ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtacacggctatcttttatatttcatggggtcatctgcttaatcattaagattttctatgatcatgattttcttcctcaaatcatattttgtcatcccagGGAGGTGCTACTCAGATGAGATTTCAACCTCGTAAGGGAAAGTATCTAGCAGCGGCCTCAGATAAAGCTATCTACATACTTGATGGGGAGACACAACATG

Basic information

species	Zea mays
transcript	GRMZM2G425377_T01
intron #	7
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G425377_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g42260.3 (Oryza sativa), 3'ss of exon 15

--gtacacggctatcttttatatttcatggggtcatctgcttaatcattaagattttctatgatcatgattttcttcctcaaatcatattttgtcatcccagGGAGGTGCTACTCAGATGAGATTTCAACCTCGTAAGGGAAAGTATCTAGCAGCGGCCTCAGATAAAGCTATCTACATACTTGATGGGGAGACACAACATG
   | ||  || |  |  | | ||||||||  || ||||||| | |||| | | ||   ||| |  |     |||   || |||||| |||||||    ||||||||||||||||||||| ||||||||||||  |||||||| ||||| ||||| |||||||| || || ||||||||||||||||| |||||||||| ||
gtatgcaatgcaacttcatgtgtttcatggtatcttctgctttaacattca-acttctgatgcttgt----ctctgtttccaatcat-ttttgtcccaacagGGAGGTGCTACTCAGATGCGATTTCAACCTCAAAAGGGAAAATATCTTGCAGCTGCCTCAGAGAAGGCCATCTACATACTTGATGGAGAGACACAACTTG

upper sequence: GRMZM2G425377_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA05G08110.1 (Glycine max), 3'ss of exon 15

gtacacggctatcttttatatttcatggggtcatctgcttaatcattaagattttcta---tgatcatgattttcttcctcaaatcatattttgtcatcccagGGAGGTGCTACTCAGATGAGATTTCAACCTCGTAAGGGAAAGTATCTAGCAGCGGCCTCAGATAAAGCTATCTACATACTTGATGGGGAGACACAACATG
    | |   ||||   | | ||  |  |  ||||    |  ||| |    | || ||   ||||    | |  |||  |      ||||||| |||     ||| ||||| ||||||||||||||||||||| |   ||||| |  ||| ||||| ||    |||||  |  | | |||  |||||| ||| || ||   | 
--gtatgaa-atctaaaaaagttgttaagcacatcctaattctcaatgtattgttataatttgattgcaaataacttatttttccaatattttatca-----gGGTGGTGCAACTCAGATGAGATTTCAACCTGGCTTGGGAAGGCTTCTTGCAGCTGCAGTGGATAATTCCGTATCCATTTTTGATGTGGAAACCCAGGGTT

upper sequence: GRMZM2G425377_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA17G12900.1 (Glycine max), 3'ss of exon 18

gtacacggctatcttttatatttcatggggtcatctgcttaatcattaagatttt-ctatgatcatgattttcttcctcaaatcatattttgtcatcccagGGAGGTGCTACTCAGATGAGATTTCAACCTCGTAAGGGAAAGTATCTAGCAGCGGCCTCAGATAAAGCTATCTACATACTTGATGGGGAGACACAACATG
    | ||  ||||   |||  |  ||  |   ||  | ||||  | ||  | || |||| ||     |     |     |||  |    | |  |  ||||| ||||| ||||||||||||||||||||| |   ||||| |  ||| ||||| ||    |||||     | | |||  |||||| ||| || |    | 
--gtatgga-atctaaaataagttgtgaagc--tcatcctaattctcaatgtattgctataatttgattgcaaataacttaattttccaatattttatcagGGTGGTGCAACTCAGATGAGATTTCAACCTTGCTTGGGAAGGCTTCTTGCAGCTGCAGTGGATAATTTCGTATCCATTTTTGATGTGGAAACCCTGGGTT

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|71304828|gb|DR788528.1|DR788528

