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

...gtatcttatcatttcaatacggcatttatttgacggttccatgaaaattggactgctgtaactgataaggagcaatctgatttcttactctgcatattagGTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACGCTTTGATGTGTTCGAAGAAGCAGAAGCTAACAAAGCTGCTGGAAAGTAT

Basic information

species	Zea mays
transcript	GRMZM2G421791_T01
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G421791_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g45490.1 (Oryza sativa), 3'ss of exon 6

gtatcttatcatttcaatacggcatttatttgacggttccatgaaaattggactgctgtaactga-taaggagc--aatctgatt---tcttactctgcatattagGTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACGCTTTGATGTGTTCGAAGAAGCAGAAGCTAACAAAGCTGCTGGAAAGTAT
      ||  ||||  |     |     ||| |   ||  | ||       | |||  ||  ||| ||  | |   | ||||| |   || ||   ||  |||||||||  |||||||||||||| | |||||||| ||||||||||| ||||||||||||||||| || ||||||||||||||||| ||||||||||| ||||||
------tagaatttggaacttaccagcttttcattattttaagatcgcaatattgcaatatttgactactgtgttgagtctgactgtgtcatatcatggctattagGTTTTTGTGGAGGAAGAATGCTACTTTTGCTATCTCTCGGCACTACAAACGCTTTGATGTATTTGAAGAAGCAGAAGCTAATAAAGCTGCTGGCAAGTAT

upper sequence: GRMZM2G421791_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA15G08090.1 (Glycine max), 3'ss of exon 6

gtatcttatcatttcaatacggcatttatttgacggttccatgaaaattggactgctgtaactgataagg-agcaatctgatttcttactctgcatattagGTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACGCTTTGATGTGTTCGAAGAAGCAGAAGCTAACAAAGCTGCTGGAAAGTAT
  |  | |||||  | || | |  ||| |   | | ||   |   | ||    || |  ||   ||      |||   | ||| ||  |        |||||||  |||||||||||||| | ||||||||||| |||   ||||| | |||||||||||| || |  || || ||||| || ||||||||||||||||||
acacataatcatacctatgccgactttgtactaggtttatgttggattttc-ttgatagaatacatgtttcggcacattaattgctctcatccttatttagGTTTTTGTGGAGGAAGAATGCAACTTTTGCAATATCTAAACATTATAGACGCTTTGATGTATTTGTTGAGGCCGAAGCAAATAAAGCTGCTGGAAAGTAT

upper sequence: GRMZM2G421791_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA13G31260.1 (Glycine max), 3'ss of exon 6

gtatcttatcatttcaatacggcatttatttgacggttccatgaaaattggactgctgtaactgataaggagcaatctgatttcttactctgcatatt-agGTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACGCTTTGATGTGTTCGAAGAAGCAGAAGCTAACAAAGCTGCTGGAAAGTAT
  |  | |||||  | || | |  ||| |   | | ||   ||| | ||    || |  ||   ||  |  |  |  | | || ||    | | |||| |||||  |||||||||||||| | ||||||||||| |||   ||||| | |||||||||||| || |  || || ||||| || ||||||||||||||||||
acacataatcatacctatgctgactttgtactaggtttatgtgagattttc-ttgatagaatacatgtgttggcacattaattgttctcatccttatttagGTTTTTGTGGAGGAAGAATGCAACTTTTGCAATATCTAAACATTATAGACGCTTTGATGTATTTGTTGAGGCCGAAGCAAATAAAGCTGCTGGAAAGTAT

upper sequence: GRMZM2G421791_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 6

gtatcttatcatttcaat--acggcatttatttgacggttccatgaaaattggactgctgtaactgataaggagcaatctgatttcttactctgcatattagGTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACGCTTTGATGTGTTCGAAGAAGCAGAAGCTAACAAAGCTGCTGGAAAGTAT
   |  | |||  | | |  ||||  || | || |     || | |   | |   |  |||  |||    | |||||| | | |     |||| |  || || ||| |||||||||| ||| | |||||||| || ||| | ||||||||||| |||||||| || |  ||||| ||||| || ||||||||||| || |||
-agttgtttcagataagttaacggt-ttgagtttagaaggccttaagcttggtggttatgtttctggactgcagcaatttaactgacatctcttctcatcagATTCTTGTGGAGGAAAAATGCTACTTTTGCTATTTCTAGACATTACAAACGATTTGATGTCTTAGTGGAAGCCGAAGCAAATAAAGCTGCTGGTAAATAT

upper sequence: GRMZM2G421791_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv19s0014g02710.t01 (Vitis vinifera), 3'ss of exon 6

gtatcttatcatttcaatacggcatttatttgacggttccatgaaaattggactgctg--taactgataaggagcaatctgatttcttactctgcatattagGTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACGCTTTGATGTGTTCGAAGAAGCAGAAGCTAACAAAGCTGCTGGAAAGTAT
  |    || |||   ||      || | |  |    |  |||     || | || |   ||  |  || ||    ||    |   ||| |||     | |||||| | ||| |  | ||| | | ||| ||||||||  | ||||| |  |||||||||||||| |||||||| |||||||| |||||||| || ||||||
acagtgcattattaggatttaattttgactatatatctgtatgcct-ctgcattgtttcttagtttctacggtatgataccttcattta-tctattattcagGTTCTTATGGCGTCAAAATGCTAGTTTGGCAATCTCAAGACATTATAGGCGCTTTGATGTGTTTGAAGAAGCTGAAGCTAATAAAGCTGCAGGGAAGTAT

upper sequence: GRMZM2G421791_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv00s0265g00120.t01 (Vitis vinifera), 3'ss of exon 6

----gtatcttatcatttcaatacggcatttatttgacggttccatgaaaattggactgctgtaactgataaggagcaatctgatttcttactctgcatattagGTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACGCTTTGATGTGTTCGAAGAAGCAGAAGCTAACAAAGCTGCTGGAAAGTAT
    | || |      || ||||     | |  ||   | ||| |       ||         || ||||     |  | || | | || | |||   | | ||||||||||||||||| ||| ||| ||||||||||||| | ||||| | ||||||||||||||| | |||||| || || || ||||||||||  ||||||
gcttgcatttgtatggttgaataaaagctatgattttagcttctagatgttctgtttcatgacaattgatgtttgggtaccttaatcct-attct---tttcagGTTCCTGTGGAGGAAAAATGCCAGTTTTGCAATCTCTAGACATTATAGACGCTTTGATGTGTTTGTAGAAGCTGAGGCAAATAAAGCTGCTGCGAAGTAT

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|22521602|gb|BU080413.1|BU080413

EST:     ATAGATGCAAAGCTTCAGCTTGTTGCGGACCCCTATCTCCTGCTTGAGAG                         GTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACG
genomic: ATAGATGCAAAGCTTCAGCTTGTTGCGGATCCCTATCTCCTGCTTGAGAGgtattcttga ... tgcatattagGTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACG

EST: gi|71439406|gb|DR820456.1|DR820456

EST:     ATAGATGCAAAGCTTCAGCTTGTTGCGGATCCCTATCTCCTGCTTGAGAG                         GTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACG
genomic: ATAGATGCAAAGCTTCAGCTTGTTGCGGATCCCTATCTCCTGCTTGAGAGgtattcttga ... tgcatattagGTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACG

EST: gi|33096912|gb|CF056872.1|CF056872

EST:     ATAGATGCAAAACTTGAGCTTGTTGTGGATCCCTATCTCCTGCTTGAGAG                         GTTCCTTTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACG
genomic: ATAGATGCAAAGCTTCAGCTTGTTGCGGATCCCTATCTCCTGCTTGAGAGgtattcttga ... tgcatattagGTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACG

EST: gi|33099543|gb|CF059503.1|CF059503

EST:     ATAGATGCAAAGCTTCAGCTTGTTGCGGACCCCTATCTCCTGCTTGAGAG                         GTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACG
genomic: ATAGATGCAAAGCTTCAGCTTGTTGCGGATCCCTATCTCCTGCTTGAGAGgtattcttga ... tgcatattagGTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACG

EST: gi|13149974|gb|BG320296.1|BG320296

EST:     ATAGATGCAAAGCTTCAGCTTGTTGCGGAYCCCTATCTCCTGCTTGAGAG                         GTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACG
genomic: ATAGATGCAAAGCTTCAGCTTGTTGCGGATCCCTATCTCCTGCTTGAGAGgtattcttga ... tgcatattagGTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACG

EST: gi|21760101|gb|BQ635642.1|BQ635642

EST:     ATAGATGCAAAGCTTCAGCTTGTTGCGGACCCCTATCTCCTGCTTGAGAG                         GTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACG
genomic: ATAGATGCAAAGCTTCAGCTTGTTGCGGATCCCTATCTCCTGCTTGAGAGgtattcttga ... tgcatattagGTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACG

EST: gi|26559312|gb|CA831547.1|CA831547

EST:     ATAGATGCAAAGCTTCAGCTTGTTGCGGACCCCTATCTCCTGCTTGAGAG                         GTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACG
genomic: ATAGATGCAAAGCTTCAGCTTGTTGCGGATCCCTATCTCCTGCTTGAGAGgtattcttga ... tgcatattagGTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACG

EST: gi|211234336|gb|FL414451.1|FL414451

EST:     ATAGATGCAAAGCTTCAGCTTGTTGCGGACCCCTATCTCCTGCTTGAGAG                         GTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACG
genomic: ATAGATGCAAAGCTTCAGCTTGTTGCGGATCCCTATCTCCTGCTTGAGAGgtattcttga ... tgcatattagGTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACG

EST: gi|87156073|gb|DY400862.1|DY400862

EST:     ATAGATGCAAAGCTTCAGCTTGTTGCGGACCCCTATCTCCTGCTTGAGAG                         GTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACG
genomic: ATAGATGCAAAGCTTCAGCTTGTTGCGGATCCCTATCTCCTGCTTGAGAGgtattcttga ... tgcatattagGTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACG

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), 48 (downstream exon)
Score: 35

CAAAACTTCTGCTCCATAGGCTTTTTCCAAACGTGAAATTTTCAGTTTGGATAGATGCAAAGCTTCAGCTTGTTGCGGATCCCTATCTCCTGCTTGAGAGgtattcttga ... tgcatattagGTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACGCTTTGATGTGTTCGAAGAAGCAGAAGCTAACAAAGCTGCTGGAAAGTAT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 80

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 109

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 158

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aattggactgctgtaactgataaggagcaatctgatttcttactctgcatattagGTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACGCTTTGATGTGTTCGAAGAAGCAGAAGCTAACAAAGCTGCTGGAAAGTAT

                                    ttcttac  putative branch site (score: 158)
                                   tttcttactct  CT-rich tract
                                  atttctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcttatcatttcaatacggcatttatttgacggttccatgaaaattggactgctgtaactgataaggagcaatctgatttcttactctgcatattagGTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACGCTTTGATGTGTTCGAAGAAGCAGAAGCTAACAAAGCTGCTGGAAAGTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - ccatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - -actgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aggagca