ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

...ccagtagcaacaaaccatgtgacagtgcagttaaaatgaactatgtgatcaaagcatatggttcaccttgattactgacaaatgctttctattaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTTTTGGATGAC

Basic information

species	Zea mays
transcript	GRMZM2G455828_T01
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G455828_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA13G37600.1 (Glycine max), 3'ss of exon 2

ccagtagcaacaaaccatgtgacagtgcagttaaaatgaa--ctatgtgatcaaagcatatggttcaccttgattactgacaaatgctttctattaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTTTTGGATGAC
   || ||   | ||  |      || ||  |  ||||||  | ||||  || |      |   ||  ||| |    | |  |||||||| | ||   |||| |||||  | ||||||||||  ||  |||| || || || |||||  | || || || ||||| |||||||| ||||| |||||||||||||||||||| 
tatgttgccctacacttttctgttgtccaaatggaatgaaagcaatgttgtccacaatccttactccacttaaca--ttatgaatgctttgtgtttgagcagGATGGAATCTCAGGTGAAGCACGCCCTTGTTGTCAAAGTTATGGGTCGTACTGGGTCTAGGGGGCAGGTGACTCAGGTTAGAGTGAAGTTTTTGGATGAT

upper sequence: GRMZM2G455828_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA03G36420.1 (Glycine max), 3'ss of exon 1

ccagtagcaacaaaccatgtgacagtg-cagttaaaatgaactatgtgatcaaagcatatggttcaccttgattactgacaaatgct--ttctattaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTTTTGGATGAC
  | |    |   | | |||||   || | | | || ||    |||   | || |||  || ||  |  |     || | || || |  || | ||    ||| |||||  | |||||||||| |||| |||| || || || |||||  | || || ||||| || |||||||| ||||| |||||||||||||||||||| 
ttattcctgatttatc-tgtgatgctgactgattaactgtg--atgcattaaacgcaattgttttccactttcatctcataactgttgattgtgtttgatcagGATGGAGTCTCAGGTGAAGCATGCTCTTGTTGTCAAAGTTATGGGTCGTACTGGATCCAGAGGACAGGTGACTCAGGTTAGAGTGAAGTTTTTGGATGAT

upper sequence: GRMZM2G455828_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA19G39070.1 (Glycine max), 3'ss of exon 1

ccagtagcaacaaaccatgtgacagtg--cagttaaa-atgaactatgtgatcaaagcatatggttcaccttgattac-tgacaaatgct--ttctattaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTTTTGGATGAC
    ||   |   ||| ||| || |||  || |||    |||   ||   | | ||   | |  | ||| || ||  | | | || || |  || | ||   |||| |||||  | ||||||||||  ||  |||| || || || |||||  | || || ||||| || || ||||||||||| ||||||||||||||||||   
gtgatacatatttacc-tgtcacggtgaccaattagctgtgatgcattaaacccaattgttt--tccacattcatctcataaaaactgttgattgtgtttgagCAGGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTACTGGATCCAGAGGACAAGTGACCCAGGTTAGAGTGAAGTTTTTGGAT---

upper sequence: GRMZM2G455828_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA03G36580.1 (Glycine max), 3'ss of exon 1

-ccagtagcaacaaaccatgtgacagtgcagttaaaatgaactatgtgatcaaagcatatggttcaccttgattac-tgacaaatgctttctattaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTTTTGGATGAC
  || | | || |    || |     |  |  |   ||  | |   | | || |   | |  | ||| || ||  | | ||   |   || | ||   |||| |||||  | ||||||||||  ||  |||| || || || |||||  | || || ||||| || |||||||||||||| |||||||||||| ||||||| 
tgcatttggaagatgttat-tcctgatttatctgtcattgattcattaaacaca-tttgttttccactttcatctcataacggtttgattgtgtttgagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTACTGGATCCAGAGGACAGGTGACCCAGGTTAGAGTGAAGTTTCTGGATGAT

upper sequence: GRMZM2G455828_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT5G03850.1 (Arabidopsis thaliana), 3'ss of exon 1

ccagtagcaacaaaccatgtgacagtgcagttaaaatgaactatgtgatcaaagcat--atggttcaccttgattactgacaaatgctttctattaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTTTTGGATGAC
 | |||  |    |     | |||    | |    |   | | |||   ||    ||  ||| || |   ||| |  | |    |    |  ||| |  ||| |||||  | ||| | ||||  ||||| ||||| ||||| ||||| ||||| || || ||||||||||| || |||||  |||||||||||   ||    
-ctgtaa-agttgattgctttacatgaaactgtgtactgattgtgtatgcatttgattgatgttttaatgtgaattttcatggttttggttgattgaatcagAATGGATTCTCAGATCAAGCACGCTGTGGTGGTTAAGGTCATGGGTAGGACTGGTTCAAGGGGTCAGGTTACTCAGGTTCGAGTGAAGTTTACCGACTCT

upper sequence: GRMZM2G455828_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT3G10090.1 (Arabidopsis thaliana), 3'ss of exon 1

ccagtagcaacaaaccatgtgacagtgcagttaaaatgaactatgtgatcaaagca-tatggttcaccttgattactgacaaatgct-ttctattaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTTTTGGATGAC
     ||     |  ||  ||  |   || ||    |   ||| |   |   |    | | ||  |  ||| |  ||||    |  | || | || |  ||| |||||  | ||| | ||||  |||||||| ||||| |||||||| ||||| || || |||||||| ||||| ||||| |||||||||||    ||    
tatacagtcttgattcaaatgtgaa--caattctctttttctaaggattttcacttcttttgtaaaatttggtctctgaatgtttttgttttgttgaatcagAATGGATTCTCAGATCAAGCACGCTGTTGTAGTGAAAGTGATGGGAAGGACTGGATCAAGGGGTCAAGTGACTCAGGTTAGAGTGAAGTTCACTGACTCG

upper sequence: GRMZM2G455828_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv08s0007g07210.t01 (Vitis vinifera), 3'ss of exon 1

ccagtagcaacaaaccatgtgacagtgcagttaaaatgaactatgtgatcaa-agcatatggttcaccttgattactgacaaatgctttctat-----taatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTTTTGGATGAC
  |  ||         ||   ||     ||  ||||  || ||  |||  ||  |    | ||     |  ||||    ||     ||||| |      | |||   |||||  ||  |||||||| |||||| |||||||| || |||||  | || || || |||||||||||||| ||||| ||||||||||||||||     
-aatgagtttgcttttatagaacttgaaaggaaaaaccaattaaatgaaaaatggtgcttagtatttatgaattataaccagcaattttctttggcagcagTGCGAAATGGATGCCGGGGTGAAGCATGCTGTGGTGGTGAAAGTTATGGGTCGAACTGGATCAAGGGGTCAGGTGACACAGGTGAGAGTGAAGTTTTTGG-----

upper sequence: GRMZM2G455828_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv08s0007g07210.t01 (Vitis vinifera), 3'ss of exon 4

-------ccagtagcaacaaaccatgtgacagtgcagttaaaatgaactatgtgatcaaagcatatggttcaccttgattactgacaaatgctttctattaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTTTTGGATGAC
           |   || |  | |||| ||     ||  || |  | || | | ||  | ||   |      |  | || | |||    || ||  |   | ||||  |||||  |   |||||||| |||||| |||||||| || |||||  | || ||||| || ||||||||||||||||| || |||||||||||||     
tatacatattctttaaatagtctatgtaactagaaagaaaatacaatct-tttaattgatgcccttatgcatctattataaatgattt-tgtttgtttgcagTGCAAAATGGAATCTGGGGTGAAGCATGCTGTGGTGGTGAAAGTTATGGGTCGAACTGGCTCAAGAGGTCAGGTGACCCAGGTGAGGGTGAAGTTTTTGG-----

upper sequence: GRMZM2G455828_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S279_27V6.1 (Physcomitrella patens), 3'ss of exon 1

ccagtagcaacaaaccatgtgacagtgcagttaaaatgaactatgtgatcaaagcatatggttcaccttgattac-tgacaaatgc-tttctattaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTTTTGGATGAC----
      |    | ||  | |        | ||  |  | ||       |   || |       |  |  || ||  |    |||   ||| | | |||       |||  ||   |||||||||||| ||||  |||||||||| ||| | ||||| ||| | |||||||||||||| ||  | ||||||||| |||||||     
------gttctatactgtttctatacctatttggatcgtacatctctttgggagaagtatccccgacaagagtatgtattgaatatatttgtgtaaatctgtgcagGATTCCGCCGTGAAGCTTGCTATTGTCATGAAGGTGATTGGCCGCACCGGGTCCCGAGGTCAGGTGACCCAAGTGCGTGTGAAGTTTCTGGATGATCAAA

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|211418582|gb|FL177387.1|FL177387

EST:     CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAG                         CATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGA
genomic: CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactct ... attaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGA

EST: gi|61117799|gb|DN558760.1|DN558760

EST:     CCTAGCGTGACTGAGAGCTCGTCGGCTTCAGTCCACGCGTGAAGCGAGAG                         CATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
genomic: CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactct ... attaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC

EST: gi|211020066|gb|FL177492.1|FL177492

EST:     CCTTGCGTGACTGANAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAG                         CATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
genomic: CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactct ... attaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC

EST: gi|31910962|gb|CD651686.1|CD651686

EST:     CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAG                         CATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
genomic: CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactct ... attaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC

EST: gi|211405825|gb|FL177316.1|FL177316

EST:     CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAASS-AGAG                         CATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
genomic: CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactct ... attaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC

EST: gi|5005545|gb|AI711607.1|AI711607

EST:     CCTTGCGTGACTGAAAGCTCGTCGGCTTCCGTCCACGCGAGAAGCGAGAG                         CATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
genomic: CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactct ... attaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC

EST: gi|31612100|gb|CD568722.1|CD568722

EST:     CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAG                         CATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
genomic: CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactct ... attaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC

EST: gi|211416039|gb|FL177376.1|FL177376

EST:     CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAA--SAGAG                         CATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
genomic: CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactct ... attaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC

EST: gi|211020060|gb|FL177486.1|FL177486

EST:     CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAG                         CATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
genomic: CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactct ... attaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC

EST: gi|31998113|gb|CD661929.1|CD661929

EST:     CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAG                         CATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
genomic: CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactct ... attaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC

EST: gi|211413482|gb|FL177356.1|FL177356

EST:     CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAG                         CATGGACACCCAGGTGAAGCTTGCTGTT
genomic: CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactct ... attaatgcagCATGGACACCCAGGTGAAGCTTGCTGTT

EST: gi|211416038|gb|FL177375.1|FL177375

EST:     CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAASS-AGAG                         CATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC
genomic: CCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactct ... attaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGAC

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 2 RNA-Seq libraries.

Block sizes: 31 (upstream exon), 49 (downstream exon)
Score: 76

TTCCTTCCTCATCCAGTGTTCTGTCCTAGCGCCGCCGCCGCCCCAGCTCGCCTTGCGTGACTGAGAGCTCGTCGGCTTCCGTCCACGCGTGAAGCGAGAGgtgcgactct ... attaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTTTTGGATGAC

Block sizes: 18 (upstream exon), 49 (downstream exon)
Score: 47

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgatcaaagcatatggttcaccttgattactgacaaatgctttctattaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTTTTGGATGAC