ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CCTTGGTGGTAGAGCTGCTGAGGAGGTGATATTTGGAGAGCCTGAGGTGACCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatacttccctttgcattgcaattttgtcaacgggaatgttaatgtttgcaaagaattttgctggtcatcacaaaccattttgcactttatgactaaga...

Basic information

species	Zea mays
transcript	GRMZM2G110408_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G110408_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os06g45820.1 (Oryza sativa), 5'ss of exon 4

CCTTGGTGGTAGAGCTGCTGAGGAGGTGATATTTGGAGAGCCTGAGGTGACCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatact-tccctttgcattgcaattttgtcaacgggaatgttaatgtttgcaaagaattttgctggtcatcacaaaccattttgcac--tttatgactaaga
|||||| ||| | |||||||||||| | || ||||| ||||||||||||||||| ||||||||||||||||||||||||||||||||| ||||||||||||||  || |   | |    |  || ||||  ||  |   |    |   ||  ||  | |       || |||        || |||||  |||||||||    
CCTTGGCGGTCGTGCTGCTGAGGAGATCATTTTTGGGGAGCCTGAGGTGACCACAGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCCTAGCCAAGCAGgtacgctatatttctattctagaactttgctaattgatctacagaaactttgaagcagtagactatgtaatctgttctgcttctgcaccttttatgactt---

upper sequence: GRMZM2G110408_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA15G17070.1 (Glycine max), 5'ss of exon 4

CCTTGGTGGTAGAGCTGCTGAGGAGGTGATATTTGGAGAGCCTGAGGTGACCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatacttcc----ctttgcattgcaattttgtcaacgggaatgttaatgtttgcaaagaattttgctggtc-atcacaaaccattttgcactttatgactaaga
 ||||| || ||||| || ||||| || || ||||| ||||||||||| || |||||||| |||||||| ||||||||||| ||  | || |||||||||||     | |    ||||   ||    |||  |  |    | |  |  ||||  |      | |||||  ||         |  |  || |   ||  | | |  
ACTTGGGGGCAGAGCAGCAGAGGAAGTTATTTTTGGTGAGCCTGAGGTTACAACTGGAGCAGCTGGTGATTTGCAGCAAATAACCAGTTTGGCCAAGCAGgttggtgttcatgactttattttctgttttaatgtatcacatttctcttgttctct----ttcttgctattctgcttttggcggtgatgaatgctagcagtgat-

upper sequence: GRMZM2G110408_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA05G26230.1 (Glycine max), 5'ss of exon 4

CCTTGGTGGTAGAGCTGCTGAGGAGGTGATATTTGGAGAGCCTGAGGTGACCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtat-acttccctttgcattgcaattttgtcaacgggaatgttaatgtttgcaaagaattttgctggtcatcacaaaccattttgcactttatgactaaga
 || ||||| || ||||| || ||  | || ||||| |||||||| || || |||||||| |||||||| ||||||||||| || || || || || |||||||   ||   | ||   |    | ||   ||        ||  | |||        |||   ||||    |    | | | |  |   ||  | |    
ACTAGGTGGAAGGGCTGCAGAAGAAATTATTTTTGGTGAGCCTGAAGTTACAACTGGAGCAGCTGGTGATTTGCAGCAAATCACCGGTTTGGCAAAACAGgtattggttaattatgtgcttttgtgttacaaaatatctcctttttctttattttatttttgtgtggtggaaaatgcctaatatttatggtaatattgtt-

upper sequence: GRMZM2G110408_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv12s0028g01600.t01 (Vitis vinifera), 5'ss of exon 4

CCTTGGTGGTAGAGCTGCTGAGGAGGTGATATTTGGAGAGCCTGAGGTGACCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgta--------tacttccctttgcattgcaattttgtcaacgggaatgttaatgtttgcaaagaattttgctggtcatcacaaaccattttgcactttatgactaaga
 || ||||| ||||||||||| || ||||| ||||| |||||||||||||| || || ||||||||||| |||||||| || ||||| || ||||| ||||||        | | ||| | ||| |     |  |  ||     | ||  |||||        | |||   |  ||| || | || |     |||  ||  ||     
ACTCGGTGGCAGAGCTGCTGAAGAAGTGATCTTTGGTGAGCCTGAGGTGACAACAGGTGCTGCTGGTGATTTGCAGCAGATCACTGGTTTGGCCAAACAGgtaataaacagttcctccatctgcttccagctggtaacatttaaactgcaaatgtc-attgtcagtttctattctcaacatatacaaa---acacagtaccacc----

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|89248872|gb|DY620658.1|DY620658

EST:     CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTGGTAACGTTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatacttcc ... ggtcctgcagATGGTGGTAACGTTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG

EST: gi|37396149|gb|CF635362.1|CF635362

EST:     CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTGGTAACGTTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatacttcc ... ggtcctgcagATGGTGGTAACGTTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG

EST: gi|32924520|gb|CF029332.1|CF029332

EST:     CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTGGTAACGTTCGGTATGTC
genomic: CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatacttcc ... ggtcctgcagATGGTGGTAACGTTCGGTATGTC

EST: gi|94472629|gb|EB701587.1|EB701587

EST:     CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTGGTAACGTTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatacttcc ... ggtcctgcagATGGTGGTAACGTTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG

EST: gi|148945969|gb|EC891262.2|EC891262

EST:     CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTGGTAACGTTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatacttcc ... ggtcctgcagATGGTGGTAACGTTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG

EST: gi|148955091|gb|EC900605.2|EC900605

EST:     CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTGGTAACGTTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatacttcc ... ggtcctgcagATGGTGGTAACGTTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG

EST: gi|22542226|gb|BU092664.1|BU092664

EST:     CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTGGTAACGTTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatacttcc ... ggtcctgcagATGGTGGTAACGTTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG

EST: gi|32850859|gb|CD990540.1|CD990540

EST:     CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTGGTAACGTTCGGTATGTCTGAAATTGGTCCATGGTCTCTGA
genomic: CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatacttcc ... ggtcctgcagATGGTGGTAACGTTCGGTATGTCTGAAATTGGTCCATGGTCTCTGA

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), 47 (downstream exon)
Score: 50

CCTTGGTGGTAGAGCTGCTGAGGAGGTGATATTTGGAGAGCCTGAGGTGACCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatacttcc ... ggtcctgcagATGGTGGTAACGTTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAGGGTGGGGCACAGAGTGGGGACGTCATCATGCGAATGATGGCAAGGAACT

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 248

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 43

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 140

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTTGGTGGTAGAGCTGCTGAGGAGGTGATATTTGGAGAGCCTGAGGTGACCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatacttccctttgcattgcaattttgtcaacgggaatgttaatgtttgcaaagaattttgctggtcatcacaaaccattttgcactttatgactaaga

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT