ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AAAATAATTTAGAAGCAAAAGCAAAACAATACAAGGATCCTGCATTGATGCACATATTTTTGATGAATAACATTCACTATATTGTCAAATCTGTCCGCAGgtatgttcttataccaagtaatgctaggaagaaagtaacaatagtgtgtgtactaccttatactctcttttctgtcactcag

Basic information

species	Zea mays
transcript	GRMZM2G074530_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G074530_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g58880.1 (Oryza sativa), 5'ss of exon 8

AAAATAATTTAGAAGCAAAAGCAAAACAATACAAGGATCCTGCATTGATGCACATATTTTTGATGAATAACATTCACTATATTGTCAAATCTGTCCGCAGgtatgttcttat-------------accaagt----aat-gctaggaagaaagtaacaata-gtgtgtgtactaccttatactctcttttctgtcactcag
| |||||| | || |||||||||||||||||||||||||| || |||||||||||||||||||||||||||||||| ||||| || ||||||||||||||||||||||||||             | ||| |    ||| || |  | |  ||||||   | | ||| |||     | || ||||||||||| ||   |||
AGAATAATCTGGATGCAAAAGCAAAACAATACAAGGATCCAGCTTTGATGCACATATTTTTGATGAATAACATTCATTATATCGTGAAATCTGTCCGCAGgtatgttcttatgaagtaaggtataaacaaattcgcaatagccaataggttagtaactggatgagtgggtatagtttaatgctctcttttctttcttccag

upper sequence: GRMZM2G074530_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT5G03540.3 (Arabidopsis thaliana), 5'ss of exon 9

AAAATAATTTAGAAGCAAAAGCAAAACAATACAAGGATCCTGCATTGATGCACATATTTTTGATGAATAACATTCACTATATTGTCAAATCTGTCCGCAGgtatgttcttataccaagtaatgctaggaagaaag---taacaatagtgtgtgtactaccttatactctcttttc-tgtcactcag---------------
|||| || || || | |||| | ||||| ||||| |||||||||||||  ||| | ||  ||||||| |||||||| || || |||| |||||| ||||||||| || || | |    | |  ||   |||   |   |     || |      |  |    |  | ||| |||    | | |||                
AAAACAACTTGGACGGAAAATCGAAACAGTACAAAGATCCTGCATTGACACACTTGTTCCTGATGAACAACATTCATTACATGGTCAGATCTGTGCGCAGgtatattatttttctcgtttaaactttaaaggctgatctggttttattaaaaaaataaaagaacgcactcatttagctttattcatatgataatttttcag

upper sequence: GRMZM2G074530_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv08s0007g02340.t01 (Vitis vinifera), 5'ss of exon 8

AAAATAATTTAGAAGCAAAAGCAAAACAATACAAGGATCCTGCATTGATGCACATATTTTTGATGAATAACATTCACTATATTGTCAAATCTGTCCGCAGgtatgttct-tataccaag--taatgctaggaagaaagtaacaatagtgtgtgtactaccttatactctcttttctgtcactcag
| ||||| || || |  ||| | || ||||| || |||||||||||||  ||  ||||| | ||||||||||||||||| ||||||| ||| || || |||| |||| | | |    ||  | ||  | |     || | |   | ||||   || |  ||  |  |   | ||||    || ||
AGAATAACTTGGATGGGAAATCCAAGCAATATAAAGATCCTGCATTGACTCAATTATTTCTTATGAATAACATTCACTACATTGTCAGATCAGTGCGAAGgtttgttatatctttttagcttgattgttgatctgaatttatgct-gtgtaaatagtttctcctttttattgttctcatccttag

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|71432760|gb|DR813810.1|DR813810

EST:     CACATATTTTTGATGAATAACATTCACTATATTGTCAAATCTGTCCGCAG                         ATCAGAAGCCAAAGATTTGTTGGGTGATGACTGGATTCAAAGGCACCGAAG
genomic: CACATATTTTTGATGAATAACATTCACTATATTGTCAAATCTGTCCGCAGgtatgttctt ... tgtcactcagATCAGAAGCCAAAGATTTGTTGGGTGATGACTGGATTCAAAGGCACCGAAG

EST: gi|211149050|gb|FK958467.1|FK958467

EST:     TAACATTCACTATATTGTCAAATCTGTCCGCAG                         ATCAGAAGCCAAAGATTTGTTGGGTGATGACTGGATTCAAAGGCACCGAAG
genomic: TAACATTCACTATATTGTCAAATCTGTCCGCAGgtatgttctt ... tgtcactcagATCAGAAGCCAAAGATTTGTTGGGTGATGACTGGATTCAAAGGCACCGAAG

EST: gi|211149052|gb|FK958469.1|FK958469

EST:     CACATATTTTTGATGAATAACATTCACTATATTGTCAAATCTGTCCGCAR                         ATCAGAAGCCAAAGATTTGTTGGGTGATGACTGGATTCAAAGGCACCGAAG
genomic: CACATATTTTTGATGAATAACATTCACTATATTGTCAAATCTGTCCGCAGgtatgttctt ... tgtcactcagATCAGAAGCCAAAGATTTGTTGGGTGATGACTGGATTCAAAGGCACCGAAG

EST: gi|5740705|gb|AI948395.1|AI948395

EST:     C-CATATTTTTGATGAATAACATTCACTATATTGTCAAATCTGTCCGCAG                         ATCAGAAGCCAAAGATTTGTTGGGTGATGACTGGATTCAAAGGCACCGAAG
genomic: CACATATTTTTGATGAATAACATTCACTATATTGTCAAATCTGTCCGCAGgtatgttctt ... tgtcactcagATCAGAAGCCAAAGATTTGTTGGGTGATGACTGGATTCAAAGGCACCGAAG

EST: gi|32925518|gb|CF030330.1|CF030330

EST:     CACATATTTTTGATGAACAACATTCACTATATTGTCAAATCTGTCCGCAG                         ATCAGAGGCCAAAGATTTGTTGGGTGATGACTGGATTCAAAGGCACCGAAG
genomic: CACATATTTTTGATGAATAACATTCACTATATTGTCAAATCTGTCCGCAGgtatgttctt ... tgtcactcagATCAGAAGCCAAAGATTTGTTGGGTGATGACTGGATTCAAAGGCACCGAAG

EST: gi|32926841|gb|CF031653.1|CF031653

EST:     CACATATTTTTGATGAACAACATTCACTATATTGTCAAATCTGTCCGCAG                         ATCAGAGGCCAAAGATTTGTTGGGTGATGACTGGATTCAAAGGCACCGAAG
genomic: CACATATTTTTGATGAATAACATTCACTATATTGTCAAATCTGTCCGCAGgtatgttctt ... tgtcactcagATCAGAAGCCAAAGATTTGTTGGGTGATGACTGGATTCAAAGGCACCGAAG

EST: gi|211159122|gb|FL458118.1|FL458118

EST:     CACATATTTTTGATGAATAACATTCACTATATTGTCAAATCTGTCCGCAG                         ATCAGAAGCCAAAGATTTGTTGGGTGATGACTGGATTCAAAGGCACCGAAG
genomic: CACATATTTTTGATGAATAACATTCACTATATTGTCAAATCTGTCCGCAGgtatgttctt ... tgtcactcagATCAGAAGCCAAAGATTTGTTGGGTGATGACTGGATTCAAAGGCACCGAAG

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: 48 (upstream exon), 49 (downstream exon)
Score: 183

AAAATAATTTAGAAGCAAAAGCAAAACAATACAAGGATCCTGCATTGATGCACATATTTTTGATGAATAACATTCACTATATTGTCAAATCTGTCCGCAGgtatgttctt ... tgtcactcagATCAGAAGCCAAAGATTTGTTGGGTGATGACTGGATTCAAAGGCACCGAAGGATTGTACAACAAAATGCCAATCAGTATAGAAGGATTGCTTGGGCGAAG

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 164

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 264