ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TTGCAACAGCCTCCCAGGTTACAAGACCAGATACGATGATGTTAACCTTGTAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattcttaaagagatgttgcttcaattattgtcaccatgattctttttcaccttgtcttaattccacttcag

Basic information

species	Zea mays
transcript	GRMZM2G120857_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G120857_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g16900.3 (Oryza sativa), 5'ss of exon 4

TTGCAACAGCCTCCCAGGTTACAAGACCAGATACGATGATGTTAACCTTGTAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattcttaaa-gagatgttgcttcaattattgtcaccatgattctttttcaccttgtcttaattccacttcag
|||||||||||||||||| ||||||||  |||| |||||||| |||||||| || |||||||||||||| || |||||||||||||| ||||||||||||||||||||||||||| |  || |   ||  |||  | |    |  ||| ||  ||||  |||  || ||   || |||
TTGCAACAGCCTCCCAGGATACAAGACTCGATATGATGATGTGAACCTTGTGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAGgtaagcattcttaaaagcaatatcattttcattggtcttgttagcattattcatcactgtgtgctatttattctccag

upper sequence: GRMZM2G120857_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA10G06590.2 (Glycine max), 5'ss of exon 2

TTGCAACAGCCTCCCAGGTTACAAGACCAGATACGATGATGTTAACCTTGTAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattcttaaagagatgttgcttcaattattgtcaccatgattctttttcaccttgtcttaattccacttcag--------
|||| |||| || ||||| ||||| ||  |||| ||| |||| || ||  | ||||||||||||||||| ||||| || || ||||| ||||| ||||||||||  |||    || |  || || | ||  || | |||   | |||||  |  |  |  | |   |  || ||  |        
TTGCTACAGTCTTCCAGGCTACAAAACTCGATATGATAATGTCAATCTAATTACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAGgtaa--atttcacaacaattgatgttaca--tactatcattttaattctgatcaatataatttgtttagcatttatgggtctcag

upper sequence: GRMZM2G120857_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA13G20790.1 (Glycine max), 5'ss of exon 2

TTGCAACAGCCTCCCAGGTTACAAGACCAGATACGATGATGTTAACCTTGTAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattcttaaagagatgttgcttcaattattgtcaccatgattctttttcaccttgtcttaattccacttcag--------
|||| |||| || ||||| ||||| ||  | || ||| |||| || ||  | ||||||||||||||||| ||||| || || ||||| ||||| ||||||||||   |||  ||  |    ||  | ||  || | ||| |   |||||  |  |  |  | |   |  || ||  |        
TTGCTACAGTCTTCCAGGCTACAAAACTCGGTATGATAATGTCAATCTAATCACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAGgtaaat-ttcacaacaa----tttatgcacgtactatcatctgaattctgatcaatataatttgtttagcatttttgggtttcag

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|74239666|gb|DT647580.1|DT647580

EST:     TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT
genomic: TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... tccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT

EST: gi|32927267|gb|CF032079.1|CF032079

EST:     TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT
genomic: TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... tccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT

EST: gi|148932534|gb|EC876336.2|EC876336

EST:     TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT
genomic: TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... tccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT

EST: gi|32929253|gb|CF034065.1|CF034065

EST:     TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT
genomic: TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... tccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT

EST: gi|149101023|gb|EE187121.2|EE187121

EST:     TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT
genomic: TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... tccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT

EST: gi|23199568|gb|BU582133.1|BU582133

EST:     T-ACAATTCG-GAAAATACTGAAGGAGAATATAG-GGTCTTGAGCATCAG                         GTTGTGAGAGG-GTTG-GGAAAGTTTGAAAATTATTACACGCCAAGCAAGT
genomic: TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... tccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT

EST: gi|148956957|gb|EC902897.2|EC902897

EST:     TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT
genomic: TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... tccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT

EST: gi|87155757|gb|DY400546.1|DY400546

EST:     TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT
genomic: TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... tccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT

EST: gi|31358416|gb|CD442773.1|CD442773

EST:     TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTGGGAAAGTTTGAATATTATTACACGCCAAGCAAG
genomic: TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... tccacttcagGTTGTGAGAGGTGTTGTGG-AAAGTTTGAAAATTATTACACGCCAAGCAAG

EST: gi|76019791|gb|DT946961.1|DT946961

EST:     TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT
genomic: TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... tccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT

EST: gi|78109386|gb|DV527802.1|DV527802

EST:     TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT
genomic: TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... tccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT

EST: gi|149089409|gb|EE178649.2|EE178649

EST:     TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT
genomic: TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... tccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT

EST: gi|9731686|gb|BE510438.1|BE510438

EST:     TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT
genomic: TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... tccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT

EST: gi|40335589|gb|CK369659.1|CK369659

EST:     TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT
genomic: TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... tccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT

EST: gi|32931400|gb|CF036212.1|CF036212

EST:     TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTGGAAAGTTTAAAAATTATTACACGCCAAGCAAGT
genomic: TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... tccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT

EST: gi|110201588|gb|EC883485.1|EC883485

EST:     TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTGGAAAGTTTGAAAAATTATTACACGCCAAGCAAG
genomic: TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... tccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAA-TTATTACACGCCAAGCAAG

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: 48 (upstream exon), 49 (downstream exon)
Score: 145

TTGCAACAGCCTCCCAGGTTACAAGACCAGATACGATGATGTTAACCTTGTAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... tccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGTTTGAGAGTGGCAGAGTATGCTTTCCATTATGCCAAGGCCAATGGCCGGG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 196

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 197

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 321

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCAACAGCCTCCCAGGTTACAAGACCAGATACGATGATGTTAACCTTGTAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattcttaaagagatgttgcttcaattattgtcaccatgattctttttcaccttgtcttaattccacttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA