ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATCCTGGACAACCGAATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAGAGCGTGGAGAGAGgtgtgtagcccccccaacttgatttccctgttaattcagcatactatacttcgtgcggtcagattcagatattgtatggtttcttgcag

Basic information

species	Zea mays
transcript	GRMZM2G132804_T01
intron #	11
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G132804_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os01g17180.2 (Oryza sativa), 5'ss of exon 11

CGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATCCTGGACAACCGAATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAGAGCGTGGAGAGAGgtgtgtagcccccccaacttgatttccctgttaattcagc-atactatacttcgtgcggtcagattcagatattgtatggtttcttgcag
| || |||||||| |||||||| ||||| || ||||| ||||| ||||||||||| ||||||||||| ||||| |||||||| ||||| ||||| || ||||| |||  |||||    ||      |   ||  |  | | || | ||   |  |  |       || |||      | |  | | ||||
CAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATTCTGGATAACCGAATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattccccctgctttttccatcacattgttctatctatgcgattgcttttctgaaggtgatccgat------tcgcatttcgcag

upper sequence: GRMZM2G132804_T01 (Zea mays), 5'ss of exon 11
lower sequence: EDP09792 (Chlamydomonas reinhardtii), 5'ss of exon 11

-----------------------------CGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATCCTGGACAACCGAATCCAAGGCCACATAGACCAGGT-CAACA-AGTTGCTAGAGCGTGGAGAGAGgtgtgtagcccccccaacttgatttccctgttaattcagcatactatacttcgtg-cggtcagattcagatattgtatggtttcttgcag
                             | | |   || ||||||||||||||||| || ||||||||||||  |||  |    ||| |||| |||||||| |  |  ||  ||  | | | |||    ||   | ||      |     | ||     |   |    |||   |  |    | | ||||| |   | || |                  
CCCCTTCATCGCCCAGAAGCTCAACATCCCCGCGCCCGACGTGGAGCAGCTGTTGGTCTCACTCATCCTGGACGGCCGCGTGGCGGGCAACATCGACCAGgtgcggcgcagcggcgggggtggggaactggggagggaggggttgcggg--gcttagttgggccacgtggcaggttgcaagctgcggcggtctg--ccggacag-----------------

upper sequence: GRMZM2G132804_T01 (Zea mays), 5'ss of exon 11
lower sequence: EFJ29478 (Selaginella moellendorffii), 5'ss of exon 11

CGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATCCTGGACAACCGAATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAGAGCGTGGAGAGAGgtgtgtagcccccccaacttgatttccctgttaattcag--catactatacttcgtgcgg-tcagattcagatattgtatggtttcttgcag
|||| |  |||||||||||||| ||||| || |||||||||||||||||  | || || |||||||| || ||  |  || | || ||||  || || ||||        | |   ||   |  | |  |||| ||  |  |  |||| ||   |||| | ||||                           
CGGAAAGAGATGTGGAGCAGCTCTTGGTGTCTCTCATCCTGGACAACCGGGTTCACGGTCACATAGATCAAGTTCATCAGCTCCTGGAGCTCGGTGACAGgtaa------ctctggacgatagattctagttagtttcgttcgaactaaacggtgtgctgctcag---------------------------

upper sequence: GRMZM2G132804_T01 (Zea mays), 5'ss of exon 11
lower sequence: EFJ28052 (Selaginella moellendorffii), 5'ss of exon 11

CGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATCCTGGACAACCGAATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAGAGCGTGGAGAGAGgtgtgtagcccccccaacttgatttccctgttaattcagc--atactatacttcgtgcggt-cagattcagatattgtatggtttcttgcag
|||| |  |||||||||||||| || || || |||||||||||||||||  | || || |||||||| || ||  |  || | || ||||  || || ||||        | |   ||   |  | |  |||| ||  |     |||| ||   |||| || |||                           
CGGAAAGAGATGTGGAGCAGCTCTTAGTGTCTCTCATCCTGGACAACCGGGTTCACGGTCACATAGATCAAGTTCATCAGCTCCTGGAGCTCGGTGACAGgtaa------ctctggacgataggttctagttagtttcgttagaactaaacggtgtgctgtgcag---------------------------

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|29945495|gb|CB815668.1|CB815668

EST:     ATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAGAGCGTGGAGAGAG                         GTCCAAGGGGATGAGGAAGTACAATGCCATCGACAAGTGGAATACTCAGCT
genomic: ATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAGAGCGTGGAGAGAGgtgtgtagcc ... tttcttgcagGTCCAAGGGGATGAGGAAGTACAATGCCATCGACAAGTGGAATACTCAGCT

EST: gi|32935315|gb|CF040127.1|CF040127

EST:     ATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAGAGCGTGGAGAAAG                         GTCCAAGGGGATGAGGAAGT
genomic: ATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAGAGCGTGGAGAGAGgtgtgtagcc ... tttcttgcagGTCCAAGGGGATGAGGAAGT

EST: gi|32937219|gb|CF042038.1|CF042038

EST:     ATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAGAGCGTGGAGAAAG                         GTCCAAGGGGATGAGGAAGTACAATGCCATCGACAAGTGGAATACTCAGCT
genomic: ATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAGAGCGTGGAGAGAGgtgtgtagcc ... tttcttgcagGTCCAAGGGGATGAGGAAGTACAATGCCATCGACAAGTGGAATACTCAGCT

EST: gi|29945633|gb|CB815739.1|CB815739

EST:     ATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAGAGCGTGGAGAGAG                         GTCCAAGGGGATGAGGAAGTACAATGCCATCGACAAGTGGAATACTCAGCT
genomic: ATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAGAGCGTGGAGAGAGgtgtgtagcc ... tttcttgcagGTCCAAGGGGATGAGGAAGTACAATGCCATCGACAAGTGGAATACTCAGCT

EST: gi|60401353|gb|DN234160.1|DN234160

EST:     ATCCAAGGCCACATAGATCAGGTCAACAAGTTGCTAGAGCGTGGAGAAAG                         GTCCAAGGGGATGAGGAAGTACAATGCCATCGACAAGTGGAATACTCAGCT
genomic: ATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAGAGCGTGGAGAGAGgtgtgtagcc ... tttcttgcagGTCCAAGGGGATGAGGAAGTACAATGCCATCGACAAGTGGAATACTCAGCT

EST: gi|14202790|gb|BG836467.1|BG836467

EST:     ATCCAAGGCCACATAGATCAGGTCAACAAGTTGCTAGAGCGTGGAGAAAG                         GTCCAAGGGGATGAGGAAGTACAATGCCATCGACAAGTGGAATACTCAGCT
genomic: ATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAGAGCGTGGAGAGAGgtgtgtagcc ... tttcttgcagGTCCAAGGGGATGAGGAAGTACAATGCCATCGACAAGTGGAATACTCAGCT

EST: gi|74244568|gb|DT652482.1|DT652482

EST:     GGCCACATAGACCAGGTCAACAAGTTGCTAGAGCGTGGAGAGAG                         GTCCAAGGGGATGAGGAAGTACAATGCCATCGACAAGTGGAATACTCAGCT
genomic: GGCCACATAGACCAGGTCAACAAGTTGCTAGAGCGTGGAGAGAGgtgtgtagcc ... tttcttgcagGTCCAAGGGGATGAGGAAGTACAATGCCATCGACAAGTGGAATACTCAGCT

EST: gi|32164838|gb|CD670156.1|CD670156

EST:     ATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAGAGCGTGGAGAGAG                         GTCCAAGGGGATGAGGAAGTACAATGCCATCGACAAGTGGAATACTCAGCT
genomic: ATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAGAGCGTGGAGAGAGgtgtgtagcc ... tttcttgcagGTCCAAGGGGATGAGGAAGTACAATGCCATCGACAAGTGGAATACTCAGCT

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: 147

CGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATCCTGGACAACCGAATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAGAGCGTGGAGAGAGgtgtgtagcc ... tttcttgcagGTCCAAGGGGATGAGGAAGTACAATGCCATCGACAAGTGGAATACTCAGCTCAAGTCCATTTACCAAACATTGTCCAACAGAGTTTGATGAGACGAATCG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 142

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 79

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATCCTGGACAACCGAATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAGAGCGTGGAGAGAGgtgtgtagcccccccaacttgatttccctgttaattcagcatactatacttcgtgcggtcagattcagatattgtatggtttcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA