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

...ccaatagtaccaaatcatgtgacagtgcagttgaaatgaaccatgcgaacaaagcaaatgattcaccttgataacttataaatgctttctgtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTCTTGGATGAC

Basic information

species	Zea mays
transcript	GRMZM2G030293_T02
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G030293_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g27174.1 (Oryza sativa), 3'ss of exon 1

--ccaatagtaccaaatcatgtgacagtgcagttgaaatgaaccatgc-gaacaaagcaaatgattcaccttgataacttataaatgctttctgtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTCTTGGATGAC
  | ||  |||  |  | |  ||||  |||  ||||| |      ||| |        | |  ||     |||      | || |||||| |||    ||||||||||| ||||| || || ||||| || ||||| |||||||||||| | |||||||||||||||||||||||||||||||||||||||||| | || |||
cacgaactgtaatat-tgaaatgac--tgcgattgaattacctgctgctggtttgtatagaacatcagttttgcctgactgtatatgcttcctgcttgtgcagCATGGATACCCAGGTCAAACTTGCCGTCGTGGTGAAGGTGATGGGCCGCACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTCCTCGACGAC

upper sequence: GRMZM2G030293_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA13G37600.1 (Glycine max), 3'ss of exon 2

ccaatagtaccaaatcatgtgacagtgcagttgaaatgaa--ccatgcgaacaaagcaaatgattcaccttgataacttataaatgctttctgtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTCTTGGATGAC
    | |  | | |   |      || ||  || ||||||  | |||    | |      | | ||  ||| | |  |||| |||||||| |||    |||| |||||  | || |||||||  ||  |||| || || || |||||  | || || || ||||| |||||||| ||||| ||||||||||| |||||||| 
tatgttgccctacacttttctgttgtccaaatggaatgaaagcaatgttgtccacaatccttactccacttaaca--ttatgaatgctttgtgtttgagcagGATGGAATCTCAGGTGAAGCACGCCCTTGTTGTCAAAGTTATGGGTCGTACTGGGTCTAGGGGGCAGGTGACTCAGGTTAGAGTGAAGTTTTTGGATGAT

upper sequence: GRMZM2G030293_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT3G10090.1 (Arabidopsis thaliana), 3'ss of exon 1

ccaatagtaccaaatcatgtgacagtgcagttgaaatgaaccatgcgaacaaagcaaatgattcaccttgataacttataaatgctttc----tgtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTCTTGGATGAC
   | |||    | |||  ||  |   || ||    |   | | |       |     |   | |  ||  |    | | |||| |||     |||  |  ||| |||||  | ||  | ||||  |||||||| || || |||||||| ||||| || || |||||||| ||||| ||||| ||||||||||||   ||    
tatacagtcttgattcaaatgtgaa--caattctctttttctaaggattttcacttcttttgtaaaatt--tggtctctgaatgtttttgttttgttgaatcagAATGGATTCTCAGATCAAGCACGCTGTTGTAGTGAAAGTGATGGGAAGGACTGGATCAAGGGGTCAAGTGACTCAGGTTAGAGTGAAGTTCACTGACTCG

upper sequence: GRMZM2G030293_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv08s0007g07210.t01 (Vitis vinifera), 3'ss of exon 1

ccaat-agtaccaaatcatgtgacagtgcagttgaaatgaaccatgcgaacaaagcaaatgattcaccttga----taacttataaatgctttctgt--caatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTCTTGGATGAC
  ||| |||      | ||   ||     ||   |||  ||  |   ||| || |    | | |     |||    ||||    || |   ||  |   || |||   |||||  ||   ||||||| |||||| ||||| || || |||||  | || || || |||||||||||||| ||||| ||||||||||| ||||     
--aatgagtttgcttttatagaacttgaaaggaaaaaccaattaaatgaaaaatggtgcttagtatttatgaattataaccagcaattttctttggcagcagTGCGAAATGGATGCCGGGGTGAAGCATGCTGTGGTGGTGAAAGTTATGGGTCGAACTGGATCAAGGGGTCAGGTGACACAGGTGAGAGTGAAGTTTTTGG-----

upper sequence: GRMZM2G030293_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv08s0007g07210.t01 (Vitis vinifera), 3'ss of exon 4

ccaatagtaccaaatcatgtgacagtgcagttgaaatgaaccatgcgaacaaagcaaatgattcaccttgataact--tataaatgctttc---tgt---caatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTCTTGGATGAC
  |    ||     | |   | |  || |  |  || |||  || | | |     || |||| | | |    | ||  |||||||| |||    |||   || ||||  |||||  |    ||||||| |||||| ||||| || || |||||  | || ||||| || ||||||||||||||||| || |||||||| ||||     
-tatacatattctttaaatagtctatgtaactagaaagaaa-atacaatcttt-taattgatgcccttatgcatctattataaatgattttgtttgtttgcagTGCAAAATGGAATCTGGGGTGAAGCATGCTGTGGTGGTGAAAGTTATGGGTCGAACTGGCTCAAGAGGTCAGGTGACCCAGGTGAGGGTGAAGTTTTTGG-----

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|5706278|gb|AI942054.1|AI942054

EST:     CGTCCCCGCTAGAAGCGAGAG                         CATGGACCCCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC
genomic: CGTCCCCGCGAGAAGCGAGAGgtgcaactct ... gtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC

EST: gi|5005768|gb|AI711830.1|AI711830

EST:     CTTCGCGTCACCCAGAGCTCGTCGGCCTCCGTCCCCGCTAGAAGCGAGAG                         CATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC
genomic: CTTCGCGTCACCGAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAGgtgcaactct ... gtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC

EST: gi|211459989|gb|FL103005.1|FL103005

EST:     CTTCGCGTCACCGAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAG                         CATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC
genomic: CTTCGCGTCACCGAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAGgtgcaactct ... gtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC

EST: gi|211502087|gb|FL054230.1|FL054230

EST:     CTTCGCGTCACCCAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAG                         CATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
genomic: CTTCGCGTCACCGAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAGgtgcaactct ... gtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC

EST: gi|32906955|gb|CF011768.1|CF011768

EST:     CTTCGCGTCACCCAGAGCTCGTCGGCCTCCGTTCCCGCGAGAAGCGAGAG                         CATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC
genomic: CTTCGCGTCACCGAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAGgtgcaactct ... gtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC

EST: gi|211459997|gb|FL103013.1|FL103013

EST:     CTTCGCGTCACCCAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAG                         CATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
genomic: CTTCGCGTCACCGAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAGgtgcaactct ... gtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC

EST: gi|32912216|gb|CF017028.1|CF017028

EST:     CTTCGCGTCACCCAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAG                         CATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC
genomic: CTTCGCGTCACCGAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAGgtgcaactct ... gtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC

EST: gi|32913339|gb|CF018151.1|CF018151

EST:     CTTCGCGTCACCCAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAG                         CATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC
genomic: CTTCGCGTCACCGAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAGgtgcaactct ... gtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC

EST: gi|211261664|gb|FK945688.1|FK945688

EST:     CTTCGCGTCACCCAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAG                         CATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
genomic: CTTCGCGTCACCGAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAGgtgcaactct ... gtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC

EST: gi|32918640|gb|CF023452.1|CF023452

EST:     CTTCGCGTCACCCAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAG                         CATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC
genomic: CTTCGCGTCACCGAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAGgtgcaactct ... gtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC

EST: gi|87156240|gb|DY401029.1|DY401029

EST:     CTTCGCGTCACCCAGAGCTCGTCGGCCTCCGTCCCCGCTAGAAGCGAGAG                         CATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC
genomic: CTTCGCGTCACCGAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAGgtgcaactct ... gtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC

EST: gi|33090887|gb|CF050881.1|CF050881

EST:     CTTCGCGTCACCCAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAG                         CATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC
genomic: CTTCGCGTCACCGAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAGgtgcaactct ... gtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC

EST: gi|14245615|gb|BG874197.1|BG874197

EST:     CTTCGCGTCACCGAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAG                         CATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC
genomic: CTTCGCGTCACCGAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAGgtgcaactct ... gtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC

EST: gi|211264098|gb|FK945699.1|FK945699

EST:     CTTCGCGTCACCCAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAG                         CATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
genomic: CTTCGCGTCACCGAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAGgtgcaactct ... gtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC

EST: gi|211261671|gb|FK945695.1|FK945695

EST:     CTTCGCGTCACCGAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGNGAGAG                         CATGGACACCCAAGTGAAGCTTGCTGTTG
genomic: CTTCGCGTCACCGAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAGgtgcaactct ... gtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTG

EST: gi|32911250|gb|CF016062.1|CF016062

EST:     TTCGCGTCACCCAGAGCTCGTCGGCCTCCGTCCCCGCGAGGAAGCGAGAG                         CATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC
genomic: TTCGCGTCACCGAGAGCTCGTCGGCCTCCGTCCCCGCGA-GAAGCGAGAGgtgcaactct ... gtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC

EST: gi|37397695|gb|CF636155.1|CF636155

EST:     CTTCGCGTCACCCAGAGCTCGTCGGCCTCCGTCCCCGCTAGAAGCGAGAG                         CATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC
genomic: CTTCGCGTCACCGAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAGgtgcaactct ... gtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC

EST: gi|211506792|gb|FL054250.1|FL054250

EST:     CTTCGCGTCACCCAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAG                         CATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
genomic: CTTCGCGTCACCGAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAGgtgcaactct ... gtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC

EST: gi|40337161|gb|CK371231.1|CK371231

EST:     CTTCGCGTCACCCAGAGCTCGTCGGCCTCCGTCCCCGCTAGAAGCGAGAG                         CATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC
genomic: CTTCGCGTCACCGAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAGgtgcaactct ... gtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC

EST: gi|32943430|gb|CF048249.1|CF048249

EST:     TTCGCGTCACCCAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCTGTTTG                         CATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGA
genomic: TTCGCGTCACCGAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGC-GAGAGgtgcaactct ... gtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGA

EST: gi|4624373|gb|AI615206.1|AI615206

EST:     CTTCGCGTCACCGAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAG                         CATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC
genomic: CTTCGCGTCACCGAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAGgtgcaactct ... gtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC

EST: gi|21987692|gb|BQ779220.1|BQ779220

EST:     CTTCGCGTCACCCAGAGCTCGTCGGCCTCCGTCCCCGCTAGAAGCGAGAG                         CATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC
genomic: CTTCGCGTCACCGAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAGgtgcaactct ... gtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGAC

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: 520

GTTTCCTTCCTGCTCAGTGTTCTCGACTCGACCGCCGCCGTCCCAGTTCGCTTCGCGTCACCGAGAGCTCGTCGGCCTCCGTCCCCGCGAGAAGCGAGAGgtgcaactct ... gtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTCTTGGATGAC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 304

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 215

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 204

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cgaacaaagcaaatgattcaccttgataacttataaatgctttctgtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTCTTGGATGAC

                       tgataac  putative branch site (score: 204)
                                       ctttctgtc  putative PPT
                      ttgataacttataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccaatagtaccaaatcatgtgacagtgcagttgaaatgaaccatgcgaacaaagcaaatgattcaccttgataacttataaatgctttctgtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTCTTGGATGAC

- - - - - - - -catgtga
- - - - - - - - - - - - - gcagttg
- - - - - - - - - - - - - - - - - - - -accatgc
- - - - - - - - - - - - - - - - - - - - - - - gaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -gcaaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctttc