ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtactgataacatctgtcattatgtgcatttctcatctcctttggtttcttgctctgacaccttcatcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCT

Basic information

species	Zea mays
transcript	GRMZM2G011923_T02
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G011923_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g41930.1 (Oryza sativa), 3'ss of exon 4

gtactgataacatctgtcattatgtgcatttctcatct-cctttggtttcttgctctgacacc--------ttcatcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCT
||| || | ||| ||| | |  |||  ||||||||| | | ||||||||| ||| |||| |          |||||  |   |||||||||||||| |||| ||||| |||||||| |||||||||||| | ||||| |||||  ||||||| || ||||| ||||||||||| || |||||||
gtaatggttacagctggcgt-gtgtttatttctcatttacttttggtttcatgcactgatattctgctatattcattctactagGTGAGGATCCGCATTAGAAAGCTCTGCAAGCCTTTGGAAGAGGATGCTTTCAGACCAGTGCTGCACCATTACGATGGTCCAAAGTTTCGTCTTGAGCTCT

upper sequence: GRMZM2G011923_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA19G25870.1 (Glycine max), 3'ss of exon 4

-----------------------gtactgataac-atctgtcattatgtgcatttctcatctcctttggtttcttgctctgacaccttcatcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCT
                        |  ||   || || | | |   | |   |   |||     |            |    |  | || || |   |||| || ||||| || |||||||| |||||| | |||||||| ||||| ||||||||||| ||||| || ||||| || ||||||||||| || || || |
gtagtagaatataggactttgaaatggtggagaccatgtatgagcttatctgtaaatcaatgaataaaacaaaaaatttgtgcctcctcttccttgtagGTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTCAGGCCAGTATTGCATCATTATGACGGGCCAAAGTTTCGTCTTGAACTGT

upper sequence: GRMZM2G011923_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA16G06100.1 (Glycine max), 3'ss of exon 4

---------------------------gtactgataacatctgtcattatgtgcatttctcatctcctttggtttcttgctctgacaccttcatcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCT
                           |    || | ||| | | |   | |   |   |||     |         |  |    |    || || |   |||| || ||||| || |||||||| |||||| | |||||||| ||||| ||||||||||| ||||| || |||||||| ||||||||||| || ||||| |
gtagtagaatatagaatattttgaaatggtgggagaccatgtatgagcttatctgtaaatcaatgaataaaacaatatttttgttccttctcttccttgtagGTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTCAGGCCAGTATTGCATCATTATGATGGGCCAAAGTTTCGTCTTGAGCTGT

upper sequence: GRMZM2G011923_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G27090.1 (Arabidopsis thaliana), 3'ss of exon 4

-----------gtactgataacatctgtcattatgtgcatttctc---atctcctttggtttcttg--ctctgacaccttcatcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCT
            |    || || |   |  || |  |  ||| |    || || | |  |    |    |||  | | |  ||  |  ||||| |||||| | || |||||  | |||||  | ||||||||||| ||||||||||||||  | |||||||||||||| ||||| || ||||| |||||||
gtgaaacttaaatcacaatgactttcattgttttaagtctttattttgatatcttgtactaatataacttctttctcttaaattgtaacagGTAAGGATCAGAGTGAGGAAAATCTGCAAAGCCTTGGAAGAGGACTCCTTCAGGCCAGTACTTCACCACTATGATGGTCCAAAATTCCGCCTTGAGCTCT

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|22490259|gb|BU050182.1|BU050182

EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTCTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

EST: gi|18655190|gb|BM499995.1|BM499995

EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTCTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

EST: gi|29544431|gb|CB604811.1|CB604811

EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGC

EST: gi|149107938|gb|EE292294.2|EE292294

EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

EST: gi|31351065|gb|CD435422.1|CD435422

EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

EST: gi|31352279|gb|CD436636.1|CD436636

EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

EST: gi|31352997|gb|CD437354.1|CD437354

EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

EST: gi|29544031|gb|CB604411.1|CB604411

EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGCAAG
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAG

EST: gi|87152915|gb|DY397704.1|DY397704

EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTCTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

EST: gi|31351326|gb|CD435683.1|CD435683

EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

EST: gi|148982112|gb|EE028161.2|EE028161

EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

EST: gi|37399688|gb|CF637177.1|CF637177

EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTCTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

EST: gi|60350260|gb|DN217233.1|DN217233

EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

EST: gi|78087740|gb|DV516133.1|DV516133

EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

EST: gi|40303492|gb|CK347879.1|CK347879

EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTCTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

EST: gi|45567374|gb|CK985540.1|CK985540

EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTCTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

EST: gi|60346554|gb|DN213527.1|DN213527

EST:     AAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: AAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

EST: gi|31352510|gb|CD436867.1|CD436867

EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

EST: gi|149082225|gb|EE171408.2|EE171408

EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

EST: gi|60401294|gb|DN234101.1|DN234101

EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTCTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

EST: gi|211413346|gb|FL280968.1|FL280968

EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTCTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

EST: gi|60358053|gb|DN225026.1|DN225026

EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

EST: gi|29544380|gb|CB604760.1|CB604760

EST:     CATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

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: 47 (upstream exon), 49 (downstream exon)
Score: 152

GCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCT

Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 133

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 116

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tatgtgcatttctcatctcctttggtttcttgctctgacaccttcatcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCT