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

...ataattaatcattttgtggcaagagcaggttgttatcattctctgttttttccctctttcgaatggttctaaattctaacctgtctcgtttttcgtccagACACATTATGTGTTGCTCCTCTGTTCATTCAAGGAACAACTCCAGCAGCATGTGCGTGTTCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGCTCGAAC

Basic information

species	Zea mays
transcript	GRMZM2G055243_T01
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G055243_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g43860.2 (Oryza sativa), 3'ss of exon 1

ataattaatcattttgt--ggcaagagcaggttgtta-tcattctctgttttttccctctttcgaatggttcta---aattctaacctgtctcgtttttcgtccagACACATTATGTGTTGCTCCTCTGTTCATTCAAGGAACAACTCCAGCAGCATGTGCGTGTTCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGCTCGAAC
      | |||||||||    || |  |   |  ||  |            | | |||    | | |  || ||   |||   ||  ||| |  |||||| | ||||| |||||||| |||||||| ||||| |||||||||||||| ||||| ||||||||||||||||||||||||||||| |||||||| ||||| || ||||
-----aagtcattttgtttatcaggtactcttctttgcttggaaatgacaatcttcctaaggcaattttttttacttaataaaaaaatgtttt-tttttcttgcagACCCATTATGTATTGCTCCTTTGTTCGTTCAAGGAACAACTACAGCAACATGTGCGTGTTCATGCAATGGAAGCAGTAATGGCTTGCTGGGAACTTGAAC

upper sequence: GRMZM2G055243_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA04G06810.1 (Glycine max), 3'ss of exon 2

--------ataattaatcattttgtggcaagagcaggttgttatcattctctgttttttccctctttcgaatggttctaaattctaacctgtctcgtttttcgtccagACACATTATGTGTTGCTCCTCTGTTCATTCAAGGAACAACTCCAGCAGCATGTGCGTGTTCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGCTCGAAC
        ||  |   | ||||| |   | | |  ||   |||||||   || || |     |    |  |   || | |      |  |   |  ||  |  | ||| | || |||||  || | |||||||| ||||| |||||||| || |||||||| || || ||||||||||||||||||||||||||||||||| | || |
gttttttcatggtgtgtgatttttt---atgtgatggagcttatcatctgctattatacatttacaactgacaattttgat-----attttcttaattgatgctgcagTCCCACTATGTTCTGTTGCTCTGTTCTTTCAAAGAACAACTTCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGATTGAGC

upper sequence: GRMZM2G055243_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA14G13750.2 (Glycine max), 3'ss of exon 1

ataattaatcattttgtggcaagagcaggttgttatcattctctgttttttccctctttcga-atggttcta----aattctaacctgtctcgtttttcg----tccagACACATTATGTGTTGCTCCTCTGTTCATTCAAGGAACAACTCCAGCAGCATGTGCGTGTTCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGCTCGAAC
         | | |||     | |   | || || |   ||| | |        |  || ||  |||| |        || |||  | | |  |  || |    | ||| | || ||||| ||| | |||||||| ||||| |||||| | ||||||||||| || || ||||||||||||||||| ||||||||||||||  | || |
---------cttcttgattataaaatggatttttttttctctatatggagaggtttgttggatgtggtacagttacggttttaatgttttttatggttggatgttgcagTCGCACTATGTTTTGTTGCTCTGTTCCTTCAAAGAACAATTGCAGCAGCATGTCCGGGTCCATGCAATGGAAGCAGTAATGGCTTGTTGGGATATAGAGC

upper sequence: GRMZM2G055243_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA17G32980.2 (Glycine max), 3'ss of exon 1

-----ataattaatcatttt--gtggcaagagcaggttgttatcattctctgttttttccctctttcgaatggttctaaattctaacctgtctcgtttttcgtccagACACATTATGTGTTGCTCCTCTGTTCATTCAAGGAACAACTCCAGCAGCATGTGCGTGTTCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGCTCGAAC
     | |||  ||  ||||  ||         | || |  |   || |  | | |    |  ||    |||||| | |  | |    ||  | | | ||    ||| | || ||||| ||| | |||||||| ||||| |||||| | || |||||||| || || ||||||||||||||||| ||||||||||||||| | || |
attgtaaaatggattttttttcgtattttttttatgtggagaagtttgttggatgtagtacattt----atggttttgatgtttcttatggttggatgtt---gcagTCGCACTATGTTTTGTTGCTCTGTTCCTTCAAAGAACAATTGCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTAATGGCTTGTTGGGAGTTAGAGC

upper sequence: GRMZM2G055243_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA06G06890.1 (Glycine max), 3'ss of exon 1

---ataattaatcattttgtggcaagagcaggttgttatcattctctgttttttccctctttcgaatggttctaaattctaacctgtctcgtttttcgtc-cagACACATTATGTGTTGCTCCTCTGTTCATTCAAGGAACAACTCCAGCAGCATGTGCGTGTTCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGCTCGAAC
    || || ||  | | |||      | | ||  |     || |||| | |    |  || | | |  | | |  || ||   | |||  ||| | |   ||| | || |||||  || | |||||||| ||||| |||||||| || |||||||| || || ||||||||||||||||||||||||||||||||| |||| |
cccctagttcatggtgt-gtgatttctg-atgtgatagagcttatctgctatgatacatttacaact--tacaattttttatattttcttatttgttgctgcagTCCCACTATGTTCTGTTGCTCTGTTCTTTCAAAGAACAACTTCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGATCGAGC

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|211317875|gb|FL083593.1|FL083593

EST:     CTGCGGCGGGCGGAGCACACTCGGGAGGCGAGGAACTCGACCTCTTCATG                         ACACATTATGTGTTGCTCCTCTGTGCATTCAAGGAACAACTCCAGCAGCAT
genomic: CTGCGGCGGGCGGAGCACACTCGGGAGGCGAGGAGCTCGACCTCTTCATGgtaagtaccc ... tttcgtccagACACATTATGTGTTGCTCCTCTGTTCATTCAAGGAACAACTCCAGCAGCAT

EST: gi|211317872|gb|FL083590.1|FL083590

EST:     CTGCGGCGGGCGGAGCACACTCGGGAGGCGAGGAACTCGACCTCTTCATG                         ACACATTATGTGTTGCTCCTCTGTTCATTCAAGGAACAACTCCAGCAGCAT
genomic: CTGCGGCGGGCGGAGCACACTCGGGAGGCGAGGAGCTCGACCTCTTCATGgtaagtaccc ... tttcgtccagACACATTATGTGTTGCTCCTCTGTTCATTCAAGGAACAACTCCAGCAGCAT

EST: gi|149109130|gb|EE293152.2|EE293152

EST:     CTGCGGCGGGCGGAGCACACTCGGGAGGCGAGGAGCTCGACCTCTTCATG                         ACACATTATGTGTTGCTCCTCTGTTCATTCAAGGAACAACTCCAGCAGCAT
genomic: CTGCGGCGGGCGGAGCACACTCGGGAGGCGAGGAGCTCGACCTCTTCATGgtaagtaccc ... tttcgtccagACACATTATGTGTTGCTCCTCTGTTCATTCAAGGAACAACTCCAGCAGCAT

EST: gi|211317871|gb|FL083589.1|FL083589

EST:     CTGCGGCGGGCGGAGCACACTCGGGAGGCGAGGAACTCGACCTCTTCATG                         ACACATTATGTGTTGCTCCTCTGTTCATTCAAGGAACAACTCCAGCAGCAT
genomic: CTGCGGCGGGCGGAGCACACTCGGGAGGCGAGGAGCTCGACCTCTTCATGgtaagtaccc ... tttcgtccagACACATTATGTGTTGCTCCTCTGTTCATTCAAGGAACAACTCCAGCAGCAT

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: 46 (upstream exon), 47 (downstream exon)
Score: 14

CGCGCAGATAGCGGCGAGGCCCCCGCCCATGGAGGCCGCGGCTGCGGCTGCTGCGGCGGGCGGAGCACACTCGGGAGGCGAGGAGCTCGACCTCTTCATGgtaagtaccc ... tttcgtccagACACATTATGTGTTGCTCCTCTGTTCATTCAAGGAACAACTCCAGCAGCATGTGCGTGTTCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGCTCGAAC

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 168

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 85

Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 37

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttttttccctctttcgaatggttctaaattctaacctgtctcgtttttcgtccagACACATTATGTGTTGCTCCTCTGTTCATTCAAGGAACAACTCCAGCAGCATGTGCGTGTTCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGCTCGAAC

                            ttctaac  putative branch site (score: 37)
                                  cctgtctcgtttttc  CT-rich tract
                        taaattctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataattaatcattttgtggcaagagcaggttgttatcattctctgttttttccctctttcgaatggttctaaattctaacctgtctcgtttttcgtccagACACATTATGTGTTGCTCCTCTGTTCATTCAAGGAACAACTCCAGCAGCATGTGCGTGTTCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGCTCGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggttct