ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaattaataaatcaactgtctgtctgtctgtctgtctgtctacgagtgagtgatccggcggcggcttccctcaaacgtcacttacttccgcgcagGGGCGCACGCGCGTCGGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACGGACCACCCGGCGACGTACTACGAGGACATGCAGCGCTCG

Basic information

species	Zea mays
transcript	GRMZM5G898668_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G898668_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g70200.1 (Oryza sativa), 3'ss of exon 3

gtaattaataaatcaactgtctgtctgtctgtctgtctgtctacgagtgagtgatccggcggcggcttccctcaaacgtcact-tacttccgcgcagGGGCGCACGCGCGTCGGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACGGACCACCCGGCGACGTACTACGAGGACATGCAGCGCTCG
        |||||   | |  | |||      |   || ||  |   | | ||   ||   ||   |    ||  | ||  || ||  |||   ||| || || ||||||||||| |||||||| ||||||||||||||||| || |||||||| || || |||||  | ||||||||||| || |||||| | || 
-------gtaaattttccgcttatctccaatacatcctatcatctgctcattggctcg-tagcatgtggagtctgatgtttctgtatgtcctatcagAGGTGCCCGCGCGTCGGTTTGGGAGAATTTCAAGAACAACCCGCTGTTTGACATCTCAACCGATCACCCACCCACGTACTACGAAGATATGCAGAGATCT

upper sequence: GRMZM5G898668_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G27440.1 (Arabidopsis thaliana), 3'ss of exon 3

-------gtaattaataaatcaactgtctgtctgtctgtctgtctgtctacgagtgagtgatccggcggcggcttccctcaaacgtcacttacttccgcgcagGGGCGCACGCGCGTCGGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACGGACCACCCGGCGACGTACTACGAGGACATGCAGCGCTCG
          |||  | | |     ||  |  | | | |  |  |  ||| ||   | |  |            |  ||  ||| || ||    |  |   || || ||| | ||  |||| |||||||||||||||||||||||  | || |||||||| || || |||||| | || |||||||| ||||||||| |  | 
acaattaagcattcctcattaggaagttaggttatatataaggttagctaagatcaaattgttttagaatctgctgactggaacttctctc---tttgtatagAGGTGCAAGAGCAGCGGTGTGGGAGAACTTCAAGAACAACCCTTTGTTTGACATCTCAACAGATCACCCGACAACATACTACGAAGACATGCAGAGAGCC

upper sequence: GRMZM5G898668_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 3

-gtaattaataaatcaactg-tctgtctgtctgtctgtctgtctacgagtgagtgatccggcgg--cggcttccctcaaacgtcacttacttccgcgcagGGGCGCACGCGCGTCGGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACGGACCACCCGGCGACGTACTACGAGGACATGCAGCGCTCG
 | ||  || |  |    || |   |   | ||||| |     || |       | |     |   |  || |  || |||     | | |      ||| || ||| | ||  | || ||||||||||| ||| ||||||||||||| |||||||| || || |||||  |||| || || || |||||||| ||  | 
aggaagcaacatcttgtatgatacatggctttgtcttttatattaggtcctttgggttgaatgaatcaactcctatctaactcttttaattgattgacagAGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGACATCTCCACTGAGCACCCAACGACATATTATGAAGACATGCAACGTGCT

upper sequence: GRMZM5G898668_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ05285 (Selaginella moellendorffii), 3'ss of exon 3

gtaattaataaatcaactgtctgtctgtctgtctgtctgtctacgagtgagtgatccggcggcggcttccctcaaac-gtcacttacttc-cgcgcagGGGCGCACGCGCGTCGGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACGGACCACCCGGCGACGTACTACGAGGACATGCAGCGCTCG
                      ||     | |||   |   ||  |  |  |  |  |       |||    |   | | || || || | |  ||||||| || || ||  | || |||||||| |||||| | || || ||||| |||||||| || || ||||||   |||||||| ||||||||||||||  | 
----------------------gtaaagttctctcaatacatagaaaagctttgtttgaaaagatcttattccgttctgacattttctgctcatgcagGGGTGCTCGTGCTGCTGTTTGGGAGAATTTCAAGGATAATCCTCTCTTTGACATCTCTACCGAGCACCCGATTACGTACTATGAGGACATGCAGCGAGCT

upper sequence: GRMZM5G898668_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ25836 (Selaginella moellendorffii), 3'ss of exon 3

gtaattaataaatcaactgtctgtctgtctgtctgtctgtctacgagtgagtgatccggcggcggcttccctcaaac-gtcacttacttc-cgcgcagGGGCGCACGCGCGTCGGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACGGACCACCCGGCGACGTACTACGAGGACATGCAGCGCTCG
                      ||     | |||   |   ||  |  |  |  |  |       |||        | | || || || | |  ||||||| || || ||  | || |||||||| |||||| | || || ||||| |||||||| || || ||||||   |||||||||||||||||||||||  | 
----------------------gtaaagttctctcaatacatagaaaagctttgtttgaaaagatcttattcggttctgacatttgctgctcatgcagGGGTGCTCGTGCTGCTGTTTGGGAGAATTTCAAGGATAATCCTCTCTTTGACATCTCTACCGAGCACCCGATTACGTACTACGAGGACATGCAGCGAGCT

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|91049522|gb|EB159940.1|EB159940

EST:     GTCTGTTCTACGACACCAGCAACGATCCCGAGGGGCG-TTACTACGCGAG                         GGGCGCACGCGCGTCGGTCTGGGAGAACTTCAAGAACA-CCCGCTCCTCGA
genomic: GTCTGTTCTACGACACCAGCAACGATCCCGAGGG-CGGTTACTACGCGAGgtaattaata ... ttccgcgcagGGGCGCACGCGCGTCGGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGA

EST: gi|91049521|gb|EB159939.1|EB159939

EST:     ATCCCGAGGGCGGTTACTACGCGAG                         GGGCGCACGCGCGTCGGTCTGGGAGAACTTCAAGAACAACCCGCTCTTGGA
genomic: ATCCCGAGGGCGGTTACTACGCGAGgtaattaata ... ttccgcgcagGGGCGCACGCGCGTCGGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGA

EST: gi|71325429|gb|DR799400.1|DR799400

EST:     GGTCTGTTCTACGACACCAGCAACGATCCCGAGGGCGGTTACTACGCGAG                         GGGCGCACGCGCGTCGGTCTGGGAGAACTTC
genomic: GGTCTGTTCTACGACACCAGCAACGATCCCGAGGGCGGTTACTACGCGAGgtaattaata ... ttccgcgcagGGGCGCACGCGCGTCGGTCTGGGAGAACTTC

EST: gi|88747218|gb|DY531359.1|DY531359

EST:     CGATCCCGAGGGCGG-TACTACGCGAG                         GGGCGCACGCGCGTCGGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGA
genomic: CGATCCCGAGGGCGGTTACTACGCGAGgtaattaata ... ttccgcgcagGGGCGCACGCGCGTCGGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGA

EST: gi|37395777|gb|CF635172.1|CF635172

EST:     GGTCTGTTCTACGACACCAGCAACGATCCCGAGGGCGGTTACTACGCGAG                         GGGCGCACGCGCGTCGGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGA
genomic: GGTCTGTTCTACGACACCAGCAACGATCCCGAGGGCGGTTACTACGCGAGgtaattaata ... ttccgcgcagGGGCGCACGCGCGTCGGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGA

EST: gi|40334794|gb|CK368864.1|CK368864

EST:     GGTCTGTTCTACGACACCAGCAACGATCCCGAGGGCGGTTACTACGCGAG                         GGGCGCACGCGCGTCGGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGA
genomic: GGTCTGTTCTACGACACCAGCAACGATCCCGAGGGCGGTTACTACGCGAGgtaattaata ... ttccgcgcagGGGCGCACGCGCGTCGGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGA

EST: gi|71325428|gb|DR799399.1|DR799399

EST:     GTCTGTTCTACGACACCAGCAACGATCCCGAGGGCGGTTACTACGCGAG                         GGGCGCACGCGCGTCGGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGA
genomic: GTCTGTTCTACGACACCAGCAACGATCCCGAGGGCGGTTACTACGCGAGgtaattaata ... ttccgcgcagGGGCGCACGCGCGTCGGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGA

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: 38 (upstream exon), 40 (downstream exon)
Score: 3

CTCACCTTATCCCTGCGGACACCCCGCGCTCCATCTTCGTCTACTTCCGCGGTCTGTTCTACGACACCAGCAACGATCCCGAGGGCGGTTACTACGCGAGgtaattaata ... ttccgcgcagGGGCGCACGCGCGTCGGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACGGACCACCCGGCGACGTACTACGAGGACATGCAGCGCTCG

Block sizes: 45 (upstream exon), 23 (downstream exon)
Score: 10

Block sizes: 42 (upstream exon), 44 (downstream exon)
Score: 30

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 191

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tacgagtgagtgatccggcggcggcttccctcaaacgtcacttacttccgcgcagGGGCGCACGCGCGTCGGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACGGACCACCCGGCGACGTACTACGAGGACATGCAGCGCTCG