EST:     GCTGGAGCATAAATAATGGTAGCTGTTTGACATGTGTTAAGGTGTTTAAG                         GGAGGTGCTACTCAGATGAGATTTC-ACCTTCGTAAGGGAAAGTATCTAGC
genomic: GCTGGAGCATAAATAATGGTAGCTGTTTGACATGTGTTAAGGTGTTTAAGgtacacggct ... gtcatcccagGGAGGTGCTACTCAGATGAGATTTCAACC-TCGTAAGGGAAAGTATCTAGC

EST: gi|78115254|gb|DV533642.1|DV533642

EST:     GCTGGAGCATAAATAATGGTAGCTGTTTGACATGTGTTAAGGTGTTTAAG                         GGAGGTGCTACTCAGATGAGATTTCAACCTCGTAAGGGAAAGTATCTAGCA
genomic: GCTGGAGCATAAATAATGGTAGCTGTTTGACATGTGTTAAGGTGTTTAAGgtacacggct ... gtcatcccagGGAGGTGCTACTCAGATGAGATTTCAACCTCGTAAGGGAAAGTATCTAGCA

EST: gi|78115253|gb|DV533641.1|DV533641

EST:     AAATAATGGTAGCTGTTTGACATGTGTTAAGGTGTTTAAG                         GGAGGTGCTACTCAGATGAGATTTCAACCTCGTAAGGGAAAGTATCTAGCA
genomic: AAATAATGGTAGCTGTTTGACATGTGTTAAGGTGTTTAAGgtacacggct ... gtcatcccagGGAGGTGCTACTCAGATGAGATTTCAACCTCGTAAGGGAAAGTATCTAGCA

EST: gi|160481532|gb|EY254364.1|EY254364

EST:     GCTGGAGCATAAATAATGGTAGCTGTTTGACATGTGTTAAGGTGTTTAAG                         GGAGGTGCTACTCAGATGAGATTTCAACCTCGTAAGGGAAAGTATC-AGTC
genomic: GCTGGAGCATAAATAATGGTAGCTGTTTGACATGTGTTAAGGTGTTTAAGgtacacggct ... gtcatcccagGGAGGTGCTACTCAGATGAGATTTCAACCTCGTAAGGGAAAGTATCTAG-C

EST: gi|60400574|gb|DN233381.1|DN233381

EST:     TTAAGGTGTTTAAG                         GGAGGTGCTACTCAGATGAGATTTCAACCTCGTAAGGGAAAGTATCTAGCA
genomic: TTAAGGTGTTTAAGgtacacggct ... gtcatcccagGGAGGTGCTACTCAGATGAGATTTCAACCTCGTAAGGGAAAGTATCTAGCA

EST: gi|60344594|gb|DN211567.1|DN211567

EST:     AGCATAAATAATGGTAGCTGTTTGACATGTGTTAAGGTGTTTAAG                         GGAGGTGCTACTCAGATGAGATTTCAACCTCGTAAGGGAAAGTATCTAGCA
genomic: AGCATAAATAATGGTAGCTGTTTGACATGTGTTAAGGTGTTTAAGgtacacggct ... gtcatcccagGGAGGTGCTACTCAGATGAGATTTCAACCTCGTAAGGGAAAGTATCTAGCA

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: 40 (upstream exon), 43 (downstream exon)
Score: 81

AAATAAAGAGGATATGATATGCTCCTGTGATAGTGATGGGGAAGTGCGCAGCTGGAGCATAAATAATGGTAGCTGTTTGACATGTGTTAAGGTGTTTAAGgtacacggct ... gtcatcccagGGAGGTGCTACTCAGATGAGATTTCAACCTCGTAAGGGAAAGTATCTAGCAGCGGCCTCAGATAAAGCTATCTACATACTTGATGGGGAGACACAACATG

Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 42

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 82

Block sizes: 42 (upstream exon), 47 (downstream exon)
Score: 97

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttaagattttctatgatcatgattttcttcctcaaatcatattttgtcatcccagGGAGGTGCTACTCAGATGAGATTTCAACCTCGTAAGGGAAAGTATCTAGCAGCGGCCTCAGATAAAGCTATCTACATACTTGATGGGGAGACACAACATG