ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CCACATTAAAGGGTTGCTGATCAACTTCATCCACTCATTCTGGCCGTCTCTTCTTAAAGTTCCATCTTTTTTGGTTGAGTTCATTACTCCAATCATCAAGgtagattactgtacgattttatctattgacatatttttatgtattttcaaattttattcttgatagtataccattttgcaccaaagggatttccccctgctagatatgtattttttttgtaaacaatttgttttgactgccatgatggattcacttgtctag

Basic information

species	Zea mays
transcript	GRMZM2G021270_T01
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G021270_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA15G43170.1 (Glycine max), 5'ss of exon 7

CCACATTAAAGGGTTGCTGATCAACTTCATCCACTCATTCTGGCCGTCTCTTCTTAAAGTTCCATCTTTTTTGGTTGAGTTCATTACTCCAATCATCAAGgtagattactgtacgattttatctattgacatatt-tttatgtattttcaaattttattcttgatagtataccattttgcaccaaagggatttccccctgctagatatgtattttttttgtaaacaatttgttttgactgccatgatggattcacttgtctag
|||||| |||||| |  |||| |||||||| || || |||||||| || || || ||||||||||||||| ||||||| || |  ||||| || || | ||||       ||| | |||| | |||   |||  | |||||  |  || |  ||||  | ||  | | || || | |  |  ||                                                                               
CCACATCAAAGGGCTATTGATAAACTTCATTCATTCGTTCTGGCCATCACTACTAAAAGTTCCATCTTTTATGGTTGAATTTACCACTCCCATAATAAGGgtaa------gtatggttttgt-tatcatcatcctgtttatagaacttgaggttttcatatt--ttgaattccctgtctctgcag------------------------------------------------------------------------------

upper sequence: GRMZM2G021270_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA10G11610.1 (Glycine max), 5'ss of exon 7

CCACATTAAAGGGTTGCTGATCAACTTCATCCACTCATTCTGGCCGTCTCTTCTTAAAGTTCCATCTTTTTTGGTTGAGTTCATTACTCCAATCATCAAGgtagattactgtacgattttatctattgacatatttttatgtattttcaaattttattcttgatagtataccattttgcaccaaagggatttccccctgctagatatgtattttttttgtaaacaatttgttttgactgccatgatggattcacttgtctag
|||||| |||||| |  |||| |||||||| || || |||||||| || || || ||||||||||||||| ||||||| || |  ||||| || || | |||    || |  |   || |   |||   ||| ||| ||    ||      ||| ||  ||   | |      || ||||                                                                                  
CCACATCAAAGGGCTATTGATAAACTTCATTCATTCGTTCTGGCCATCACTGCTAAAAGTTCCATCTTTTATGGTTGAATTTACCACTCCTATAATAAGGgt----tagtagagttttgttgttatcatcatgtttatagaacttcatggttttcatattttgaattccctgtttctgcag---------------------------------------------------------------------------------

upper sequence: GRMZM2G021270_T01 (Zea mays), 5'ss of exon 7
lower sequence: PP1S33_203V6.1 (Physcomitrella patens), 5'ss of exon 9

CCACATTAAAGGGTTGCTGATCAACTTCATCCACTCATTCTGGCCGTCTCTTCTTAAAGTTCCATCTTTTTTGGTTGAGTTCATTACTCCAATCATCAAGgtagattactgtacgattttatctattgacatatttttatgtattttcaaattttattcttgatagtataccattttgcaccaaagggatttccccctgctagatatgtattttttttgtaaacaatttgttttgactgccatgatggattcacttgtctag
 || || ||||| ||| | |||||||||||||||||||||||||| ||  | || ||| ||||||| ||  | || |||||||| ||||||||| | ||||||  ||     | |  |||   | ||| |     ||   |  || | | | |   ||||     |||| |   | | | |  | |   |   | | |||                                                              
TCATATCAAAGGATTGTTAATCAACTTCATCCACTCATTCTGGCCCTCGTTGCTCAAAATTCCATCATTCCTCGTGGAGTTCATCACTCCAATCGTTAAGgtaagttgt--gatggatttggttgttgtc----cttggggccttgtgatactagcttct-----gtatgctcatct-cgctgatgacttcgacgcgtgcag------------------------------------------------------------

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|18654823|gb|BM499628.1|BM499628

EST:     TTCTTAAAGTTCCATC-TTTTTGGTTGAGTTCATTACTCCAATCATCAAG                         GCAACCAGAGGTCAAACTACGAAATCATTTTACACAATGCCAGAGTATGAA
genomic: TTCTTAAAGTTCCATCTTTTTTGGTTGAGTTCATTACTCCAATCATCAAGgtagattact ... acttgtctagGCAACCAGAGGTCAAACTACGAAATCATTTTACACAATGCCAGAGTATGAA

EST: gi|18963118|gb|BM660250.1|BM660250

EST:     CCAA-CATCAA-                         GCAACCAGAGG-CAAACTACGAAATCA-TTTACACAATGCCAGAGTATGAA
genomic: CCAATCATCAAGgtagattact ... acttgtctagGCAACCAGAGGTCAAACTACGAAATCATTTTACACAATGCCAGAGTATGAA

EST: gi|31354680|gb|CD439037.1|CD439037

EST:     CATCTTTTTTGGTTGAGTTCATTACTCCAATCACTCTAG                         GCAACCAGAGGTCAAACTACGAAATCATTTTACACAATGCCAGAGTATGA
genomic: CATCTTTTTTGGTTGAGTTCATTACTCCAATCA-TCAAGgtagattact ... acttgtctagGCAACCAGAGGTCAAACTACGAAATCATTTTACACAATGCCAGAGTATGA

EST: gi|18655210|gb|BM500015.1|BM500015

EST:     TTCTTAAAGTTCCATCTTTTTTGGTTGAGTTCATTACTCCAATCATCAAG                         GCAACCAGAGGTCAAACTACGAAATCATTTTACACAATGCCAGAGTATGAA
genomic: TTCTTAAAGTTCCATCTTTTTTGGTTGAGTTCATTACTCCAATCATCAAGgtagattact ... acttgtctagGCAACCAGAGGTCAAACTACGAAATCATTTTACACAATGCCAGAGTATGAA

EST: gi|18662206|gb|BM501800.1|BM501800

EST:     TTCTTAAAGTTCCATCTTTTTTGGTTGAGTTCATTACTCCAATCATCAAG                         GCAACCAGAGGTCAAACTACGAAATCATTTTACACAATGCCAGAGTATGAA
genomic: TTCTTAAAGTTCCATCTTTTTTGGTTGAGTTCATTACTCCAATCATCAAGgtagattact ... acttgtctagGCAACCAGAGGTCAAACTACGAAATCATTTTACACAATGCCAGAGTATGAA

EST: gi|18661837|gb|BM501604.1|BM501604

EST:     TTCTTAAAGTTCCATCTTTTTTGGTTGAGTTCATTACTCCAATCATCAAG                         GCAACCAGAGGTCAAACTACGAAATCATTTTACACAATGCCAGAGTATGAA
genomic: TTCTTAAAGTTCCATCTTTTTTGGTTGAGTTCATTACTCCAATCATCAAGgtagattact ... acttgtctagGCAACCAGAGGTCAAACTACGAAATCATTTTACACAATGCCAGAGTATGAA

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), 46 (downstream exon)
Score: 256

CCACATTAAAGGGTTGCTGATCAACTTCATCCACTCATTCTGGCCGTCTCTTCTTAAAGTTCCATCTTTTTTGGTTGAGTTCATTACTCCAATCATCAAGgtagattact ... acttgtctagGCAACCAGAGGTCAAACTACGAAATCATTTTACACAATGCCAGAGTATGAAGAATGGAGAAAGAATTTAGGAGCAAGTGCAAGTTCGTGGACTATAAAAT

Block sizes: 39 (upstream exon), 42 (downstream exon)
Score: 18

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 32