ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtatatatgttactgagttaaacgaggagatcaattctatgctatttgatgttatgatgtattatcaataatttcatatcatagttcatttgaacttgtgttgttctgctgcagTTGAATCGACTTGTGACAGAGAAGTGGGTAGATGGGTGGGATGATCCCCGCTTGTTGACACTGGCTGGTCTCCGGCGACGGGGAGTATCATCAACTGCAA

Basic information

species	Zea mays
transcript	GRMZM2G032049_T01
intron #	14
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G032049_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os01g09000.1 (Oryza sativa), 3'ss of exon 14

gtatatatgttactgagttaaacgaggagatcaattctatgctatttgatgttatgatgtattatcaataatttcatatcatagttcatttgaacttgtgttgttctgctgcagTTGAATCGACTTGTGACAGAGAAGTGGGTAGATGGGTGGGATGATCCCCGCTTGTTGACACTGGCTGGTCTCCGGCGACGGGGAGTATCATCAACTGCAA
     |  |||||||| |     ||  |||| |||  ||  ||  || ||  |||| | ||  | || |          ||| |||              |||||||| ||||||||||||||||||||||||| ||||||||||||||||||||||| || || ||||||||||| || ||  | |||||||| ||||| |||||||||||||
----gtg-gttactgaatcttttgacaagataaatgttacactgcttcat-ctatggtttaagaacact----------catggttt-------------ttgttctgttgcagTTGAATCGACTTGTGACAGAAAAGTGGGTAGATGGGTGGGATGACCCTCGTTTGTTGACACTAGCAGGATTGCGGCGACGTGGAGTGTCATCAACTGCAA

upper sequence: GRMZM2G032049_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA20G25120.1 (Glycine max), 3'ss of exon 15

gtatatatgttactgagttaaacgaggagatcaattctatgctatttgatgttatgatgtattatcaataatttcatatcatagttcatttgaacttgtgttgttctgctgcagTTGAATCGACTTGTGACAGAGAAGTGGGTAGATGGGTGGGATGATCCCCGCTTGTTGACACTGGCTGGTCTCCGGCGACGGGGAGTATCATCAACTGCAA
                || || | |  |  |     | |||  ||    ||||  | | |||||| |    | | || |   | | | |    || | |  |  | || |  || | ||||| || || |||||||||||||| ||||||||||||||||| || ||| ||||||| |||||| | |||||  | ||  |  |  |||||||||
----------------gtgaagcaacaattttg-cacaatgtaataatttgttgagttctattattatgcttatgatttgccattccctaactacatattattctttgttaaagCTAAATCGTCTAGTTACAGAGAAGTGGGTTGATGGGTGGGATGATCCTCGTTTGATGACACTAGCTGGTTTGCGGCGTAGAGGCATGACCCCAACTGCAA

upper sequence: GRMZM2G032049_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA10G41920.2 (Glycine max), 3'ss of exon 15

gtatatatgttactgagttaaacgaggagatcaattctatgctatttgatgttatgatgtattatcaataatttcatatcatagttcatttgaacttgtgttgttct--gctgcagTTGAATCGACTTGTGACAGAGAAGTGGGTAGATGGGTGGGATGATCCCCGCTTGTTGACACTGGCTGGTCTCCGGCGACGGGGAGTATCATCAACTGCAA
                || || | |  |  |     | |||  ||    ||||  | | |||||| | |  || ||  |     |||   | |     | || ||||  | |  || | ||||| || || |||||||||||||| ||||||||||||||||| || ||| ||||||| |||||| | |||||  | ||  |  |  |||||||||
----------------gtgaagcaacaattttg-cacaatgtaataatttgttgagttctattatta-tgcttacaatttgccattc-cctaactacatattattctttgttaaagCTAAATCGTCTAGTTACAGAGAAGTGGGTTGATGGGTGGGATGATCCTCGTTTGATGACACTAGCTGGTTTGCGGCGTAGAGGCATGACTCCAACTGCAA

upper sequence: GRMZM2G032049_T01 (Zea mays), 3'ss of exon 14
lower sequence: Vv15s0021g01230.t01 (Vitis vinifera), 3'ss of exon 15

gtatatatgttactgagttaaacgaggagatcaattctatgctatttgatgttatgatgtat-tatcaataatttcatatcatagttcatttgaacttgtgttgttctgctgcagTTGAATCGACTTGTGACAGAGAAGTGGGTAGATGGGTGGGATGATCCCCGCTTGTTGACACTGGCTGGTCTCCGGCGACGGGGAGTATCATCAACTGCAA
     |  | |  ||  || |||    | ||  || | | |||   |||   || | | | | | |  ||| ||||| ||  |   ||           |  ||| ||| |||||||||| || || |||||||| |||||||| ||||| ||||||||||| ||  |  ||||| | |||||| | || ||  |||| ||  | |||||  |||
----gtgagctgatgcattgaacatctatat--atgcaaagct---tgaaactaagctttttgtgtttatattttcacatattgactc-----------taatgtgctgttgcagTTGAACCGCCTGGTGACAGAAAAGTGGGTTGATGGTTGGGATGATCCTCGTCTTATGACATTAGCTGGTTTGCGACGTAGGGGGGTGACTTCAACATCAA

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|32933496|gb|CF038308.1|CF038308

EST:     GGGAATATTCGAGGCTAAACATATCAAATACTGTGATGTCTAAAAGAAAG                         CTGAATCGACTTGTGACAGAGAAGTGGGTAGATGGGTGGGATGATCCTCGC
genomic: GGGAATATTCGAGGCTAAACATATCAAATACTGTGATGTCTAAAAGAAAGgtatatatgt ... tctgctgcagTTGAATCGACTTGTGACAGAGAAGTGGGTAGATGGGTGGGATGATCCCCGC

EST: gi|32934107|gb|CF038919.1|CF038919

EST:     GGGAATATTCGAGGCTAAACATATCAAATACTGTGATGTCTAAAAGAAAG                         CTGAATCGACTTGTGACAGAGAAGTGGGTAGATGGGTGGGATGATCCTCGC
genomic: GGGAATATTCGAGGCTAAACATATCAAATACTGTGATGTCTAAAAGAAAGgtatatatgt ... tctgctgcagTTGAATCGACTTGTGACAGAGAAGTGGGTAGATGGGTGGGATGATCCCCGC

EST: gi|32933499|gb|CF038311.1|CF038311

EST:     GGGAATATTCGAGGCTAAACATATCAAATACTGTGATGTCTAAAAGAAAG                         CTGAATCGACTTGTGACAGAGAAGTGGGTAGATGGGTGGGATGATCCCCGC
genomic: GGGAATATTCGAGGCTAAACATATCAAATACTGTGATGTCTAAAAGAAAGgtatatatgt ... tctgctgcagTTGAATCGACTTGTGACAGAGAAGTGGGTAGATGGGTGGGATGATCCCCGC

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: 233

TTCATACTACTGGCTACTTGTTGCCTTGGGCCTTTATCAACCATATGTGTGGGAATATTCGAGGCTAAACATATCAAATACTGTGATGTCTAAAAGAAAGgtatatatgt ... tctgctgcagTTGAATCGACTTGTGACAGAGAAGTGGGTAGATGGGTGGGATGATCCCCGCTTGTTGACACTGGCTGGTCTCCGGCGACGGGGAGTATCATCAACTGCAA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 184

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 268

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 160

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tattatcaataatttcatatcatagttcatttgaacttgtgttgttctgctgcagTTGAATCGACTTGTGACAGAGAAGTGGGTAGATGGGTGGGATGATCCCCGCTTGTTGACACTGGCTGGTCTCCGGCGACGGGGAGTATCATCAACTGCAA