ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtactggtaacatcatttgtcattacgttcattcctcatttccttttgattccttgctctgacgtttccttcaccatgttagGTGAGGATCTGCATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCATTATGATGGGCCAAAGTTCCGCCTTGAGCTCT

Basic information

species	Zea mays
transcript	GRMZM2G033117_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G033117_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g41930.1 (Oryza sativa), 3'ss of exon 4

gtactggtaacatcatttgtcattacgttcattcctcatttccttttgattccttgctctgacgttt-----ccttcaccatgttagGTGAGGATCTGCATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCATTATGATGGGCCAAAGTTCCGCCTTGAGCTCT
||| |||| ||| |   || | |   ||| ||| ||||||| |||||| || | ||| ||||  ||        ||||   |  |||||||||||| ||||||| ||||| |||||||| |||||||||||| | ||||| |||||  |||||||||| ||||| |||||||| || ||||||||||
gtaatggttacagc---tggcgt-gtgtttatttctcatttacttttggtttcatgcactgatattctgctatattcattctactagGTGAGGATCCGCATTAGAAAGCTCTGCAAGCCTTTGGAAGAGGATGCTTTCAGACCAGTGCTGCACCATTACGATGGTCCAAAGTTTCGTCTTGAGCTCT

upper sequence: GRMZM2G033117_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA19G25870.1 (Glycine max), 3'ss of exon 4

--------------------gtactggta-acatcatttgtcattacgttcattcctcatttccttttgattccttgctctgacgtttccttcaccatgttagGTGAGGATCTGCATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCATTATGATGGGCCAAAGTTCCGCCTTGAGCTCT
                    | | ||||  | | ||| | | |     |   |   ||| |      | |  |       |   |  ||||   || ||| |||| || ||| |  | |||||||| |||||| | |||||||| ||||| ||||||||||| ||||| |||||||| ||||||||||| || ||||| || |
gtagtagaatataggactttgaaatggtggagaccatgtatgagcttatctgtaaatcaatga---ataaaacaaaaaatttgtgcctcctcttccttgt-agGTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTCAGGCCAGTATTGCATCATTATGACGGGCCAAAGTTTCGTCTTGAACTGT

upper sequence: GRMZM2G033117_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA16G06100.1 (Glycine max), 3'ss of exon 4

----------------------gtactggta--acatcatttgtcattacgttcattcctcatttccttttgattccttgctctgacgtttccttcaccatgttagGTGAGGATCTGCATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCATTATGATGGGCCAAAGTTCCGCCTTGAGCTCT
                      | | ||||   | | ||| | | |     |   |   ||| |      | |  |  |  | |      | ||   || ||| |||| || ||| |  | |||||||| |||||| | |||||||| ||||| ||||||||||| ||||| |||||||||||||||||||| || |||||||| |
gtagtagaatatagaatattttgaaatggtgggagaccatgtatgagcttatctgtaaatcaatga---ataaaacaatatttttgttccttctcttccttgt-agGTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTCAGGCCAGTATTGCATCATTATGATGGGCCAAAGTTTCGTCTTGAGCTGT

upper sequence: GRMZM2G033117_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G27090.1 (Arabidopsis thaliana), 3'ss of exon 4

-----gtactggtaacatcatttgtcattacgttcattcctcatttccttttgattccttgctctgacgtttccttc----accatgttagGTGAGGATCTGCATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCATTATGATGGGCCAAAGTTCCGCCTTGAGCTCT
            | |||     | |||||   || | || | ||||   | |  |    |  | | || | |   ||    |   |   |||| |||||| |  | |||||  | |||||  | ||||||||||| ||||||||||||||  | ||||| |||||||| ||||| ||||||||||||||||
gtgaaacttaaatcacaatgactttcattgttttaagtctttattttgatatcttgtactaatataacttctttctcttaaattgtaacagGTAAGGATCAGAGTGAGGAAAATCTGCAAAGCCTTGGAAGAGGACTCCTTCAGGCCAGTACTTCACCACTATGATGGTCCAAAATTCCGCCTTGAGCTCT

upper sequence: GRMZM2G033117_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S168_104V6.2 (Physcomitrella patens), 3'ss of exon 4

-------------------------------------------gtactggtaacatcatttgtcattacgttcattcctcatttccttttgattccttgctctgacgtttccttcaccatgttagGTGAGGATCTGCATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCATTATGATGGGCCAAAGTTCCGCCTTGAGCTCT
                                            | |  |  |||   ||    | || ||  |    |  ||   |      |  |       |  |||  || |||    |||||| |||   | ||| | |||| ||| ||||| || |||||||| || |||||||||||  |||| || ||||||||||| |||||||| ||| ||||||
gttgaatctcaaagcattgcgatgttaaatagtgattcacggtttgccagatacaaatttaaatagtaggtagaacatttgttaagtcactgcttatccactcaatttttatttgaccg---tagGTGCGGACTCGTATTCGAAAGCAGTGTAAGCCTTTAGAAGAGGACTCATTCAGGCCAGTGCTGCATCACTATGATGGGCCCAAGTTCCGTCTTCAGCTCT

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|60399109|gb|DN231923.1|DN231923

EST:     TCTAGATTCCCAGCGCAG                         GTGAGGATCTGCATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: TCTAGATTCCCAGCGCAGgtactggtaa ... accatgttagGTGAGGATCTGCATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

EST: gi|211180981|gb|FL324627.1|FL324627

EST:     TGAATCTAGATTCCCAGCGCAG                         GTGAGGATCTGCATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: TGAATCTAGATTCCCAGCGCAGgtactggtaa ... accatgttagGTGAGGATCTGCATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

EST: gi|60401049|gb|DN233856.1|DN233856

EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCTGCATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactggtaa ... accatgttagGTGAGGATCTGCATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

EST: gi|28361820|gb|CB240176.1|CB240176

EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCTGCATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactggtaa ... accatgttagGTGAGGATCTGCATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

EST: gi|60350290|gb|DN217263.1|DN217263

EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCTGCATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactggtaa ... accatgttagGTGAGGATCTGCATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

EST: gi|211531442|gb|FL327582.1|FL327582

EST:     TGAATCTAGATTCCCAGCGCAG                         GTGAGGATCTGCATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: TGAATCTAGATTCCCAGCGCAGgtactggtaa ... accatgttagGTGAGGATCTGCATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

EST: gi|60357783|gb|DN224756.1|DN224756

EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCTGCATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactggtaa ... accatgttagGTGAGGATCTGCATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

EST: gi|60338189|gb|DN205162.1|DN205162

EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCTGCATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactggtaa ... accatgttagGTGAGGATCTGCATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

EST: gi|211531841|gb|FL338637.1|FL338637

EST:     TGAATCTAGATTCCCAGCGCAG                         GTGAGGATCTGCATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: TGAATCTAGATTCCCAGCGCAGgtactggtaa ... accatgttagGTGAGGATCTGCATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

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), 47 (downstream exon)
Score: 236

GCTGCCAGTTTTGGTGGGTCCAATATCGATCCTACTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactggtaa ... accatgttagGTGAGGATCTGCATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCATTATGATGGGCCAAAGTTCCGCCTTGAGCTCT

Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 204

Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 173

Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 99

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttcattcctcatttccttttgattccttgctctgacgtttccttcaccatgttagGTGAGGATCTGCATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCATTATGATGGGCCAAAGTTCCGCCTTGAGCTCT