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

gtaggttcgccacaattgtcattcagttttcgtaccagcagtggattactcctgctaaccgttgacctcacatatcaaccagATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATGTGCCCGGGTGGGTGGAAGGTTCTTGTTGACTACTACAACAGCCTGCAAGCTG

Basic information

species	Zea mays
transcript	GRMZM2G158147_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G158147_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g02050.1 (Oryza sativa), 3'ss of exon 4

gtaggttcgccacaattgtcattcagtt--ttcgtaccagcagtggattactcctgctaaccgttgacctcacatatcaa--ccagATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATGTGCCCGGGTGGGTGGAAGGTTCTTGTTGACTACTACAACAGCCTGCAAGCTG
    || |     |||| |||   |  |  || | | |||       ||  | ||| |||    | || | ||| |||||  |||||||||  ||| ||| |||| ||||||||| ||||| ||||||||||||||||| ||||||||||| |||||||| ||||||||||| ||  ||||| | |
----gtacagataaattttcacataagtgctttgcagcagagacaattttgttctgttaaaaactaactttacaaatcaaaaccagATGCGGGCTTTTGCGAAAAGTGGAGAGAACCCTCCTGACGGTTTCATGTGCCCTGGTGGGTGGAAAGTTCTTGTGGACTACTACAATAGTTTGCAAACCG

upper sequence: GRMZM2G158147_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA13G06940.1 (Glycine max), 3'ss of exon 4

---------------gtaggttcgccacaattgtcattcagt--tttcgtaccagcagtggattactcctgctaac--cgttgacctcacatatcaaccagATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATGTGCCCGGGTGGGTGGAAGGTTCTTGTTGACTACTACAACAGCCTGCAAGCTG
                 | ||| |   |     || ||      ||  | | | |   |  |  | |  |  |     | || |      ||||   |||||||||  ||| ||| |||| ||| |||||||| ||||| ||||||||||||||  |||||||||||||||||||  | || ||  | ||  |||| || |
acatcacatgtagcaacaagttggtttctgaaatcctttgacaattgggcatctgttctttacaaattttcgtggtttctttaatgatttatattt-ccagATGCGGGCTTTTGCAAAAAGTGGGGAGAATCCGCCAGAAGGTTTCATGTGCCCAAGTGGGTGGAAGGTTCTTGTCAAATATTATGAAAGTTTGCAGGCAG

upper sequence: GRMZM2G158147_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT1G19920.1 (Arabidopsis thaliana), 3'ss of exon 4

--------------------gtaggttcgccacaattgtcattcagttt-----tcgtaccagcagtggattactcctg-----ctaaccgttgacctcacatat-caaccagATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATGTGCCCGGGTGGGTGGAAGGTTCTTGTTGACTACTACAACAGCCTGCAAGCTG
                     || | |    |     | |    |||||     |  | |        |||||| ||||      ||  || ||   |    | | |   |||||||| |||||||| | ||| || |||||||||||||| || || ||||| ||| |||| ||||| ||||||||  | |||||  | ||| ||||||   
gtaagagacagttttgagacttaagattcttattgaaggctccaagtttcgaggttctgcttatgtgcgattacacctgagtttttattcggtgttttttgttgtgcttacagATGCGAACTTATGCAAGAACAGGGGAGAATCCTCCAGATGGATTTATGTGTCCGAGTGGATGGAATGTTCTTGTCAAATACTATGAGAGCTTGCAAGAGA

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|149016052|gb|EE154221.2|EE154221

EST:     AGTCAAGTTTTTCTGTTCATCTCTGGAACCAAG                         AGGCGCACTTATTCCAAAACTGGAGAGAATCCTCCAGCCGGTTTCATGTGC
genomic: AGTCAAGATTTTCTGTTCATCTCTGGAACCAAGgtaggttcgc ... tatcaaccagATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATGTGC

EST: gi|211399264|gb|FL448232.1|FL448232

EST:     TTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTGATCTCTGGAACCAAG                         ATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATGTGC
genomic: TTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAGgtaggttcgc ... tatcaaccagATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATGTGC

EST: gi|32830226|gb|CD969904.1|CD969904

EST:     TTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAG                         ATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATG
genomic: TTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAGgtaggttcgc ... tatcaaccagATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATG

EST: gi|32828661|gb|CD968339.1|CD968339

EST:     TTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAG                         ATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATG
genomic: TTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAGgtaggttcgc ... tatcaaccagATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATG

EST: gi|211401799|gb|FL448233.1|FL448233

EST:     TTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAG                         ATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATGTGC
genomic: TTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAGgtaggttcgc ... tatcaaccagATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATGTGC

EST: gi|32829799|gb|CD969477.1|CD969477

EST:     TTTTTGATCCTTCACGCA-TCAAGATTTTCTGTTCATCTCTGGAACCAAG                         ATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATG
genomic: TTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAGgtaggttcgc ... tatcaaccagATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATG

EST: gi|32829244|gb|CD968922.1|CD968922

EST:     TTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAG                         ATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATGTGC
genomic: TTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAGgtaggttcgc ... tatcaaccagATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATGTGC

EST: gi|32828636|gb|CD968314.1|CD968314

EST:     TTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAG                         ATGCGCACTTATGCCAAAACTGGAAAGAATCCTCCAGACGGTTTCATG
genomic: TTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAGgtaggttcgc ... tatcaaccagATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATG

EST: gi|148974683|gb|EE025486.2|EE025486

EST:     ACGCAGTCAAGATTTTCTGTTCATTTCTGGAACCAAG                         ATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATGTGC
genomic: ACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAGgtaggttcgc ... tatcaaccagATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATGTGC

EST: gi|32830289|gb|CD969967.1|CD969967

EST:     TTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAG                         ATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATG
genomic: TTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAGgtaggttcgc ... tatcaaccagATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATG

EST: gi|60346069|gb|DN213042.1|DN213042

EST:     TTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAG                         ATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATGTGC
genomic: TTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAGgtaggttcgc ... tatcaaccagATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATGTGC

EST: gi|32830236|gb|CD969914.1|CD969914

EST:     TTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAG                         ATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATG
genomic: TTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAGgtaggttcgc ... tatcaaccagATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATG

EST: gi|60357884|gb|DN224857.1|DN224857

EST:     TTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAG                         ATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATGTGC
genomic: TTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAGgtaggttcgc ... tatcaaccagATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATGTGC

EST: gi|32829367|gb|CD969045.1|CD969045

EST:     TTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAG                         ATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATGTTC
genomic: TTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAGgtaggttcgc ... tatcaaccagATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATGTGC

EST: gi|148942989|gb|EC888037.2|EC888037

EST:     TTTTTGATCCTTCACGCAGTCAAGATTTTTTGTTCATTTCTGGAACCAAG                         ATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATGTGC
genomic: TTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAGgtaggttcgc ... tatcaaccagATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATGTGC

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), 48 (downstream exon)
Score: 36

GTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAGgtaggttcgc ... tatcaaccagATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATGTGCCCGGGTGGGTGGAAGGTTCTTGTTGACTACTACAACAGCCTGCAAGCTG

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 81

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 35

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 25

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tttcgtaccagcagtggattactcctgctaaccgttgacctcacatatcaaccagATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATGTGCCCGGGTGGGTGGAAGGTTCTTGTTGACTACTACAACAGCCTGCAAGCTG

                                            atatcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggttcgccacaattgtcattcagttttcgtaccagcagtggattactcctgctaaccgttgacctcacatatcaaccagATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATGTGCCCGGGTGGGTGGAAGGTTCTTGTTGACTACTACAACAGCCTGCAAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG