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

gtttgtgtaatcattacgacctgcatacaaaaacaaataacctgtggagccaattataacttctcacgtattggtgatgcagGTGCAGCTGCAACAAATAACTGTTCAAGTAGCATGGAGAGTCCATCTGGTACTTGGCCAACTTCTGAAGCAGTCGAGCAAGAAAATATGGTTCCACCACT

Basic information

species	Zea mays
transcript	GRMZM2G057408_T02
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G057408_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g45840.2 (Oryza sativa), 3'ss of exon 4

gtttgtgtaatcattacg-------acctgcatacaaaa------acaaataacctgtggagccaattataacttctcacgtattggtgatgcagGTGCAGCTGCAACAAATAACTGTTCAAGTAGCATGGAGAGTCCATCTGGTACTTGGCCAACTTCTGAAGCAGTCGAGCAAGAAAATATGGTTCCACCACT
|| ||| ||   | || |       ||||   | |||||      | ||| | ||     |  | |||   ||     |  | | |  | | ||||||| | ||| ||||||||||| || |||||||| |||||||| |||  |||||||||||||||||||||||| || |||||||||||| ||| ||||||
gtatgtttacctactatgctcataaacctctgtccaaaattaatgagaaaaatccaacaaatgccattg--acgaactaaatttggcaggtacagGTGCTGTTGCTACAAATAACTGCTCTAGTAGCATAGAGAGTCCTTCTACTACTTGGCCAACTTCTGAAGCAGTTGAACAAGAAAATATGCTTCGACCACT

upper sequence: GRMZM2G057408_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g45840.1 (Oryza sativa), 3'ss of exon 4

gtttgtgtaatcattacg-------acctgcatacaaaa------acaaataacctgtggagccaattataacttctcacgtattggtgatgcagGTGCAGCTGCAACAAATAACTGTTCAAGTAGCATGGAGAGTCCATCTGGTACTTGGCCAACTTCTGAAGCAGTCGAGCAAGAAAATATGGTTCCACCACT
|| ||| ||   | || |       ||||   | |||||      | ||| | ||     |  | |||   ||     |  | | |  | | ||||||| | ||| ||||||||||| || |||||||| |||||||| |||  |||||||||||||||||||||||| || |||||||||||| |||       
gtatgtttacctactatgctcataaacctctgtccaaaattaatgagaaaaatccaacaaatgccattg--acgaactaaatttggcagGTACAGGTGCTGTTGCTACAAATAACTGCTCTAGTAGCATAGAGAGTCCTTCTACTACTTGGCCAACTTCTGAAGCAGTTGAACAAGAAAATATGCTTCG------

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|78118281|gb|DV536668.1|DV536668

EST:     TTCCTGGGACAATACTCTTGCTCAACCTTTCAGCGCTGGTCATGTTCAAG                         GTGCAGCTGCAACAAATAACTGTTCAAGTAGCATGGAGAGTCCATCTGGTA
genomic: TTCCTGGGACAATACTCTTGCTCAACCTTTCAGCGCTGGTCATGTTCAAGgtttgtgtaa ... ggtgatgcagGTGCAGCTGCAACAAATAACTGTTCAAGTAGCATGGAGAGTCCATCTGGTA

EST: gi|101392321|gb|EB818090.1|EB818090

EST:     TTCCTGGGACAATACTCTTGCTCAACCTTTCAGCGCTGGTCATGTTCAAG                         GTGCAGCTGCAACAAATAACTGTTCAAGTAGCATGGAGAGTCCATCTGGTA
genomic: TTCCTGGGACAATACTCTTGCTCAACCTTTCAGCGCTGGTCATGTTCAAGgtttgtgtaa ... ggtgatgcagGTGCAGCTGCAACAAATAACTGTTCAAGTAGCATGGAGAGTCCATCTGGTA

EST: gi|91876492|gb|EB406449.1|EB406449

EST:     TTCCTGGGACAATACTCTTGCTCAACCTTTCAGCGCTGGTCATGTTCAAG                         GTGCAGCTGCCACAAATAACTGTTCAAGTAGCATGGAGAGTCCATCTGGTA
genomic: TTCCTGGGACAATACTCTTGCTCAACCTTTCAGCGCTGGTCATGTTCAAGgtttgtgtaa ... ggtgatgcagGTGCAGCTGCAACAAATAACTGTTCAAGTAGCATGGAGAGTCCATCTGGTA

EST: gi|78118283|gb|DV536669.1|DV536669

EST:     TTCCTGGGACAATACTCTTGCTCAACCTTTCAGCGCTGGTCATGTTCAAG                         GTGCAGCTGCAACAAATAACTGTTCAAGTAGCATGGAGAGTCCATCTGGTA
genomic: TTCCTGGGACAATACTCTTGCTCAACCTTTCAGCGCTGGTCATGTTCAAGgtttgtgtaa ... ggtgatgcagGTGCAGCTGCAACAAATAACTGTTCAAGTAGCATGGAGAGTCCATCTGGTA

EST: gi|89757689|gb|DY687184.1|DY687184

EST:     TTCCTGGGACAATACTCTTGCTCAACCTTTCAGCGCTGGTCATGTTCAAG                         GTGCAGCTGCAACAAATAACTGTTCAAGTAGCATGGAGAGTC
genomic: TTCCTGGGACAATACTCTTGCTCAACCTTTCAGCGCTGGTCATGTTCAAGgtttgtgtaa ... ggtgatgcagGTGCAGCTGCAACAAATAACTGTTCAAGTAGCATGGAGAGTC

EST: gi|78076508|gb|DV504942.1|DV504942

EST:     TTCCTGGGACAATACTCTTGCTCAACCTTTCAGCGCTGGTCATGTTCAAG                         GTGCAGCTGCAACAAATAACTGTTCAAGTAGCATGGAGAGTCCATCTGGTA
genomic: TTCCTGGGACAATACTCTTGCTCAACCTTTCAGCGCTGGTCATGTTCAAGgtttgtgtaa ... ggtgatgcagGTGCAGCTGCAACAAATAACTGTTCAAGTAGCATGGAGAGTCCATCTGGTA

EST: gi|71763063|gb|DR961000.1|DR961000

EST:     TTCCTGGGACAATACTCTTGCTCAACCTTTCAGCGCTGGTCATGTTCAAG                         GTGCAGCTGCAACAAATAACTGTTCAAGTAGCATGGAGAGTCCATCTGGTA
genomic: TTCCTGGGACAATACTCTTGCTCAACCTTTCAGCGCTGGTCATGTTCAAGgtttgtgtaa ... ggtgatgcagGTGCAGCTGCAACAAATAACTGTTCAAGTAGCATGGAGAGTCCATCTGGTA

EST: gi|148956892|gb|EC902815.2|EC902815

EST:     TTCCTGGGACAATACTCTTGCTCAACCTTTCAGCGCTGGTCATGTTCAAG                         GTGCAGCTGCAACAAATAACTGTTNCA-GTAGCATGGAGAGTCCATCTGGT
genomic: TTCCTGGGACAATACTCTTGCTCAACCTTTCAGCGCTGGTCATGTTCAAGgtttgtgtaa ... ggtgatgcagGTGCAGCTGCAACAAATAACTGTT-CAAGTAGCATGGAGAGTCCATCTGGT

EST: gi|71441161|gb|DR822211.1|DR822211

EST:     TCCTGGGACAATACTCTTGCTCAACCTTTCAGCGCTGGTCATGTTNCA-G                         GTGCAGCTGCAACAAATAACTGGTTCA-GTAGCATGGAGAGTCCATCTGG
genomic: TCCTGGGACAATACTCTTGCTCAACCTTTCAGCGCTGGTCATGTT-CAAGgtttgtgtaa ... ggtgatgcagGTGCAGCTGCAACAAATAACTG-TTCAAGTAGCATGGAGAGTCCATCTGG

EST: gi|71428977|gb|DR810027.1|DR810027

EST:     TCCTGGGACAATACTCTTGGCTCA-CCTTTCAGCGCTGGTCATGTTCAAG                         GTGCAGCTGCAACAAATAACTGTTCAAGTAGCATGGAGAGTCCATCTGGTA
genomic: TCCTGGGACAATACTCTTG-CTCAACCTTTCAGCGCTGGTCATGTTCAAGgtttgtgtaa ... ggtgatgcagGTGCAGCTGCAACAAATAACTGTTCAAGTAGCATGGAGAGTCCATCTGGTA

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), 48 (downstream exon)
Score: 57

CCTATGGATACTGCTACTGTGAGAAACACAAATGCGAATGTGGCGGTGCCTTCCTGGGACAATACTCTTGCTCAACCTTTCAGCGCTGGTCATGTTCAAGgtttgtgtaa ... ggtgatgcagGTGCAGCTGCAACAAATAACTGTTCAAGTAGCATGGAGAGTCCATCTGGTACTTGGCCAACTTCTGAAGCAGTCGAGCAAGAAAATATGGTTCCACCACT

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 62

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 55

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 44

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

caaaaacaaataacctgtggagccaattataacttctcacgtattggtgatgcagGTGCAGCTGCAACAAATAACTGTTCAAGTAGCATGGAGAGTCCATCTGGTACTTGGCCAACTTCTGAAGCAGTCGAGCAAGAAAATATGGTTCCACCACT

                                 ttctcac  putative branch site (score: 44)
                        aattataactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgtaatcattacgacctgcatacaaaaacaaataacctgtggagccaattataacttctcacgtattggtgatgcagGTGCAGCTGCAACAAATAACTGTTCAAGTAGCATGGAGAGTCCATCTGGTACTTGGCCAACTTCTGAAGCAGTCGAGCAAGAAAATATGGTTCCACCACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA