ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtacgtcgaacaatcggatcatcgtcagcgagtgttagttatccgagctagctaggtgacgaccccgcgctgacctcatcagctggcatggtgatcggtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACCGCAAGTACCCGAATGGCTCCAGGCCTAACCGGGCGGCCGGGACAGGGTA

Basic information

species	Zea mays
transcript	GRMZM2G123667_T01
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G123667_T05 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g08210.1 (Oryza sativa), 3'ss of exon 1

gtacgtcgaacaatcggatcatcgtcagcgagtgttagtt-atccgagctagctaggtgacgaccccgcgctgacctcatcagctggcatggtgatcggtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACCGCAAGTACCCGAATGGCTCCAGGCCTAACCGGGCGGCCGGGACAGGGTA
                  | | |   ||| |  |    |  |  |||       |  |      |     |  |    || |  |||     ||     | |||||||||| |||| | || |||||||||||||||||||||||||||||||| ||||| ||||||||||| ||     |||| ||| ||||||| ||||| |||||
-----------------gtaagcaagagcaaaagcagatcgaatcgaatcgaggaaattgaagtcgaattcaaattcaattaattggggatttgg--aattgttgcagAGAGGGCGATGGGAGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGGGACCGGAAGTACCCGAACGGGCAGCGGCCGAACAGGGCGGCGGGGACGGGGTA

upper sequence: GRMZM2G123667_T05 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA04G42800.1 (Glycine max), 3'ss of exon 1

gtacgtcgaacaatcggatcatcgtcagcgagtgttagttatccgagctagctaggtgacgaccccgcgctgacctcatcagctggcatggtgatcggtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACCGCAAGTACCCGAATGGCTCCAGGCCTAACCGGGCGGCCGGGACAGGGTA
                       || |     | ||     || ||  ||      |    |   |    |    ||||    ||  || || || |     | |||    ||| | |   || ||||| |||||||||||||| || || || ||||| || |||||||| || |||||||| ||||||||||| || || || ||
-----------------------gtaacattatcttcaacttctgatatattcttattcttaattcttaattcattcattttttga-attgttattg-----tacagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACCGGAAATACCCGAACGGTTCCAGGCCGAACCGGGCGGCGGGAACCGGTTA

upper sequence: GRMZM2G123667_T05 (Zea mays), 3'ss of exon 1
lower sequence: Vv07s0031g02610.t01 (Vitis vinifera), 3'ss of exon 1

gtacgtcgaacaatcggatcatcgtcagcgagtgttagttatccgagctagctaggtgacgaccccgcg-ctgacctcatcagctggcatggtgatcggtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACCGCAAGTACCCGAATGGCTCCAGGCCTAACCGGGCGGCCGGGACAGGGTA
  |  |   ||||    || ||||  |     ||| | |  ||    |||| |  |  |     | |   ||||  |       |    |||   | |||   |||||  | |||  |    || || |||||||||||||||||||| ||  | |||||||| || || || || || ||||||||||||||||||||  | || ||
-aatttttgacaaat--atgatcgaaact--ctgtaaatcgtctct-ctagttcagcaaattttcagaaactgaatttggatatt--tttggaattgggtttctgcagGAATGGCTCTGTACGGTGAAAAGGAGTGGTACTTCTTCTCTCCAAGGGACCGCAAATATCCCAACGGTTCAAGGCCTAACCGGGCGGCCGGATCCGGCTA

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|211322211|gb|FL322860.1|FL322860

EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC

EST: gi|38687829|gb|CK144860.1|CK144860

EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC

EST: gi|211331126|gb|FL341576.1|FL341576

EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC

EST: gi|211518019|gb|FL144160.1|FL144160

EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC

EST: gi|211165931|gb|FL144172.1|FL144172

EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC

EST: gi|17921555|gb|BM259206.1|BM259206

EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC

EST: gi|149078700|gb|EE167497.2|EE167497

EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC

EST: gi|211165934|gb|FL144175.1|FL144175

EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGAGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC

EST: gi|211165936|gb|FL144177.1|FL144177

EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC

EST: gi|211329589|gb|FL022638.1|FL022638

EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC

EST: gi|211145460|gb|FL359539.1|FL359539

EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAAGAAGGAGTGGTACTTCTTCTCGCCGCGCGAC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGA-GAAGGAGTGGTACTTCTTCTCGCCGCGCGAC

EST: gi|211449319|gb|FL365458.1|FL365458

EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC

EST: gi|211518024|gb|FL144165.1|FL144165

EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC

EST: gi|19351281|gb|BM895813.1|BM895813

EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC

EST: gi|211127219|gb|FL366470.1|FL366470

EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC

EST: gi|211165928|gb|FL144169.1|FL144169

EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAAAAAAGGAGTGGTACTTCTTCTCGCCGCGCGA
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAA--GGAGTGGTACTTCTTCTCGCCGCGCGA

EST: gi|89756736|gb|DY686654.1|DY686654

EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC

EST: gi|211285411|gb|FL349550.1|FL349550

EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC

EST: gi|88756318|gb|DY540459.1|DY540459

EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC

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: 11 (upstream exon), 39 (downstream exon)
Score: 1

GTGATGTACTATCTCCTCCGCAAGTGCGGCGGCCTGCCGCTCGCCGCGCCGGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACCGCAAGTACCCGAATGGCTCCAGGCCTAACCGGGCGGCCGGGACAGGGTA

Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 32

Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 25

Block sizes: 49 (upstream exon), 27 (downstream exon)
Score: 2

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

taggtgacgaccccgcgctgacctcatcagctggcatggtgatcggtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACCGCAAGTACCCGAATGGCTCCAGGCCTAACCGGGCGGCCGGGACAGGGTA