ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAGGAGCAGAGGTGGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatccttataagtgctgtttggttttccactctgaattttatgatcttaactgtttttttggggtccgttgctcatgttag

Basic information

species	Zea mays
transcript	GRMZM2G062635_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G062635_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g10290.2 (Oryza sativa), 5'ss of exon 3

AGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAGGAGCAGAGGTGGTTCTCG------ATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatccttataagtgctgttt--ggttttc---cactctgaattttatgatcttaactgtttttttggggtccgttgctcatgt-tag
      ||  | ||| |||| ||||||||||||||||||||||| ||||| |||||||      ||||||| || |||||||||||||| ||||||||||||||||||  |  ||     | |   |||||  |  ||||   ||||||   || |||   || ||||   ||||   | || |||| | |||| |||
------GCTGTTTCGCTTGAAGAAGAGTATGATGCAGCAGGAGCTGAGGTAGTTCTCGGTGATGATGAGGACGGTGAAGGCTGGCTTGCCACACATGGAGTGCAAGgttgacctctcagaatgccttgtttcagtgtttcgcgcactctcttttgtataggctaaactccctttt---gttctgttggtaatgtatag

upper sequence: GRMZM2G062635_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g41110.1 (Oryza sativa), 5'ss of exon 3

AGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAGGAGCAGAGGTGGTTCTCG------ATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatccttataagtgctgttt-ggttttccac----tctgaattttatgatcttaactgtttttttggggtccgttgctcatgt-tag
      ||  ||||  |||| ||||||||||||||||||||||| ||||| |||||||      ||||||| || |||||||||||||| ||||||||||||||||||  |  || | | ||    |||||  || || |||    |||   || ||| | || |||||  ||||   | || |||| | |||| |||
------GCTGTCTCACTTGAAGAAGAGTATGATGCAGCAGGAGCTGAGGTAGTTCTCGGTGATGATGAGGACGGTGAAGGCTGGCTTGCCACACATGGAGTGCAAGgttgacctc-tcacaatgcttgtttcagtgtttcacgtgctctcttttgtataagctaaactgcctttt---gttctgttggtaatgtatag

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|211324986|gb|FL012755.1|FL012755

EST:     GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAG                         CATCAAAGACAGAAGAGGAGGAAGACA
genomic: GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatcc ... ctcatgttagCATCAAAGCCGGAAGAGGAGGAAGACA

EST: gi|211327143|gb|FL012762.1|FL012762

EST:     GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAG                         CATCAAAGACAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA
genomic: GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatcc ... ctcatgttagCATCAAAGCCGGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA

EST: gi|89250718|gb|DY622504.1|DY622504

EST:     GTTCTCCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAG                         CATCAAAGACAGAAGAGGAGGAAGACATTTCCCTCTATGGACACCTTGGAC
genomic: GTTCTC-GATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatcc ... ctcatgttagCATCAAAGCCGGAAGAGGAGGAAGACATT-CCCTCTATGGACACCTTGGAC

EST: gi|211329316|gb|FL012778.1|FL012778

EST:     GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAG                         CATCAAAGACAGAAGAGGAGGAAGACATTCCCTCTATGGACACC
genomic: GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatcc ... ctcatgttagCATCAAAGCCGGAAGAGGAGGAAGACATTCCCTCTATGGACACC

EST: gi|211329314|gb|FL012776.1|FL012776

EST:     GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAG                         CATCAAAGACAGAAGAGGAGGAAGACATTCCCTCTATG
genomic: GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatcc ... ctcatgttagCATCAAAGCCGGAAGAGGAGGAAGACATTCCCTCTATG

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: 174

AGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAGGAGCAGAGGTGGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatcc ... ctcatgttagCATCAAAGCCGGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACATAGGGAGATCTGATGGAATAAAGTCTATCCCCTCTTACTTTAGCGGTGG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 345

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 242

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 233

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAGGAGCAGAGGTGGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatccttataagtgctgtttggttttccactctgaattttatgatcttaactgtttttttggggtccgttgctcatgttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA