ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtattggtaacccagatgtcctgctcccagcctattgaggtcaatggaactgggagcggagcacactgttcactcatcgcttgggttggaacctaatctgtcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTTCTCTTCATCCTTGGTATCACTCATGTGTTGTACAGTTTTGTAACAGTGG

Basic information

species	Zea mays
transcript	GRMZM2G089259_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G089259_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g07912.1 (Oryza sativa), 3'ss of exon 3

gtattggtaacccagatgtcctgctcccagcctattgaggtcaatggaactgggagcggagcacactgttcactcatcgcttgggttggaacctaatctgtcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTTCTCTTCATCCTTGGTATCACTCATGTGTTGTACAGTTTTGTAACAGTGG
      |||  |    ||      | ||| || |    |||| || | ||   |  ||  |||      |   |  | | ||  | |||    |  ||||   ||||||||| ||||| ||||||||||| || || |||||||| |||||||| |||||  | || |||||||||||||| ||||||||||||| ||||||||| || |
------gtagtcggtctggttctattccatccaaggatggtcgattggac---gttcgaggcatggcactttttggt-gattcagctggtgttttctctg---cttgcagGGTCATGAGCCTTTTGTTTCATATGAAGGCCTTGAACAGCTGCATCGGTTCTTGTTTATCCTTGGTATCACCCATGTGTTGTACACTTTTGTAACTGTTG

upper sequence: GRMZM2G089259_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA12G29080.1 (Glycine max), 3'ss of exon 2

gtattggtaacccagatgtcctgctcccagcctattgaggtcaatggaactgggagcggagcacactgttcactcatcgcttgggttggaacctaatctgtcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTTCTCTTCATCCTTGGTATCACTCATGTGTTGTACAGTTTTGTAACAGTGG
        || |   | | | |  ||     || ||||    | ||  |              || |  | ||  ||| |     |   ||  | |         |||||||||||||||| ||||||||||| ||||| ||||||||||||||||||||  | ||  | || || |||||||||||  |||| |||| | |  | || |
------acaaacttcagggcattatctt---ctgttgaacaaactgagatcaaatattctttgcaatact-acaaatcacccttctgaaaattttaataaatgaatgcagGGCCATGAACCATTTGTTTCGTATGAGGGTCTTGAGCAGCTGCACCGGTTCTTATTTGTTCTCGGGATCACTCATGTTCTGTATAGTTGTCTGGCTGTTG

upper sequence: GRMZM2G089259_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G20120.1 (Glycine max), 3'ss of exon 3

------------------------------------------------------------------------------gtattggtaacccagatgtcctgc-tcccagcctattgaggtcaatggaactgggagcggagcacactgt----tcactcatcgcttgggttggaacctaatctgtcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTTCTCTTCATCCTTGGTATCACTCATGTGTTGTACAGTTTTGTAACAGTGG
                                                                               ||  || || | |   |    || |      || ||||    | ||  |              |  ||       ||  |  |||    |   ||  | |         |||||||||||||||| |||||||| || ||||| |||||||||||||| |||||  | ||  | ||||| |||||||||||  |||| |||| | |  | || |
gtaacagtctgctgtaaagtgatttctgccttcacaagaaattcatttacaaaaaaaaattagttgaagattgaaaacatacaggaaaacaaacggcagggcattatcttctgttgaacaaactgagatcaaatatctgtttctttgaaatactacaaagtgctcttctgataattttaataaatgaatgcagGGCCATGAACCATTTGTTTCATATGAGGGTCTTGAGCAGCTGCATCGGTTCTTATTTGTTCTTGGGATCACTCATGTTCTGTATAGTTGTCTGGCTGTTG

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|74237070|gb|DT644984.1|DT644984

EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT

EST: gi|211183324|gb|FK979377.1|FK979377

EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCTGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT

EST: gi|87157614|gb|DY402403.1|DY402403

EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT

EST: gi|71428557|gb|DR809607.1|DR809607

EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT

EST: gi|94475718|gb|EB704676.1|EB704676

EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT

EST: gi|50336816|gb|CO531942.1|CO531942

EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT

EST: gi|211180923|gb|FK979371.1|FK979371

EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT

EST: gi|22546168|gb|BU098479.1|BU098479

EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGA
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGA

EST: gi|71321201|gb|DR797302.1|DR797302

EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT

EST: gi|71329466|gb|DR801453.1|DR801453

EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT

EST: gi|87157722|gb|DY402511.1|DY402511

EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT

EST: gi|148957093|gb|EC903064.2|EC903064

EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGGCCATGAACCTTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCCGG
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGG-CCATGAACCTTTT-GTTTCGTACGAGGGCCTTGAGCAGCTGCACC-GG

EST: gi|22819833|gb|BU499923.1|BU499923

EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT

EST: gi|37421156|gb|CF648275.1|CF648275

EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGATGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT

EST: gi|71428023|gb|DR809073.1|DR809073

EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT

EST: gi|76012907|gb|DT940077.1|DT940077

EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT

EST: gi|26558674|gb|CA830909.1|CA830909

EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT

EST: gi|33466850|gb|CF243899.1|CF243899

EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT

EST: gi|148994788|gb|EE034233.2|EE034233

EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT

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: 86

CGAGAGCGACTACCAGGACCTGCTGCGCAACACGGACGCCAACCAGACGGCGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTTCTCTTCATCCTTGGTATCACTCATGTGTTGTACAGTTTTGTAACAGTGG

Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 28

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 15

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

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gcggagcacactgttcactcatcgcttgggttggaacctaatctgtcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTTCTCTTCATCCTTGGTATCACTCATGTGTTGTACAGTTTTGTAACAGTGG