ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaattacggttctggtcatgtcccaatgtgttcatttttatggtttttgtggcctttgtgattatttgcaaacattattggtggtgcatggatatagctgtgtttggtgcatcaagttggtgaaaaggaaactagatatgctcactttagatctttatttgcag

Basic information

species	Zea mays
transcript	GRMZM5G862101_T02
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G862101_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g12220.1 (Oryza sativa), 5'ss of exon 3

AGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaattacggttctggtcatgtcccaatgtgttcatttttatggtttttgtggcctttgtgattatttgcaaacattattggtggtgcatggatatagctgtgtttggtgcatcaagttggtgaaaaggaaactagatatgctcactttagatctttatttgcag
| ||||||  |||||| ||||||||||| |||||||||||||||||| ||||||| ||| |||||||||||||||| |||||||||||| | || || |||||| | ||  || |   |  |  |    |  ||  ||||| |  |  |  |  ||||| || |||       |  |   |      |    ||| ||||                                                                  
AAACAAAATCTCCTGTTGATGATCAGCAATGGCTCACTTACTGGGTGCTGTACTCGTTTATCACTTTGTTTGAGCTTACTTTTGCTCCAGTAATTGAATGgtaa-tgaccatttt--cctgggtcaggagattttttttttgtcttactcatttccttt-tgtttagcatttgatttccctcaaaaagttcagatttagcaaca--------------------------------------------------------------

upper sequence: GRMZM5G862101_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA05G01160.1 (Glycine max), 5'ss of exon 3

AGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaattacggttctggtcatgtcccaatgtgttcatttttatggtt--tttgtggcctttgtgattatttgcaaacattattggtggtgcatggatatagctgtgtttggtgcatcaagttggtgaaaaggaaactagatatgctcactttagatctttatttgcag
|||  ||   |||| | |||||||||||||||||||||||||||||  | ||||| ||  ||||  | ||||| || |||||||||  | |  | ||||||||   | |  || | || || ||    | ||||  || |  |  ||  ||||      | ||  | | |   |||| |    |  | |  |     | || || | ||                                                           
AGAGCAAGTCTCCTATTGATGATCAGCAGTGGCTCACTTACTGGGTTCTCTACTCCTTGATCACCCTCTTTGAACTTACTTTTGCTAAAGTCCTTGAGTGgta---tgcattttttgt-atatctttttatgttgtttatgttaattgatttgcaagaatagtactcagtgataaacgt----gacgataaacct-cagagttgagatt-----------------------------------------------------------

upper sequence: GRMZM5G862101_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA17G10730.1 (Glycine max), 5'ss of exon 3

AGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaattacggttctggtcatgtcccaatgtgttcatttttatggtttttgtggcctttgtgattatttgcaaacattattggtggtgcatggatatagctgtgtttggtgcatcaagttggtgaaaaggaaactagatatgctcactttagatctttatttgcag
|||  ||   |||  | |||||||||||||||||||||||||||||  | ||||| ||  ||||  | ||||| || || ||||||  | |  | || |||||  |||    | |  |    ||      |||| || || || ||||| |  |   |||||| || |    ||      |  |    | ||    | |   | |||||                                                         
AGAGCAAGTCTCCCATTGATGATCAGCAGTGGCTCACTTACTGGGTTCTCTACTCCTTGATCACACTCTTTGAACTTACCTTTGCTAGAGTCCTTGAATGgta--ttaacccttttttttcttct-----tgtttatgttaattgttttggaagg--ttgtgagtactcattaaatgccataataa-acttgagacttgagatttttggg--------------------------------------------------------

upper sequence: GRMZM5G862101_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv17s0000g05990.t01 (Vitis vinifera), 5'ss of exon 3

AGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaattacggttctggtcatgtcccaatgtgttcatttttatggtttttgtggcctttgtgattatttgcaaacattattggtggtgcatggatatagctgtgtttggtgcatcaagttggtgaaaaggaaactagatatgctcactttagatctttatttgcag
|||| ||    ||||| ||||||||||| |||||||| |||||||| ||||| ||  |  ||||  | || ||||| || ||||||  | | || || |||||| |     ||      ||||   ||    |||     | ||||   || |  ||||     |  |||     | |||   |    |||   |  | |  |  | |                                                          
AGACCAAGTCCCCTGTTGATGATCAGCAATGGCTCACATACTGGGTTTTGTATTCTATGATCACACTCTTCGAGCTCACCTTTGCTAAAGTCATTGAATGgtaa-tcgtatttt-----atgttt-aacactttccccaatgtggt---tgggctcttttcttctccttgagtggagtatcttttcctcattcttgaatcaataatggaa--------------------------------------------------------

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|211223200|gb|FL136732.1|FL136732

EST:     TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTT
genomic: TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaattacg ... ttatttgcagGCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTT

EST: gi|211223194|gb|FL136726.1|FL136726

EST:     TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTT
genomic: TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaattacg ... ttatttgcagGCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTT

EST: gi|211223203|gb|FL136735.1|FL136735

EST:     TACTCATTTGNCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCATATGCAAAACTGNTCTTTAACTGCTGGTTGGNCTT
genomic: TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaattacg ... ttatttgcagGCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTT

EST: gi|211223202|gb|FL136734.1|FL136734

EST:     TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGG
genomic: TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaattacg ... ttatttgcagGCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGG

EST: gi|211223197|gb|FL136729.1|FL136729

EST:     TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTT
genomic: TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaattacg ... ttatttgcagGCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTT

EST: gi|211221143|gb|FL136724.1|FL136724

EST:     TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTT
genomic: TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaattacg ... ttatttgcagGCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTT

EST: gi|211223201|gb|FL136733.1|FL136733

EST:     TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTT
genomic: TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaattacg ... ttatttgcagGCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTT

EST: gi|211223204|gb|FL136736.1|FL136736

EST:     TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCNATTATCGAGTG                         GCTTCCATTTTGGTCATATGCAAAANTGTTCTTTAACTGCTGGTTGG
genomic: TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaattacg ... ttatttgcagGCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGG

EST: gi|211223195|gb|FL136727.1|FL136727

EST:     TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTT
genomic: TACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaattacg ... ttatttgcagGCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTT

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: 335

AGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaattacg ... ttatttgcagGCTTCCATTTTGGTCATATGCAAAACTGTTCTTTAACTGCTGGTTGGTCTTACCTTGGTTCAATGGTGCTGCTTATGTTTACGACCATTTTGTGCGGCCA

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 150

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 219