaatcttgtacatatgtcctctgtcattagttataggtttaaattcctctttctcttaatgaagGAAATGCTGCGACCGATTCCTGCTGCACTTGCTTCCTGCACCCGGTTCTTCGAGGCAATGTCTGCGATGAGGGAATCCTTTTCTACTCTTCAGAAACTAC

- - - - - - - -acatgcc
- - - - - - - - - - - - -caacaac
- - - - - - - - - - - - - - - - -caaaaatc