ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgctgtactttcttgtttaaacctttgccctctgcatggttaattatgttgtgttaatattgagtttctgttcttgcag

Basic information

species	Zea mays
transcript	GRMZM2G134109_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G134109_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g46490.1 (Oryza sativa), 5'ss of exon 2

TTGCTGCTGCGGTAGTCCC-----CAACCATCATCATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgttt--gctgtactttcttgtttaaacctttgccctctgcatggttaattatg---ttgtgttaatattgagtttctgttcttgcag
|||||| || |||  |  |     | ||| ||||||||||||||||||||||| ||| |||||||||||||||||||||||||||||| ||||  |   | |||  |  |||      |    |      || |||  | |    ||   |   | ||| |||  | ||| |||||
TTGCTGTTGTGGTGTTTTCTTCATCTACCGTCATCATGCAGAACGAGGAGGGTCAGATGGTGGACCTCTACGTCCCCAGGAAGTGgtatgtttctgtcattcttgatgttttggtgtctaattcaactggtgtttagatgtacttttacatgcgtgttgtgttggt-ttcctgcag

upper sequence: GRMZM2G134109_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S306_29V6.1 (Physcomitrella patens), 5'ss of exon 1

--------------------TTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgctgtactt-tcttgtttaaacctttgccctctgca--tggttaattatgttgtgttaatattgagtttctgttcttgcag-----------
                    ||  ||  |||     | ||| |   || ||||||||||||||| ||| | |  |||||||||||| |||| ||||||||||| || ||     |   | ||||||   | ||||   | |     |  | ||||||  | |     |   || ||      ||  |||           
CTGCCCGTTTCGTCTGTCGTTTCGTGTAGCGTGTAGCGCCAGCAGCCAACATGCAGAACGAGGAAGGTGATAATGTGGACCTCTACATCCCGAGGAAGTGgtaagtgtgtaactcgcgttttgtttccgcttttgttgtttatggtttatgaattataatttagggcttgggaattcggtggctgacaggtagtttgttc

upper sequence: GRMZM2G134109_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S287_34V6.1 (Physcomitrella patens), 5'ss of exon 1

--------------------TTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttg---ctgtactttcttgtt--taaacctttg----------ccctctgcatggttaattatgttgtgttaa-tattgagtttctgttcttgcag
                    |  ||    |  |    |  | |   || ||||||||||||||||||| | |  ||||| |||||| ||||||||||||||| ||| |    |  |  | |||  ||      | ||||          ||  || |||  ||   |  | ||   |||    |   ||||  ||| | |  
CTTTTCTCTCGATCTCTCTCTCTCTCTCTCTCTCTCGCTTATCTTGCACCATGCAGAACGAGGAGGGTGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgcgtataagaccatcttctctcattatctttcttttgttggaaatatcctgctccatcatttcctccgatggactaaaccctagatttcatttcatcc--

upper sequence: GRMZM2G134109_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S372_10V6.1 (Physcomitrella patens), 5'ss of exon 1

------------------TTGCTGCT-GCGGTAGTCCCCAACCAT-CATCATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgctgtactttcttgtttaaacctttgccc-tctgca----tggttaattatgttgtgttaatattgagt-----ttctgttcttgcag----
                   |||  || || |   || || |     || ||||||||||||||||||  | |  ||||| |||||| |||||||||||||||  ||||  | |  ||  | ||   | | |   ||| | |  |    |  ||| || |  | |  |  ||||   |      |   ||| | | |    
TCTCTCGTCTTTCAATTTCTGCGTCTCGCTGATCTCGCCGATTTCGCACCATGCAGAACGAGGAGGGCGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgggttttttttgtttcatcgtcgtatcttccccccatttagagtttttcttacttctactttcctcctatttgataaaccctagattcattccggatt

upper sequence: GRMZM2G134109_T01 (Zea mays), 5'ss of exon 2
lower sequence: EFJ15472 (Selaginella moellendorffii), 5'ss of exon 1

--------------------TTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgctgtactttcttgtttaa--acctttgccctctgcatggttaattatgttgtgttaatattgagtttctgttcttgcag
                     ||| |||| ||  |      | |  |||||||||||||||||||||  |||  || || |||||| |||||||||||||||| |   |     |   |||  ||     ||  |  | || ||  | || ||| | ||| |                          
ATTAGGGTTCTTTCGTTGTGCTGCGGCTGAGGAGGAGAAAGAGCGCCATCATGCAGAACGAGGAGGGCGAGAACGTCGATCTCTACATCCCCAGGAAGTGgtaagcgcgaatctcccgcttcctttgtggccgctctcatcagcgcgattgattttcttgcgcag-----------------------

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:     ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTG                         CTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT
genomic: ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgc ... gttcttgcagCTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT

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

EST:     ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACTTCCCCAGGAAGTG                         CTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT
genomic: ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgc ... gttcttgcagCTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT

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

EST:     ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTG                         CTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT
genomic: ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgc ... gttcttgcagCTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT

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

EST:     ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACTTCCCCAGGAAGTG                         CTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT
genomic: ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgc ... gttcttgcagCTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT

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

EST:     ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTG                         CTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT
genomic: ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgc ... gttcttgcagCTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT

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

EST:     ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTG                         CTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT
genomic: ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgc ... gttcttgcagCTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT

EST: gi|9742525|gb|BE518637.1|BE518637

EST:     TGCAGAACGAGGAGGGCTAAGACGGTGGACCTCTACGTCCCCAGGAAGTG                         CTCGGCCACGAACAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT
genomic: TGCAGAACGAGGAGGG-TAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgc ... gttcttgcagCTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT

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

EST:     ACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTG                         CTCGGCCACGAACAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT
genomic: ACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgc ... gttcttgcagCTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT

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

EST:     ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTG                         CTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT
genomic: ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgc ... gttcttgcagCTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT

EST: gi|211239555|gb|FL220645.1|FL220645

EST:     ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTG                         CTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT
genomic: ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgc ... gttcttgcagCTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT

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

EST:     ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTG                         CTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT
genomic: ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgc ... gttcttgcagCTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT

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

EST:     AACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTG                         CTCGGCCACGAACAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT
genomic: AACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgc ... gttcttgcagCTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT

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

EST:     ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTG                         CTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT
genomic: ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgc ... gttcttgcagCTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT

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

EST:     ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTG                         CTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT
genomic: ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgc ... gttcttgcagCTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT

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

EST:     ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTG                         CTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT
genomic: ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgc ... gttcttgcagCTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT

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

EST:     ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTG                         CTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT
genomic: ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgc ... gttcttgcagCTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT

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

EST:     ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTG                         CTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT
genomic: ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgc ... gttcttgcagCTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT

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

EST:     ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTG                         CTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT
genomic: ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgc ... gttcttgcagCTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT

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

EST:     ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTG                         CTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT
genomic: ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgc ... gttcttgcagCTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT

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

EST:     ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTG                         CTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT
genomic: ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgc ... gttcttgcagCTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT

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

EST:     ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTG                         CTCGGCCACGAACAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT
genomic: ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgc ... gttcttgcagCTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT

EST: gi|33093009|gb|CF053003.1|CF053003

EST:     ATGCAGAACGAGGAGGGTAAGACGGCGGACCTCTACGTCCCCAGGAAGTG                         CTCGGCCACGAACAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAC
genomic: ATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgc ... gttcttgcagCTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGAT

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: 613

TTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgc ... gttcttgcagCTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGATCAACATTGGCCACTTGGATGCGAATGGCCTGTACGATGGTCACTTCACC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 431

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 306

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 510

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTGgtacgtttgctgtactttcttgtttaaacctttgccctctgcatggttaattatgttgtgttaatattgagtttctgttcttgcag

- - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA