ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCGTTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaataacacttgtggtcatgtcccaatgtgttcaattttatgttctttgggtgggcttcgtgattatttggaaacattactggtggtacatggatatagctgtttagtgcaacaagttggtgaatagaaaactaaatatgcttactttagatctttgtttgcag

Basic information

species	Zea mays
transcript	GRMZM2G047860_T02
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G047860_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g12220.1 (Oryza sativa), 5'ss of exon 3

AGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCGTTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaataacacttgtggtcatgtcccaatgtgttcaattttatgttctttgggtgggcttcgtgattatttggaaacattactggtggtacatggatatagctgtttagtgcaacaagttggtgaatagaaaactaaatatgcttactttagatctttgtttgcag
| ||||||  |||||| ||||||||||| |||||||||||||||||| |||||||||||||||||||||||||||| |||||||||||| | || || ||||||  | || ||        |||   |  | ||   |||| | ||  |    |    ||  | |  |||||   |  |  ||           ||| ||||                                                                
AAACAAAATCTCCTGTTGATGATCAGCAATGGCTCACTTACTGGGTGCTGTACTCGTTTATCACTTTGTTTGAGCTTACTTTTGCTCCAGTAATTGAATGgtaatgaccattttc--ctgggtcaggagatttttt-ttttgtcttactcatttccttttgtttagcatttg---atttccctcaaaaagttcagatttagcaaca------------------------------------------------------------

upper sequence: GRMZM2G047860_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA05G01160.1 (Glycine max), 5'ss of exon 3

AGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCGTTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaataacacttgtggtcatgtcccaatgtgttcaattttatgttctttgggtgggcttcgtgattatttggaaacattactggtggtacatggatatagctgtttagtgcaacaagttggtgaatagaaaactaaatatgcttactttagatctttgtttgcag
|||  ||   |||| | |||||||||||||||||||||||||||||  | ||||| || |||||  | ||||| || |||||||||  | |  | ||||||||   |    ||||    || |    ||||  |  || |||  |  ||||   |    | ||  | | |   |||| | || | |   || |     | |   ||                                                            
AGAGCAAGTCTCCTATTGATGATCAGCAGTGGCTCACTTACTGGGTTCTCTACTCCTTGATCACCCTCTTTGAACTTACTTTTGCTAAAGTCCTTGAGTGgtatgcattttttgta--tatctttttatgttgtttatgttaattgatttgcaagaa--tagtactcagtgataaacgtgac-gataa-acctcagagttgagatt------------------------------------------------------------

upper sequence: GRMZM2G047860_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA17G10730.1 (Glycine max), 5'ss of exon 3

AGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCGTTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaataacacttgtggtcatgtcccaatgtgttcaattttatgttctttgggtgggcttcgtgattatttgg-aaacattactggtggtacatggatatagctgtttagtgcaacaagttggtgaatagaaaactaaatatgcttactttagatctttgtttgcag
|||  ||   |||  | |||||||||||||||||||||||||||||  | ||||| || |||||  | ||||| || || ||||||  | |  | || |||||  |||| |||    |  | ||    ||| |   || |||  |  |||||  ||   | |||| || |    |||    |            |  |  || | ||| |                                                         
AGAGCAAGTCTCCCATTGATGATCAGCAGTGGCTCACTTACTGGGTTCTCTACTCCTTGATCACACTCTTTGAACTTACCTTTGCTAGAGTCCTTGAATGgtat-taaccctt----ttttttcttcttgttt---atgttaattgttttggaagg---ttgtgagtactcattaaatgccataataaacttgagacttgagatttttggg--------------------------------------------------------

upper sequence: GRMZM2G047860_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv17s0000g05990.t01 (Vitis vinifera), 5'ss of exon 3

AGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCGTTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaataacacttgtggtca-----tgtcccaatgtgttcaa----ttttatgttctttgggtgggct---tcgtgattatt-tggaaacattactggtggtacatggatatagctgtttagtgcaacaagttggtgaatagaaaactaaatatgcttactttagatctttgtttgcag
|||| ||    ||||| ||||||||||| |||||||| |||||||| ||||| ||  | |||||  | || ||||| || ||||||  | | || || ||||||       || || | |     |  ||||||||| |       |||| |  || ||| ||||  |   |  |  | ||| | ||| || || |||                                                                                 
AGACCAAGTCCCCTGTTGATGATCAGCAATGGCTCACATACTGGGTTTTGTATTCTATGATCACACTCTTCGAGCTCACCTTTGCTAAAGTCATTGAATGgtaatcgtattttatgtttaacactttccccaatgtggttgggctcttttcttctccttgagtggagtatcttttcctcattcttgaatcaataatggaa-------------------------------------------------------------------------------

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|211371979|gb|FL186724.1|FL186724

EST:     TACTCATTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
genomic: TACTCGTTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaataaca ... ttgtttgcagGCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT

EST: gi|32808662|gb|CD960896.1|CD960896

EST:     TGCTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTA
genomic: TACTCGTTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaataaca ... ttgtttgcagGCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTA

EST: gi|33103480|gb|CF063440.1|CF063440

EST:     TACTCATTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCATATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
genomic: TACTCGTTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaataaca ... ttgtttgcagGCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT

EST: gi|33103463|gb|CF063423.1|CF063423

EST:     TACTCATTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCATATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
genomic: TACTCGTTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaataaca ... ttgtttgcagGCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT

EST: gi|211371978|gb|FL186723.1|FL186723

EST:     TACTCATTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
genomic: TACTCGTTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaataaca ... ttgtttgcagGCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT

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: 395

AGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCGTTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaataaca ... ttgtttgcagGCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTTGCCTTGGTTCAATGGTGCTGCCTATGTTTACGACCATTTTGTGCGGCCA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 218

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 286