ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaacctgaggaaacagatccacatcatgcatcatcatcagtaacaccacagtattttttttaccgagaacaccacagtataattgcttcaagtaacctgaaaattctccatctgcagGGAAACCGGTGTACATGTATAGTATGGGAGGGCTTGCAGAGTATTGTGTTGTCCCAGCCAATGCGCTAGCAGTTCTCCCTGACTCACTGCCATACACAGA

Basic information

species	Zea mays
transcript	GRMZM2G024303_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G024303_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g01760.1 (Oryza sativa), 3'ss of exon 4

gtaacctgaggaaacagatccacatcatgcatcatcatcagtaacaccacagtattttttttaccgagaacaccacagtataattgcttcaagtaacctgaaaattctccatctgcagGGAAACCGGTGTACATGTATAGTATGGGAGGGCTTGCAGAGTATTGTGTTGTCCCAGCCAATGCGCTAGCAGTTCTCCCTGACTCACTGCCATACACAGA
                 |||   |  || || |  |     | | |     ||| |  |            |  || ||    ||||||  || |  ||     || | ||| | |||| || || |||||||||||||||||||| ||||||||||| ||||| ||||| |||||||| || ||||||||||| ||  ||||  |||||||||||||
--------------gtaatcttaaatatacaactcctcacatgatatgtgggtaatgatac------aggtataactgtgcctttgcttacagcattcttt---ttatgcatttccagGAAAGCCAGTGTACATGTATAGTATGGGTGGGCTTGCAGAATATTGCGTTGTGCCAGCCAACGCACTAGCAGTTCTTCCCAACTCTTTGCCATACACAGA

upper sequence: GRMZM2G024303_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G00740.2 (Glycine max), 3'ss of exon 5

gtaacctgaggaaacagatccacatcatgcatcatcatcagtaacaccacagtattttttttaccgagaacaccacagtataattgcttcaagtaacctgaaaattctcca-tctgcagGGAAACCGGTGTACATGTATAGTATGGGAGGGCTTGCAGAGTATTGTGTTGTCCCAGCCAATGCGCTAGCAGTTCTCCCTGACTCACTGCCATACACAGA
              |   | || ||  |  ||  || |||    ||      |||   |  |   | || ||   || |||      ||     |||   |||| | | || | |  ||| ||||| |  |||||||||||||||||||||||||| || || |||||||| ||||| ||||   |  | ||  | || |||||| ||||||| |||||
-------------gctagtacaaatt-tcaatgttcttcaagtgcatt----tatccctaattatgggatcatt-cattattgaaaatttggaaaactgaaaaagtttgcaatttatagGAAAACCAGCATACATGTATAGTATGGGAGGGCTTGCTGAATACTGTGTTGTGCCAGCAAATGGAGTGTCTGTGTTACCAGACTCATTGCCATATACAGA

upper sequence: GRMZM2G024303_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA05G33140.1 (Glycine max), 3'ss of exon 4

gtaacctgaggaaacagatccacatcatgcatcatcatcagtaacaccacagtattttttttaccgagaacac-cacagtataattgcttcaagtaacctgaaaattct-ccatctgcagGGAAACCGGTGTACATGTATAGTATGGGAGGGCTTGCAGAGTATTGTGTTGTCCCAGCCAATGCGCTAGCAGTTCTCCCTGACTCACTGCCATACACAGA
                  | || ||  |  ||  || |||    ||      |||   |  |   | || ||  ||   |   |    ||  | ||     |||| | | | |  | |||| ||||| |  | |||||||||||||||||||||||| || || || ||||| ||||| ||||   |  | ||  | || |||||| ||||||| |||||
---------------tagtacatatt-tcaatgttcttcaagtgcatt----tatccctaattgtgggatcattcattattggaaaatttggaatactgaaaaaagtttgctacttacagGAAAACCAGCATTCATGTATAGTATGGGAGGGCTTGCTGAATACTGCGTTGTGCCAGCAAATGGAGTGTCTGTATTACCAGACTCATTGCCATATACAGA

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|6021295|gb|AW066223.1|AW066223

EST:     CAAGGGGACACTCTATGATGGCGAGACACGGCTGTTTCTAAGGGGCAATG                         GGAAACCGGTGTACATGTATAGTATGGGAGGGCTTGCAGAGTATTGTGTTG
genomic: CAAGGGGACACTCTATGATGGCGAGACACGGCTGTTTCTAAGGGGCAATGgtaacctgag ... ccatctgcagGGAAACCGGTGTACATGTATAGTATGGGAGGGCTTGCAGAGTATTGTGTTG

EST: gi|6020969|gb|AW065897.1|AW065897

EST:     CAAGGGGACACTCTATGATGGCGAGACACGGCTGTTTCTAAGGGGCAATG                         GGAAACCGGTGTACATGTATAGTATGGGAGGGCTTGCAGAGTATTGNGTTG
genomic: CAAGGGGACACTCTATGATGGCGAGACACGGCTGTTTCTAAGGGGCAATGgtaacctgag ... ccatctgcagGGAAACCGGTGTACATGTATAGTATGGGAGGGCTTGCAGAGTATTGTGTTG

EST: gi|18660089|gb|BM500681.1|BM500681

EST:     GGCGAGACACGGCTGTTTCTAAGGGGCAATG                         GGAAACCGGTGTACATGTATAGTATGGGAGGGCTTGCAGAGTATTGTGTTG
genomic: GGCGAGACACGGCTGTTTCTAAGGGGCAATGgtaacctgag ... ccatctgcagGGAAACCGGTGTACATGTATAGTATGGGAGGGCTTGCAGAGTATTGTGTTG

EST: gi|20301156|gb|BQ164099.1|BQ164099

EST:     CAAGGGGACACTCTATGATGGAGAGACACGGCTGTTTCTAAGGGGCAATG                         GGAAACCGGTGTACATGTATAGTATGGGAGGGCTTGCAGAGTATTGTGTTG
genomic: CAAGGGGACACTCTATGATGGCGAGACACGGCTGTTTCTAAGGGGCAATGgtaacctgag ... ccatctgcagGGAAACCGGTGTACATGTATAGTATGGGAGGGCTTGCAGAGTATTGTGTTG

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: 129

GGCCAAGAAGATCTGTGTGAGTCTTTCTTCGCGTATAATCGTGCCAAGGGGACACTCTATGATGGCGAGACACGGCTGTTTCTAAGGGGCAATGgtaacctgag ... ccatctgcagGGAAACCGGTGTACATGTATAGTATGGGAGGGCTTGCAGAGTATTGTGTTGTCCCAGCCAATGCGCTAGCAGTTCTCCCTGACTCACTGCCATACACAGA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 310

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 266

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 138

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ccgagaacaccacagtataattgcttcaagtaacctgaaaattctccatctgcagGGAAACCGGTGTACATGTATAGTATGGGAGGGCTTGCAGAGTATTGTGTTGTCCCAGCCAATGCGCTAGCAGTTCTCCCTGACTCACTGCCATACACAGA