ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CCGGCTGCCGACGGTCATCGGCGGCTCCTACGCGTTCGTCATCCCGATAATGGCCATCATCCAGGACCCGTCGCTTTCTGGGATACCCGACGGTCATGAGgtgagcagcagcagttgcctgtgactgtccgttctgcctgttgcttctgatggaggcggtggcgtgtgtgtaatctgaaagtttttttccccatctgtggttgagcag

Basic information

species	Zea mays
transcript	GRMZM2G437859_T04
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G437859_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g55500.4 (Oryza sativa), 5'ss of exon 3

CCGGCTGCCGACGGTCATCGGCGGCTCCTACGCGTTCGTCATCCCGATAATGGCCATCATCCAGGACCCGTCGCTTTCTGGGATACCCGACGGTCATGAGgtgagcagcagcag----------ttgcctgtgactgtccgttctgcctgttgcttctgatggaggcggt--ggcgtgtgtg-------taatctga-----aagtttttttccccatctgtggttgagcag
 || ||||| ||||| |||||||| ||||||||||||||  ||||||||||||||||||| |||||| | |||||  | |  ||||||||||  || ||||| ||||| |||||          ||   | || |  ||| | |  ||  | || |||  ||     | |  ||||||| ||       | |||||      |  | | | || |  ||| |   |||||||
GCGCCTGCCCACGGTGATCGGCGGATCCTACGCGTTCGTGGTCCCGATAATGGCCATCATACAGGACTCATCGCTCGCCGCCATACCCGACGACCACGAGgtaagcag-agcaggcggacgctcttctttctgtccatccatccgtccaatcgcctctactgttttagattaggcgtgtctgatcacaatcatctgctgttcatctctctctctctctctctctctgagcag

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|74244049|gb|DT651963.1|DT651963

EST:     TGGCCATCATCCAGGACCCGTCGCTTTCTGGGATACCCGACGGTCATGAG                         AGGTTCCTCGAGACCATGAAGGCCATACAGGGGGCACTGATAGTGTCCTCC
genomic: TGGCCATCATCCAGGACCCGTCGCTTTCTGGGATACCCGACGGTCATGAGgtgagcagca ... ggttgagcagAGGTTCCTCGAGACCATGAAGGCCATACAGGGGGCACTGATAGTGTCCTCC

EST: gi|149001123|gb|EE038382.2|EE038382

EST:     TGGCCATCATCCAGGACCCGTCGCTTTCTGGGATACCCGACGGTCATGAG                         AGGTTCCTCGAGACCATGAAAGCCATACAGGGGGCACTGATAGTG
genomic: TGGCCATCATCCAGGACCCGTCGCTTTCTGGGATACCCGACGGTCATGAGgtgagcagca ... ggttgagcagAGGTTCCTCGAGACCATGAAGGCCATACAGGGGGCACTGATAGTG

EST: gi|78084450|gb|DV512843.1|DV512843

EST:     TGGCCATCATCCAGGACCCGTCGCTTTCTGGGATACCCGACGGTCATGAG                         AGGTTCCTCGAGACCATGAAGGCCATACAGGGGGCACTGATAGTGTCCTCC
genomic: TGGCCATCATCCAGGACCCGTCGCTTTCTGGGATACCCGACGGTCATGAGgtgagcagca ... ggttgagcagAGGTTCCTCGAGACCATGAAGGCCATACAGGGGGCACTGATAGTGTCCTCC

EST: gi|71439895|gb|DR820945.1|DR820945

EST:     TGGCCATCATCCAGGACCCGTCGCTTTCTGGGATACCCGACGGTCATGAG                         AGGTTCCTCGAGACCATGAAGGCCATACAGGGGGCACTGATAGTGTCCTCC
genomic: TGGCCATCATCCAGGACCCGTCGCTTTCTGGGATACCCGACGGTCATGAGgtgagcagca ... ggttgagcagAGGTTCCTCGAGACCATGAAGGCCATACAGGGGGCACTGATAGTGTCCTCC

EST: gi|76923378|gb|DV169457.1|DV169457

EST:     TGGCCATCATCCAGGACCCGTCGCTTTCTGGGATACCCGACGGTCATGAG                         AGGTTCCTCGAGACCATGAAGGCCATACAGGGGGCACTGATAGTGTCCTCC
genomic: TGGCCATCATCCAGGACCCGTCGCTTTCTGGGATACCCGACGGTCATGAGgtgagcagca ... ggttgagcagAGGTTCCTCGAGACCATGAAGGCCATACAGGGGGCACTGATAGTGTCCTCC

EST: gi|74238882|gb|DT646796.1|DT646796

EST:     TGGCCATCATCCAGGACCCGTCGCTTTCTGGGATACCCGACGGTCATGAG                         AGGTTCCTCGAGACCATGAAGGCCATACAGGGGGCACTGATAGTGTCCTCC
genomic: TGGCCATCATCCAGGACCCGTCGCTTTCTGGGATACCCGACGGTCATGAGgtgagcagca ... ggttgagcagAGGTTCCTCGAGACCATGAAGGCCATACAGGGGGCACTGATAGTGTCCTCC

EST: gi|74240437|gb|DT648351.1|DT648351

EST:     TGGCCATCATCCAGGACCCGTCGCTTTCTGGGATACCCGACGGTCATGAA                         AGGTTCCTCGAGACCATGAAGGCCATACAGG
genomic: TGGCCATCATCCAGGACCCGTCGCTTTCTGGGATACCCGACGGTCATGAGgtgagcagca ... ggttgagcagAGGTTCCTCGAGACCATGAAGGCCATACAGG

EST: gi|91049745|gb|EB160163.1|EB160163

EST:     TGGCCATCATCCAGGACCCGTCGCTTTCTGGGATACCCGACGGTCATGAG                         AGGTTCCTCGAGACCATGAAGGCCATACAGGGGGCACTGATAGTGTCCTCC
genomic: TGGCCATCATCCAGGACCCGTCGCTTTCTGGGATACCCGACGGTCATGAGgtgagcagca ... ggttgagcagAGGTTCCTCGAGACCATGAAGGCCATACAGGGGGCACTGATAGTGTCCTCC

EST: gi|211102809|gb|FL069927.1|FL069927

EST:     TGGCCATCATCCAGGACCCGTCGCTTTCTGGGATACCCGACGGTCATGAG                         AGGTTCCTCGAGACCATGAAGGGCATACAGGGGGCACTGATAGTGTCCTCC
genomic: TGGCCATCATCCAGGACCCGTCGCTTTCTGGGATACCCGACGGTCATGAGgtgagcagca ... ggttgagcagAGGTTCCTCGAGACCATGAAGGCCATACAGGGGGCACTGATAGTGTCCTCC

EST: gi|71310987|gb|DR791795.1|DR791795

EST:     TGGCCATCATCCAGGACCCGTCGCTTTCTGGGATACCCGACGGTCATGAG                         AGGTTCCTCGAGACCATGAAGGCCATACAGGGGGCACTGATAGTGTCCTCC
genomic: TGGCCATCATCCAGGACCCGTCGCTTTCTGGGATACCCGACGGTCATGAGgtgagcagca ... ggttgagcagAGGTTCCTCGAGACCATGAAGGCCATACAGGGGGCACTGATAGTGTCCTCC

EST: gi|71438783|gb|DR819833.1|DR819833

EST:     TGGCCATCATCCAGGACCCGTCGCTTTCTGGGATACCCGACGGTCATGAG                         AGGTTCCTCGAGACCATGAAGGCCATACAGGGGGCACTGATAGTGTCCTCC
genomic: TGGCCATCATCCAGGACCCGTCGCTTTCTGGGATACCCGACGGTCATGAGgtgagcagca ... ggttgagcagAGGTTCCTCGAGACCATGAAGGCCATACAGGGGGCACTGATAGTGTCCTCC

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: 169

CCGGCTGCCGACGGTCATCGGCGGCTCCTACGCGTTCGTCATCCCGATAATGGCCATCATCCAGGACCCGTCGCTTTCTGGGATACCCGACGGTCATGAGgtgagcagca ... ggttgagcagAGGTTCCTCGAGACCATGAAGGCCATACAGGGGGCACTGATAGTGTCCTCCAGCATTCAGATCATTCTGGGCTACAGCCAGCTGTGGGGTATTTTCTCCA

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 39

Block sizes: 47 (upstream exon), 41 (downstream exon)
Score: 10