ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtctgccttgcatacttgcactgcagtgtgttttgattattctgtacgtgtatgcttctgttcttatgtattatgatgactctttgttctttcagGCTTCTATCTTTGTACAGTCTCATGTCCGTGCTCATGTTGAGTTGATGTGGCTATTGAGTTCTTCTACTCCTATTGGCTGGCTGAATAGAATGATCCAGT

Basic information

species	Zea mays
transcript	GRMZM2G177970_T01
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G177970_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g54020.2 (Oryza sativa), 3'ss of exon 5

gtctgccttgcatacttgcactgcagtgtgttttgattattctgtacgtgtatgcttctgttcttatgtattatgatgactctttgttctttcagGCTTCTATCTTTGTACAGTCTCATGTCCGTGCTCATGTTGAGTTGATGTGGCTATTGAGTTCTTCTACTCCTATTGGCTGGCTGAATAGAATGATCCAGT------------------
|||||| |  |||| || || |  |   || | |  || ||  | | |||      |        |||| ||||| ||  | | |||  || ||||||||||| ||||||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||| ||||| || ||||||||||| |                  
gtctgcttcacatatttacattatatgatgatgt--ttgtt--gcaggtgcccttgtggagctgaatgttttatgttg-ttttgtgtctttacaggcttctatatttgtacagTCTCATGTCCGTGCTCATGTTGAGTTGATGTGGCTTCTGAGTTCTTCTACTCCTATTGGTTGGCTCAACAGAATGATCCAATTCAAAGAGAAGTCACGCA

upper sequence: GRMZM2G177970_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g54020.1 (Oryza sativa), 3'ss of exon 5

gtctgccttgcatacttgcactgcagtgtgttttgattattctgtacgtgtatgcttctgttcttatgtattatgatgactctttgttctttcagGCTTCTATCTTTGTACAGTCTCATGTCCGTGCTCATGTTGAGTTGATGTGGCTATTGAGTTCTTCTACTCCTATTGGCTGGCTGAATAGAATGATCCAGT
|||||| |  |||| || || |  |   || | |  || ||  | | |||      |        |||| ||||| ||  | | |||  || ||||||||||| ||||||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||| ||||| || ||||||||||| |
gtctgcttcacatatttacattatatgatgatgt--ttgtt--gcaggtgcccttgtggagctgaatgttttatgttg-ttttgtgtctttacagGCTTCTATATTTGTACAGTCTCATGTCCGTGCTCATGTTGAGTTGATGTGGCTTCTGAGTTCTTCTACTCCTATTGGTTGGCTCAACAGAATGATCCAAT

upper sequence: GRMZM2G177970_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv04s0008g00200.t01 (Vitis vinifera), 3'ss of exon 5

gtctgccttgcatacttgcactgcagtgtgttttgattattctgtacgtgtatgcttctgttcttatgtattatgatgactctttgttctttcagGCTTCTATCTTTGTACAGTCTCATGTCCGTGCTCATGTTGAGTTGATGTGGCTATTGAGTTCTTCTACTCCTATTGGCTGGCTGAATAGAATGATCCAGT
               ||    |  | | |   ||  ||||| ||| |    | | || | | | |   | ||||||      | |||     ||||| ||| ||||||| ||||||||||| ||||| |||   || ||||||||| || |||||||| ||||||| ||||| ||| |||| | |||||| ||||
--------------gtttagtttaactattcattctttattgtgtgcca--aggtttatatgcatgcttgttatgactcagatctgtatgggcagGCCTCTGTCTTTGTTCAGTCTCATGTTCGTGCCCATTCAGAATTGATGTGGTTACTGAGTTCTGCTACTCCAATTGGTTGGTTGAACAAAATGATTCAGT

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|76294199|gb|DV033767.1|DV033767

EST:     CAAGAAGCACTGCTGCAATATATCTTGCATGTGGCGTCGACAGCTCCAAG                         GCTTCTATCTTTGTACAGTCTCATGTCCGTGCTCATGTTGAGTTGATGTGG
genomic: CAAGAAGCACTGCTGCAATATATCTTGCATGTGGCGTCGACAGCTCCAAGgtctgccttg ... gttctttcagGCTTCTATCTTTGTACAGTCTCATGTCCGTGCTCATGTTGAGTTGATGTGG

EST: gi|211458161|gb|FL127573.1|FL127573

EST:     CAAGAAGCACTGCTGCAATATATCTTGCATGTGGCGTCGACAGCTCCAAG                         GCTTCTATCTTTGTACAGTCTCATGTCCGTGC
genomic: CAAGAAGCACTGCTGCAATATATCTTGCATGTGGCGTCGACAGCTCCAAGgtctgccttg ... gttctttcagGCTTCTATCTTTGTACAGTCTCATGTCCGTGC

EST: gi|50331394|gb|CO526520.1|CO526520

EST:     CAAGAAGCACTGCTGCAATATATCTTGCATGTGGCGTCGACAGCTCCAAG                         GCTTCTATCTTTGTACAGTCTCATGTCCGTGCTCATGTTGAGTTGATGTGG
genomic: CAAGAAGCACTGCTGCAATATATCTTGCATGTGGCGTCGACAGCTCCAAGgtctgccttg ... gttctttcagGCTTCTATCTTTGTACAGTCTCATGTCCGTGCTCATGTTGAGTTGATGTGG

EST: gi|60398533|gb|DN231349.1|DN231349

EST:     CAAGAAGCACTGCTGCAATATATCTTGCATGTGGCGTCGACAGCTCCAAG                         GCTTCTATCTTTGTACAGTCTCATGTCCGTGCTCATGTTGAGTTGATGTGG
genomic: CAAGAAGCACTGCTGCAATATATCTTGCATGTGGCGTCGACAGCTCCAAGgtctgccttg ... gttctttcagGCTTCTATCTTTGTACAGTCTCATGTCCGTGCTCATGTTGAGTTGATGTGG

EST: gi|78120428|gb|DV538812.1|DV538812

EST:     CAAGAAGCACTGCTGCAATATATCTTGCATGTGGCGTCGACAGCTCCAAG                         GCTTCTATCTTTGTACAGTCTCATGTCCGTGCTCATGTTGAGTTGATGTGG
genomic: CAAGAAGCACTGCTGCAATATATCTTGCATGTGGCGTCGACAGCTCCAAGgtctgccttg ... gttctttcagGCTTCTATCTTTGTACAGTCTCATGTCCGTGCTCATGTTGAGTTGATGTGG

EST: gi|71449704|gb|DR830754.1|DR830754

EST:     CAAGAAGCACTGCTGCAATATATCTTGCATGTGGCGTCGACAGCTCCAAG                         GCTTCTATCTTTGTACAGTCTCATGTCCGTGCTCATGTTGAGTTGATGTGG
genomic: CAAGAAGCACTGCTGCAATATATCTTGCATGTGGCGTCGACAGCTCCAAGgtctgccttg ... gttctttcagGCTTCTATCTTTGTACAGTCTCATGTCCGTGCTCATGTTGAGTTGATGTGG

EST: gi|211458163|gb|FL127575.1|FL127575

EST:     CAAGAAGCACTGCTGCAATATATCTTGCATGTGGCGTCGACAGCTCCAAG                         GCTTCTATCTTTGTACAGTCTCATGT
genomic: CAAGAAGCACTGCTGCAATATATCTTGCATGTGGCGTCGACAGCTCCAAGgtctgccttg ... gttctttcagGCTTCTATCTTTGTACAGTCTCATGT

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: 46 (upstream exon), 47 (downstream exon)
Score: 30

ATTACTTTACCATATGAGGCGCCACTGCTTTCTAAAGCAACAAGAAGCACTGCTGCAATATATCTTGCATGTGGCGTCGACAGCTCCAAGgtctgccttg ... gttctttcagGCTTCTATCTTTGTACAGTCTCATGTCCGTGCTCATGTTGAGTTGATGTGGCTATTGAGTTCTTCTACTCCTATTGGCTGGCTGAATAGAATGATCCAGT

Block sizes: 38 (upstream exon), 49 (downstream exon)
Score: 56

Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 19

Block sizes: 37 (upstream exon), 49 (downstream exon)
Score: 22

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tctgtacgtgtatgcttctgttcttatgtattatgatgactctttgttctttcagGCTTCTATCTTTGTACAGTCTCATGTCCGTGCTCATGTTGAGTTGATGTGGCTATTGAGTTCTTCTACTCCTATTGGCTGGCTGAATAGAATGATCCAGT