ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtatgtatatagaagcatgtcttcttgcgctagtcttgttaaatatcataaactacctttttcatctataagcattaatttccatttatctgttttagGATGAACTTCTTGAGTAATATTCTACGGGAAGAGGGTGGATTCGAGTATAAGAAAGCCATAGTTGATTCAATTATTATACTCATTAGAGATATTCCTGAT

Basic information

species	Zea mays
transcript	GRMZM2G036034_T01
intron #	9
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G036034_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os07g10150.1 (Oryza sativa), 3'ss of exon 9

gtatgtatatagaagcatgtcttcttgcgctagtcttgttaaatatcataaactacctttttcatctataagcattaatttccatttatctgttttagGATGAACTTCTTGAGTAATATTCTACGGGAAGAGGGTGGATTCGAGTATAAGAAAGCCATAGTTGATTCAATTATTATACTCATTAGAGATATTCCTGAT
   |   || |  ||| | | |||||   |     || ||||| |||   ||||| ||| | ||||    | |||| |  |   ||  | | ||  ||||||||||| ||||||||||| ||||||||||||||||| || ||||| ||||| || || |||||||||||||| ||||||||||||||||||||||||
--gtacgtagaatagcgtatattcttatacagaaatttttaaagatccagaactagcttgt-catcag--aacattgaactttgtt-gtgt-ttgcagGATGAACTTTTTGAGTAATATCCTACGGGAAGAGGGTGGCTTTGAGTACAAGAAGGCTATTGTTGATTCAATTATCATACTCATTAGAGATATTCCTGAT

upper sequence: GRMZM2G036034_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 9

gtatgtatatagaagcatgtcttcttgcgctagtcttgttaaatatcataaactacctttttcat--ctataagcat------------taatttccatt----tatctgttttagGATGAACTTCTTGAGTAATATTCTACGGGAAGAGGGTGGATTCGAGTATAAGAAAGCCATAGTTGATTCAATTATTATACTCATTAGAGATATTCCTGAT
|||||| |     |  ||   || |  | |    | ||  | || | | |   | | | |||  |  ||| | | ||            |  |||  |||    |||   ||| |||||||||||| |||||||||||||  ||||||| || || || || || ||||| || || || ||||||||| | || |||||||||||||| ||||||
gtatgtgtccctgaatatagtttttgactccccacatgccatatgttacatcgtgcatatttatttcctagaggaatgttttatgatgatggtttgtattctgctattattttcagGATGAACTTCCTGAGTAATATTCTTAGGGAAGAAGGGGGTTTTGATTACAAGAAGGCAATTGTAGATTCAATTGTGATTCTCATTAGAGATATCCCTGAT

upper sequence: GRMZM2G036034_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA12G04820.1 (Glycine max), 3'ss of exon 9

------gtatgtatatagaa----gcatgtcttcttgcgctagtcttgttaaatatcata-aactacctttttca---------tctataagcattaatttccatt----tatctgttttagGATGAACTTCTTGAGTAATATTCTACGGGAAGAGGGTGGATTCGAGTATAAGAAAGCCATAGTTGATTCAATTATTATACTCATTAGAGATATTCCTGAT
       |||||  ||   |      | || |  || | | ||   |   | || ||||   | |   |||   |         |||| ||  | |  ||||  ||    |||   ||| |||||||| ||| | ||||| |||||  ||||||| ||||| || || || |||||||| || || ||||||||| | || || ||||||||||| ||||||
gtgagtatatgtcaatgtcattctataggtttctttcccccagaagttacatatttcatttgaatgtttttcctagatgaatggtcta-aattactggtttcttttctgttattattttcagGATGAATTTCCTAAGTAACATTCTTAGGGAAGAAGGTGGCTTTGATTACAAGAAAGCAATTGTAGATTCAATTGTGATTCTTATTAGAGATATCCCTGAT

upper sequence: GRMZM2G036034_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA04G01470.1 (Glycine max), 3'ss of exon 9

gtatgtatatagaagcatgtcttcttgcgctagtcttgttaaatatcataaactacctttttca--------tctata---agcattaatttccatttatctgttttagGATGAACTTCTTGAGTAATATTCTACGGGAAGAGGGTGGATTCGAGTATAAGAAAGCCATAGTTGATTCAATTATTATACTCATTAGAGATATTCCTGAT
|||||| |     |  ||   || |  | |       |    || |   | | |   ||  | |        | |||    |   ||  | | |   |||   ||| |||||||| ||| |||||||||||||  |||| || ||||| || || || ||||| || || || ||||||||| | || |||||||||||||| ||| ||
gtatgtgtccctgaatatagtttttgactccccatacgccttatgttgcatatttatttcctaaaggaatgttttatgctgatggtttgtattctgctattattttcagGATGAATTTCCTGAGTAATATTCTTAGGGAGGAAGGTGGTTTTGATTACAAGAAGGCAATTGTAGATTCAATTGTGATTCTCATTAGAGATATCCCTAAT

upper sequence: GRMZM2G036034_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 9

---------------------gtatgtatatagaagcat----gtcttcttgcgctagtcttgttaaat----atcataaactacctttttcatctataa-gcattaatttccatttatctgtttt--agGATGAACTTCTTGAGTAATATTCTACGGGAAGAGGGTGGATTCGAGTATAAGAAAGCCATAGTTGATTCAATTATTATACTCATTAGAGATATTCCTGAT
                      | |    ||  || |||    || || ||    |    || ||||||    |   |||| |   |   |||| |  ||   | |||      ||    || |||  |||||||||||||| || || |||||  ||||||| |||||||| ||||| || || || || |||||||||||  | || ||||| |||||||||||||||
gtaagtgatatcctgtttttgatgtcatcattaaaacatttgggttttatttttatgtcttttttaaatgaacagtgtaaaatgtttccgtcatgtgaaatagaataaccctttttcccttgcttttcagGATGAACTTCTTAAGCAACATTCTTAGGGAAGAAGGTGGATTTGAGTACAAAAAGGCGATTGTTGATTCAATCGTGATCCTCATAAGAGATATTCCTGAT

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|89106351|gb|DY576568.1|DY576568

EST:     GAAATATCGCTCATT                         GATGAACTTCTTGAGTAATATTCTACGGGAAGAGGGAGGATTCGAGTACAA
genomic: GAAATATCGCTCATTgtatgtatat ... tctgttttagGATGAACTTCTTGAGTAATATTCTACGGGAAGAGGGTGGATTCGAGTATAA

EST: gi|18963611|gb|BM660532.1|BM660532

EST:     GAAATATCGCTCATT                         GATGAACTTCTTGAGTAATATTCTACGGGAAGAGGGAGGATTCGAGTACAA
genomic: GAAATATCGCTCATTgtatgtatat ... tctgttttagGATGAACTTCTTGAGTAATATTCTACGGGAAGAGGGTGGATTCGAGTATAA

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: 462

TGACCAACTTTATGTCAGACATAGCTGATGAGTTTAAGATTGTTGTTGTTGAAGCAATAAGATCTCTGTGCTTGAAGTTCCCTCTGAAATATCGCTCATTgtatgtatat ... tctgttttagGATGAACTTCTTGAGTAATATTCTACGGGAAGAGGGTGGATTCGAGTATAAGAAAGCCATAGTTGATTCAATTATTATACTCATTAGAGATATTCCTGAT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 398

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 313

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 478

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tatcataaactacctttttcatctataagcattaatttccatttatctgttttagGATGAACTTCTTGAGTAATATTCTACGGGAAGAGGGTGGATTCGAGTATAAGAAAGCCATAGTTGATTCAATTATTATACTCATTAGAGATATTCCTGAT