ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

...atatatataatgcctacattaatgcttagtttgtatcctgttgaccccatgcctggattcagtaactcacattagaaactatttgcacctttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGATCTCGAGACAACTTCTTTTTCGCCGGGATTGACAAAGTTAGGTTCAGGA

Basic information

species	Zea mays
transcript	GRMZM2G024482_T02
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G024482_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g12840.1 (Oryza sativa), 3'ss of exon 3

atatatata-atgcctacattaatgcttagtttgtatcctgttgaccccatgcctggattcagt--aactcacattagaaactatttgcacctttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGATCTCGAGACAACTTCTTTTTCGCCGGGATTGACAAAGTTAGGTTCAGGA
| ||    | ||| ||  ||   |  | | |   |||  |  |  |  || |     |  ||    ||||  | | |        |   |||||||| ||||||||||||||||||||||||||||||||||| |||| |||||| |||| |||||||| ||||| ||||| || || || ||||| ||||| |||||| | |
agatgaggacatggctggatgttttttaattgcttattgttctatcatcaagtagacaaacatctgaacttccctcatgtgaggct---acctttatgcacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGTTGCAGCCTGAAATTGGCGGATCTCGGGACAATTTCTTCTTTGCAGGAATTGATAAAGTGAGGTTCCGTA

upper sequence: GRMZM2G024482_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv12s0055g01100.t01 (Vitis vinifera), 3'ss of exon 3

-atatatataatgcctacattaatgcttagtttgtatcctgttgaccccatgcctggattcagtaactcacattagaaactatttgcacct-ttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGATCTCGAGACAACTTCTTTTTCGCCGGGATTGACAAAGTTAGGTTCAGGA
   |    | |  | || ||  |   | ||  | ||| || |  ||    || ||    || | |        || |   | |||     | ||    |||||| ||||| |||||||| ||  |||| ||||| ||||||||||| || || ||||| || || ||||| || || || ||||||||||| || ||| |||
ggaaggccttacacataaatatactgtaaggctttatact-taaacatgctgtctttggtctg-atggagtggtaaattttttttctgtttgttggatacagGCAATGGCACAGGTTGGTGGCTTGGTAATGCTACAACCTGAAGTGGGAGGCTCTCGTGAAAATTTCTTCTTTGCTGGAATTGACAAAGTAAGATTCCGGA

upper sequence: GRMZM2G024482_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv00s0357g00070.t01 (Vitis vinifera), 3'ss of exon 3

-------atatatataatgcctacattaatgcttagtttgtatcctgttgaccccatgcctggattcagtaactcacattagaaactatttgcacctttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGATCTCGAGACAACTTCTTTTTCGCCGGGATTGACAAAGTTAGGTTCAGGA
       ||   | | |   |    ||  |    |||||| ||   | | ||   |    ||  |  ||||| |     |  ||    || |    |       ||||| ||||| |||||||||||  |||| ||||| |||||||||||||| || ||||| || || ||||| || || || || |||||||| ||||||  ||
ttgttaaattctttttacaaccctgtttctatcaagtttggatttggat-acattacatgtgcctctagtaattgctgatgaaagtggttggtgggtc------cagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCAGA

upper sequence: GRMZM2G024482_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv00s0357g00020.t01 (Vitis vinifera), 3'ss of exon 3

-------atatatataatgcctacattaatgcttagtttgtatcctgttgaccccatgcctggattcagtaactcacattagaaactatttgcacctttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGATCTCGAGACAACTTCTTTTTCGCCGGGATTGACAAAGTTAGGTTCAGGA
       ||   | | |   |    ||  |    |||| | ||   | | ||   |    ||  |  ||||| |     |  ||    || |    |       ||||| ||||| |||||||||||  |||| ||||| |||||||||||||| || ||||| || || ||||| || || || || |||||||| |||||| |||
ttgttaaattctttttacaaccctgtttctatcaagttcgcatttggat-acattacatgtgcctctagtaattgctgatgaaagtggttggtgggtc------cagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCGGA

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|18179048|gb|BM380258.1|BM380258

EST:     AGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAG                         GCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA
genomic: AGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAGgtatgcacca ... ttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA

EST: gi|71762142|gb|DR960079.1|DR960079

EST:     CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAG                         GCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA
genomic: CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAGgtatgcacca ... ttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA

EST: gi|211091572|gb|FL457274.1|FL457274

EST:     CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAG                         GCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA
genomic: CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAGgtatgcacca ... ttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA

EST: gi|60345198|gb|DN212171.1|DN212171

EST:     CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAG                         GCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA
genomic: CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAGgtatgcacca ... ttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA

EST: gi|33092892|gb|CF052886.1|CF052886

EST:     CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAG                         GCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA
genomic: CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAGgtatgcacca ... ttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA

EST: gi|166536311|gb|EG218725.1|EG218725

EST:     CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAG                         GCTATGGCCCAGGTTGGGGGTCTGGTGA
genomic: CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAGgtatgcacca ... ttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGA

EST: gi|50338308|gb|CO533434.1|CO533434

EST:     CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAG                         GCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA
genomic: CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAGgtatgcacca ... ttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA

EST: gi|40334305|gb|CK368375.1|CK368375

EST:     CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAG                         GCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA
genomic: CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAGgtatgcacca ... ttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA

EST: gi|37396344|gb|CF635461.1|CF635461

EST:     CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAG                         GCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA
genomic: CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAGgtatgcacca ... ttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA

EST: gi|37377757|gb|CF625513.1|CF625513

EST:     CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAG                         GCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA
genomic: CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAGgtatgcacca ... ttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA

EST: gi|211091571|gb|FL457273.1|FL457273

EST:     CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAG                         GCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA
genomic: CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAGgtatgcacca ... ttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA

EST: gi|211283730|gb|FL464726.1|FL464726

EST:     CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAG                         GCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA
genomic: CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAGgtatgcacca ... ttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA

EST: gi|113669978|gb|DW819268.1|DW819268

EST:     CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAG                         GCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAAC-TGAAGTTGG
genomic: CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAGgtatgcacca ... ttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGG

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: 45 (upstream exon), 49 (downstream exon)
Score: 210

AGAATATGCAGTGGGGATCAAGAATGTTACAATAAATGATAATTTCTTCCCAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAGgtatgcacca ... ttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGATCTCGAGACAACTTCTTTTTCGCCGGGATTGACAAAGTTAGGTTCAGGA

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 212

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 161

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 457

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cccatgcctggattcagtaactcacattagaaactatttgcacctttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGATCTCGAGACAACTTCTTTTTCGCCGGGATTGACAAAGTTAGGTTCAGGA