ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

...attactgtttgtcaagtgaattgttacatgttgcttttgctgtgtcatggattcttctgcttggttatggttctgatttcgtgttttttgttgtgcctagGGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAGATCAAGCAGTAGGTCTTTGCACGTAGTTCCACCGGTAATGGCCTTTTTT

Basic information

species	Zea mays
transcript	GRMZM2G134109_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G134109_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g46490.1 (Oryza sativa), 3'ss of exon 3

-----attactgtttgtcaagtgaat-tgttacatgt-tgcttttgctgtgtcatggattcttctgcttggttatggttctgatttcgtgttttttgttgtgcctagGGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAGATCAAGCAGTAG--GTCTTTGCACGTAGTTCCACCGGTAATGGCCTTTTTT
      |  |||||| ||  |   || || ||      |       || |||       |   || |||   ||  ||||| ||||  | | ||| |        |||| || || |||||| |  |||| |||||||||||||||| |||||||||| |||||||| ||  |   ||||   |||||  ||| ||||   |   ||  
aggacctagctgtttttcttgctcatatgctatgcacataaaaagactttgttgcaatgttgcctccttcagta-agttctcatttgatttatttcgac------agGGAGACGCCGACAGTGCTCTGGATAGGCTGTGGCAGAAGAGGAAGGCTGAGGTCAAGCAGCAGTAGATGTTGCTACTAGTTTTACCTGTAAGAACTCGTT--

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|211241797|gb|FL220663.1|FL220663

EST:     ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG
genomic: ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgatagtcc ... ttgtgcctagGGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG

EST: gi|211239565|gb|FL220655.1|FL220655

EST:     ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG
genomic: ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgatagtcc ... ttgtgcctagGGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG

EST: gi|5597227|gb|AI891220.1|AI891220

EST:     CGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGTGATGCTGACAGCTCGTTGGACAGGCTGTGGCAGAAAAAGAAGGCTGAG
genomic: CGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgatagtcc ... ttgtgcctagGGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG

EST: gi|211244033|gb|FL220677.1|FL220677

EST:     ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG
genomic: ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgatagtcc ... ttgtgcctagGGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG

EST: gi|211241800|gb|FL220666.1|FL220666

EST:     ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGTGATGCTGACAGTTCGTTGGACA
genomic: ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgatagtcc ... ttgtgcctagGGTGATGCTGACAGTTCGTTGGACA

EST: gi|84980738|gb|DW531087.1|DW531087

EST:     ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG
genomic: ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgatagtcc ... ttgtgcctagGGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG

EST: gi|211235091|gb|FL220624.1|FL220624

EST:     ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG
genomic: ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgatagtcc ... ttgtgcctagGGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG

EST: gi|18385131|gb|BM418330.1|BM418330

EST:     ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGTGATGCTGACAGCTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG
genomic: ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgatagtcc ... ttgtgcctagGGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG

EST: gi|211241802|gb|FL220668.1|FL220668

EST:     ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG
genomic: ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgatagtcc ... ttgtgcctagGGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG

EST: gi|211244035|gb|FL220679.1|FL220679

EST:     ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG
genomic: ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgatagtcc ... ttgtgcctagGGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG

EST: gi|18649856|gb|BM498675.1|BM498675

EST:     ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGTGATGCTGACAGCTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG
genomic: ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgatagtcc ... ttgtgcctagGGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG

EST: gi|211239552|gb|FL220642.1|FL220642

EST:     ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG
genomic: ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgatagtcc ... ttgtgcctagGGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG

EST: gi|211244039|gb|FL220683.1|FL220683

EST:     ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG
genomic: ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgatagtcc ... ttgtgcctagGGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG

EST: gi|211241790|gb|FL220656.1|FL220656

EST:     ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG
genomic: ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgatagtcc ... ttgtgcctagGGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG

EST: gi|211237336|gb|FL220639.1|FL220639

EST:     ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG
genomic: ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgatagtcc ... ttgtgcctagGGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG

EST: gi|211237328|gb|FL220631.1|FL220631

EST:     ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG
genomic: ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgatagtcc ... ttgtgcctagGGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG

EST: gi|211244040|gb|FL220684.1|FL220684

EST:     ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG
genomic: ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgatagtcc ... ttgtgcctagGGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG

EST: gi|211244030|gb|FL220674.1|FL220674

EST:     ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG
genomic: ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgatagtcc ... ttgtgcctagGGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG

EST: gi|211239560|gb|FL220650.1|FL220650

EST:     ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG
genomic: ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgatagtcc ... ttgtgcctagGGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG

EST: gi|18649857|gb|BM498676.1|BM498676

EST:     ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAG                         GGTGATGCTGACAGCTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG
genomic: ACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgatagtcc ... ttgtgcctagGGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAG

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: 580

TCATGCCTCTGTCCAGATCAACATTGGCCACTTGGATGCGAATGGCCTGTACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgtgatagtcc ... ttgtgcctagGGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAGATCAAGCAGTAGGTCTTTGCACGTAGTTCCACCGGTAATGGCCTTTTTT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1208

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1009

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 373

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

catggattcttctgcttggttatggttctgatttcgtgttttttgttgtgcctagGGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAGATCAAGCAGTAGGTCTTTGCACGTAGTTCCACCGGTAATGGCCTTTTTT

                         ttctgat  putative branch site (score: 373)
                                      ttttttgtt  putative PPT
                                      ttttttgtt  TA-rich tract

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attactgtttgtcaagtgaattgttacatgttgcttttgctgtgtcatggattcttctgcttggttatggttctgatttcgtgttttttgttgtgcctagGGTGATGCTGACAGTTCGTTGGACAGGCTGTGGCAGAAGAAGAAGGCTGAGATCAAGCAGTAGGTCTTTGCACGTAGTTCCACCGGTAATGGCCTTTTTT

- - -tgtttgt
- - - - - - - - tgaattg
- - - - - - - - - - - - - - tgttgct
- - - - - - - - - - - - - - - - - -tttgctg
- - - - - - - - - - - - - - - - - - - - - tgtcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttt