ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaactcctagcagcgatagggtttcgaacgcccgttaggggggcttgccgcttacggatctgggcgcctccgcgcagGGGTGTCGAGGAAGACGCAGGAGCTGTACATGTTGGTGTTCGTGGCGAGGTACCTCGACCTCTTCACGGACTACGTCTCGCTCTACAACTCAGTGATGAA

Basic information

species	Zea mays
transcript	GRMZM2G408989_T01
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G408989_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g45310.1 (Oryza sativa), 3'ss of exon 1

--------gtaactcctagcagcgatagggtttcgaacgcccgtt--------aggggggcttgccgcttacggatctgggcgcctccgcgcagGGGTGTCGAGGAAGACGCAGGAGCTGTACATGTTGGTGTTCGTGGCGAGGTACCTCGACCTCTTCACGGACTACGTCTCGCTCTACAACTCAGTGATGAA
        |   |    ||  | | ||||||||||  |||  | |         |||||  |  ||||| ||||||||| | |  |  |||||||||||||||||||||||||||||||||||||| |||||||||||||||||||| | ||||| |||||||||||| |||||||||||||||| ||||||||
gtgagcccgagccgtacagtgggggtagggtttcggccgcttggttgggggtgggggggattctccgctcacggatctgtgtg--ttggcgcagGGGTGTCGAGGAAGACGCAGGAGCTGTACATGCTGGTGTTCGTGGCGAGGTACATGGACCTGTTCACGGACTACATCTCGCTCTACAACTCGGTGATGAA

upper sequence: GRMZM2G408989_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ37620 (Selaginella moellendorffii), 3'ss of exon 1

gtaactcctagcagcgatagggtttcgaacgcccgttaggggggcttgccgcttacggatctgggcgcctccgcgcagGGGTGTCGAGGAAGACGCAGGAGCTGTACATGTTGGTGTTCGTGGCGAGGTACCTCGACCTCTTCACGGACTACGTCTCGCTCTACAACTCAGTGATGAA
                 || ||| | |  |  |  | |  | |||  |   |||     ||    |  ||   ||||||| | |||   |||||||||||||| |||  | |||| ||||||||| | ||||||||  | ||||| ||||  ||||||||||||||||  || |||||
----------------gtatggtatgg--catcgatcaaagaggc--gattcttc----tcaaaacttctaaacgcagGGATCTCGCTCAAGACGCAGGAGCTCTACGCGCTGGTTTTCGTGGCGCGCTACCTCGATTTGTTCACAGACTTTGTCTCGCTCTACAACTTCGTCATGAA

upper sequence: GRMZM2G408989_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ15071 (Selaginella moellendorffii), 3'ss of exon 1

gtaactcctagcagcgatagggtttcgaacgcccgttaggggggct-tgccgcttacggatctgggcgcctccgcgcagGGGTGTCGAGGAAGACGCAGGAGCTGTACATGTTGGTGTTCGTGGCGAGGTACCTCGACCTCTTCACGGACTACGTCTCGCTCTACAACTCAGTGATGAA
                 || ||| | |  |  |  | |  | |||  | |  || |    | |           ||||||| | |||   |||||||||||||| |||  | |||| ||||||||| | ||||||||  | ||||| ||||  ||||||||||||||||  || |||||
----------------gtatggtatgg--catcgatcaaagaggcgattcttctcaaaactttaaa-------acgcagGGATCTCGCTCAAGACGCAGGAGCTCTACGCGCTGGTTTTCGTGGCGCGCTACCTCGATTTGTTCACAGACTTTGTCTCGCTCTACAACTTCGTCATGAA

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|211036981|gb|FL384634.1|FL384634

EST:     CTCGGTCCTCGTGCTCCTCCTCAAGATCTACGCCACCAAGTCCTGCTCAG                         GGGTGTCGAGGAAGACGCAGGAGCTGTACATGTTGGTGTTCGTGGCGAGGT
genomic: CTCGGTCCTCGTGCTCCTCCTCAAGATCTACGCCACCAAGTCCTGCTCAGgtaactccta ... ctccgcgcagGGGTGTCGAGGAAGACGCAGGAGCTGTACATGTTGGTGTTCGTGGCGAGGT

EST: gi|211443736|gb|FK945786.1|FK945786

EST:     CTCGGTCCTCGTGCTCCTCCTCAAGATCTACGCCACCAAGTCCTGCTCAG                         GGGTGTCGAGGAAGACGCAGGAGCTGTACATGTTGGTGTTCGTGGCGAGGT
genomic: CTCGGTCCTCGTGCTCCTCCTCAAGATCTACGCCACCAAGTCCTGCTCAGgtaactccta ... ctccgcgcagGGGTGTCGAGGAAGACGCAGGAGCTGTACATGTTGGTGTTCGTGGCGAGGT

EST: gi|91871430|gb|EB401416.1|EB401416

EST:     CTCGGTCCTCGTGCTCCTCCTCAAGATCTACGCCACCAAGTCCTGCTCAG                         GGGTGTCGAGGAAGACGCAGGAGCTGTACATGTTGGTGTTCGTGGCGAGGT
genomic: CTCGGTCCTCGTGCTCCTCCTCAAGATCTACGCCACCAAGTCCTGCTCAGgtaactccta ... ctccgcgcagGGGTGTCGAGGAAGACGCAGGAGCTGTACATGTTGGTGTTCGTGGCGAGGT

EST: gi|211057285|gb|FL401200.1|FL401200

EST:     CTCGGTCCTCGTGCTCCTMCTCAAGATCTACGCCACCAAGTCCTGCTCAG                         GGGTGTCGAGGAAGACGCAGGAGCTGTACATGTTGGTGTTCGTGGCGAGGT
genomic: CTCGGTCCTCGTGCTCCTCCTCAAGATCTACGCCACCAAGTCCTGCTCAGgtaactccta ... ctccgcgcagGGGTGTCGAGGAAGACGCAGGAGCTGTACATGTTGGTGTTCGTGGCGAGGT

EST: gi|50330722|gb|CO525848.1|CO525848

EST:     CTCGGTCCTCGTGCTCCTCCTCAAGATCTACGCCACCAAGTCCTGCTCAG                         GGGTGTCGAGGAAGACGCAGGAGCTGTACATGTTGGTGTTCGTGGCGAGGT
genomic: CTCGGTCCTCGTGCTCCTCCTCAAGATCTACGCCACCAAGTCCTGCTCAGgtaactccta ... ctccgcgcagGGGTGTCGAGGAAGACGCAGGAGCTGTACATGTTGGTGTTCGTGGCGAGGT

EST: gi|211455869|gb|FL373116.1|FL373116

EST:     CTCGGTCCTCGTGCTCCTCCTCAAGATCTACGCCACCAAGTCCTGCTCAG                         GGGTGTCGAGGAAGACGCAGGAGCTGTACATGTTGGTGTTCGTGGCGAGGT
genomic: CTCGGTCCTCGTGCTCCTCCTCAAGATCTACGCCACCAAGTCCTGCTCAGgtaactccta ... ctccgcgcagGGGTGTCGAGGAAGACGCAGGAGCTGTACATGTTGGTGTTCGTGGCGAGGT

EST: gi|31354771|gb|CD439128.1|CD439128

EST:     CTCGGTCCTCGTGCTCCTCCTCAAGATCTACGCCACCAAGTCCTGCTCAG                         GGGTGTCGAGGAAGACGCAGGAGCTGTACATGTTGGTGTTCGTGGCGAGGT
genomic: CTCGGTCCTCGTGCTCCTCCTCAAGATCTACGCCACCAAGTCCTGCTCAGgtaactccta ... ctccgcgcagGGGTGTCGAGGAAGACGCAGGAGCTGTACATGTTGGTGTTCGTGGCGAGGT

EST: gi|211150047|gb|FL377204.1|FL377204

EST:     CTCGGTCCTCGTGCTCCTCCTCAAGATCTACGCCACCAAGTCCTGCTCAG                         GGGTGTCGAGGAAGACGCAGGAGCTGTACATGTTGGTGTTCGTGGCGAGGT
genomic: CTCGGTCCTCGTGCTCCTCCTCAAGATCTACGCCACCAAGTCCTGCTCAGgtaactccta ... ctccgcgcagGGGTGTCGAGGAAGACGCAGGAGCTGTACATGTTGGTGTTCGTGGCGAGGT

EST: gi|211176140|gb|FL381693.1|FL381693

EST:     CTCGGTCCTCGTGCTCCTCCTCAAGATCTACGCCACCAAGTCCTGCTCAG                         GGGTGTCGAGGAAGACGCAGGAGCTGTACATGTTGGTGTTCGTGGCGAGGT
genomic: CTCGGTCCTCGTGCTCCTCCTCAAGATCTACGCCACCAAGTCCTGCTCAGgtaactccta ... ctccgcgcagGGGTGTCGAGGAAGACGCAGGAGCTGTACATGTTGGTGTTCGTGGCGAGGT

EST: gi|211379193|gb|FL377345.1|FL377345

EST:     CTCGGTCCTCGTGCTCCTCCTCAAGATCTACGCCACCAAGTCCTGCTCAG                         GGGTGTCGAGGAAGACGCAGGAGCTGTACATGTTGGTGTTCGTGGCGAGGT
genomic: CTCGGTCCTCGTGCTCCTCCTCAAGATCTACGCCACCAAGTCCTGCTCAGgtaactccta ... ctccgcgcagGGGTGTCGAGGAAGACGCAGGAGCTGTACATGTTGGTGTTCGTGGCGAGGT

EST: gi|78080744|gb|DV509156.1|DV509156

EST:     CTCGGTCCTCGTGCTCCTCCTCAAGATCTACGCCACCAAGTCCTGCTCAG                         GGGTGTCGAGGAAGACGCAGGAGCTGTACATGTTGGTGTTCGTGGCGAGGT
genomic: CTCGGTCCTCGTGCTCCTCCTCAAGATCTACGCCACCAAGTCCTGCTCAGgtaactccta ... ctccgcgcagGGGTGTCGAGGAAGACGCAGGAGCTGTACATGTTGGTGTTCGTGGCGAGGT

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: 130

GCTGCGGCCATGAACGCCTTCCGGTTCCTCGGGGACATGACCCACCTCTTCTCGGTCCTCGTGCTCCTCCTCAAGATCTACGCCACCAAGTCCTGCTCAGgtaactccta ... ctccgcgcagGGGTGTCGAGGAAGACGCAGGAGCTGTACATGTTGGTGTTCGTGGCGAGGTACCTCGACCTCTTCACGGACTACGTCTCGCTCTACAACTCAGTGATGAA

Block sizes: 39 (upstream exon), 47 (downstream exon)
Score: 75

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 91

Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 114

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttcgaacgcccgttaggggggcttgccgcttacggatctgggcgcctccgcgcagGGGTGTCGAGGAAGACGCAGGAGCTGTACATGTTGGTGTTCGTGGCGAGGTACCTCGACCTCTTCACGGACTACGTCTCGCTCTACAACTCAGTGATGAA