ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtgaattattagaattgtatttgtttcttggagatctgcgtgccttaatatttttgacccatttgagctaatggaataaaatggaaaccattttgaaggctgcgttgggaccacttgtataaatcagtaaatctaacccctctaatataatttccatgtcacagGACTCGAGTGACACTAAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACCACTAACAAAGGTTAACAACCTGATATTTGGGCGCACTTGGGTTGATTCT

Basic information

species	Zea mays
transcript	GRMZM2G174644_T02
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 6

gtgaattattagaattgtatttgtttcttggagatctgcgtgccttaatatttttgacccatttgagctaatggaataaaatggaaaccattttgaaggctgcgttgggaccacttgtataaatcagtaaatctaacccctctaatataatttccatgtcacagGACTCGAGTGACACTAAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACCACTAACAAAGGTTAACAACCTGATATTTGGGCGCACTTGGGTTGATTCT
                                                                    ||||    | |||  |  |   |||  | |  |  |     ||||  | | || |||       ||||    | |  | |   |||    |||||||||| ||||| |||| || || || ||||||  | |||| ||||| |||||||| || ||||| |||||| ||||||||||||| |||||||||||||||
-------------------------------------------------------------------gtaattttgtcaaactgtgattgtttc-aggattatgaataaaccagctctttatatc-------ctaaatggttttttgt---ttctgcatcacagGACTAGAGTGTCACTTAAGAAGTCCGGTGTCAAGCTGGAATTGGTACCACCACTCACGAAGGTCAACAACTTGATATTTGGGCGTACTTGGGTTGATTCT

upper sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA12G06690.1 (Glycine max), 3'ss of exon 6

gtgaattattagaattgtatttgtttcttggagatctgcgtgccttaatatttttgacccatttgagctaatggaataaaatggaaaccattttgaaggctgcgttgggaccacttgtataaatcagtaaatctaacccctctaatataatttccatgtc-acagGACTCGAGTGACACTAAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACCACTAACAAAGGTTAACAACCTGATATTTGGGCGCACTTGGGTTGATTCT
                                                        |   |||   |||  |  | |  |||   |    || |||   ||| |||        |||| |  ||  |  | | |||       || |  | ||  ||||   ||| || || ||||| || || | |  |||||| || || |||||||||||||| |  ||||||||||||||||| |||||||| || |||||| ||||||| 
-----------------------------------------------------caaaataattcttgct--taaattttaatcctagttgttctgat--ctgagttatcctgttttgtttttatttgcta-tttaa-------aaaaggacttgtatgtttgcagAACACGTGTGACCCTTAAGAGAGATGGTGTTGTCTTAGATTTGGTGCCACCTCCTACAAAGGTTAACAACCTCATATTTGGCCGAACTTGGATTGATTCA

upper sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA11G14770.1 (Glycine max), 3'ss of exon 6

gtgaattattagaattgtatttgtttcttggagatctgcgtgccttaatatttttgacccatttgagctaatggaataaaatggaaaccattttgaa---ggctgcgttgggaccacttgtataaatcagtaaat-ctaacccctctaatataatttccatgtc-acagGACTCGAGTGACACTAAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACCACTAACAAAGGTTAACAACCTGATATTTGGGCGCACTTGGGTTGATTCT
                                                                      ||| || ||||          ||| |     | ||   ||     | || |     |  ||   |  |  |   |  || |  | ||  ||||   ||| ||||| ||||| || || | |  |||||| || || |||||||||||||| |  ||||||||||||||||| |||||||| || |||||| ||||||| 
---------------------------------------------------------------------tatgcaacaaaacaattcttgatttaatcctagttgttctgatctgaattatcctgttttgttgttatttgctatttaaaaaggacttgtatgtttgcagAACTCGTGTGACCCTTAAGAGAGATGGTGTTGTCTTAGATTTGGTGCCACCTCCTACAAAGGTTAACAACCTCATATTTGGCCGAACTTGGATTGATTCA

upper sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 6

gtgaattattagaattgtatttgtttcttggagatctgcgtgccttaatatttttgacccatttgagctaatggaataaaatggaaaccattttgaaggctgcgttgggaccacttgtataaatcagtaaatctaacccctctaatataatttccatgtcacagGACTCGAGTGACACTAAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACCACTAACAAAGGTTAACAACCTGATATTTGGGCGCACTTGGGTTGATTCT
                                                        ||   | ||  |    |   | |  |     |||| |  || |||  |||      |    | | || |   | || |      ||   | | ||   ||| |  ||| || || || || ||||||| |  |||||| ||  | |||||||||||||| |  |||||||||||||||||||| ||||| || || ||||||||||| 
--------------------------------------------------------acttgtatgtacctcagtgtttatttt---tccatctgtaaagctttgtttcctttaaaattctgaa-cgacatatttggtgattcactttttat---cat-ttgcagAACACGTGTTACTCTAAAAAGAGATGGTGTTGTCCTAGATTTGGTGCCACCTCCCACAAAGGTTAACAACCTGATTTTTGGACGGACATGGGTTGATTCA

upper sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv08s0007g00480.t01 (Vitis vinifera), 3'ss of exon 6

gtgaattattagaattgtatttgtttcttggagatctgcgtgccttaatatttttgacccatttgagctaatggaataaaatggaaaccattttgaaggctgcgttgggaccacttgtataaatcagtaaatctaacccctctaatataatttccatgtcacagGACTCGAGTGACACTAAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACCACTAACAAAGGTTAACAACCTGATATTTGGGCGCACTTGGGTTGATTCT
                                      ||   || | | || |||     | |    || ||   ||      | || |||||  |  || |||          ||| | | |            ||  | ||||  |   ||||| |  |||||| || ||||| || |||| |  |||||| ||  | ||||||||||| ||    ||||| ||||||||||| |||||||| || |||||||||||||| 
--------------------------------------cggatctcagt-ttgttgcttgttctc--ttattgttttagttcatagacaattttagaaactacgtg--------ctgtcttattt-----------cctttttaatgaa---tccatat-gcagGACACGTGTGACGCTCAAAAGAGATGGTGTAGTCCTAGATTTGGTGCCCCCTGCTACAAAAGTTAACAACCTCATATTTGGACGTACTTGGGTTGATTCA

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|31349767|gb|CD434124.1|CD434124

EST:     TTGAAGACCAAGCTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAG                         GACTCGAGTGACACTNNNNNNNTCTGGTGTCGTGCTGGATTTGGTGCCACC
genomic: TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAGgtgaattatt ... catgtcacagGACTCGAGTGACACTAAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACC

EST: gi|211409590|gb|FL109891.1|FL109891

EST:     TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAG                         GACTCGAGTGACACTNNNNNNNTCTGGTGTCGTGTTGGATTTGGTGCCACC
genomic: TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAGgtgaattatt ... catgtcacagGACTCGAGTGACACTAAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACC

EST: gi|78025234|gb|DV493621.1|DV493621

EST:     TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAG                         GACTCGAGTGACACTNNNNNNNTCTGGTGTCGTGTTGGATTTGGTGCCACC
genomic: TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAGgtgaattatt ... catgtcacagGACTCGAGTGACACTAAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACC

EST: gi|5499280|gb|AI855147.1|AI855147

EST:     TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAG                         GACTCGAGTGACACTNNNNNNNTCTGGTGTCGTGTTGGATTTGGTGCCACC
genomic: TTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAGgtgaattatt ... catgtcacagGACTCGAGTGACACTAAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACC

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), 49 (downstream exon)
Score: 155

GTGTTGCTCACTGCGAGAATGAACATTTTACTTACGATATCACGTCTAAGTTGAAGACCAAGTTTTTGGGAAATTCAGTGGAAATTTACCCAGTTGGAAGgtgaattatt ... catgtcacagGACTCGAGTGACACTAAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACCACTAACAAAGGTTAACAACCTGATATTTGGGCGCACTTGGGTTGATTCT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 359

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 339

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 179

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

accacttgtataaatcagtaaatctaacccctctaatataatttccatgtcacagGACTCGAGTGACACTAAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACCACTAACAAAGGTTAACAACCTGATATTTGGGCGCACTTGGGTTGATTCT