ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CTGCTCTGCCCACTTCCTATGGGTCGGAGAGCGCACTCGCCAGCTTGATGGTGCTCACGTTGAGTTCCTTCGAGGCATTGCCAACCCTCTTGGTATCAAGgtaaatctaatgctcaacatttagcaagtcctgtttgacctctgcatttgtaaagctcaaggtttaggcattgtctgagaaatttctcctcacccaacaatgtaatacag

Basic information

species	Zea mays
transcript	GRMZM5G828182_T02
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G828182_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g37790.1 (Oryza sativa), 5'ss of exon 3

CTGCTCTGCCCACTTCCTATGGGTCGGAGAGCGCACTCGCCAGCTTGATGGTGCTCACGTTGAGTTCCTTCGAGGCATTGCCAACCCTCTTGGTATCAAGgtaaatct-aatgctca-acatttagcaagtcctgtttgacctctgcatttgtaaagctcaaggtttaggcattgtctgagaaatttctcctcacccaacaatgtaatacag-------------------------
||| ||||| |||||||| ||||| |||||||| || || ||||||||| |||| || || ||||| || ||||| ||||| |||||||| |||||||||||||||   |||  ||  ||| ||  |||| |   |            | |   ||| ||||  || |           ||  | ||| |          || | ||| ||                          
CTGTTCTGCTCACTTCCTTTGGGTTGGAGAGCGTACACGTCAGCTTGATTGTGCCCATGTGGAGTTTCTCCGAGGAATTGCGAACCCTCTGGGTATCAAGgtaaataggaatattcctacacttgtcaagacagataaatagataatgtataccaagttcaaacttcatttgaaagtgcaggtaattcacactttgtcctaaaggaattcaccctaaactcatcaaactaaatgcag

upper sequence: GRMZM5G828182_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT4G33510.2 (Arabidopsis thaliana), 5'ss of exon 3

CTGCTCTGCCCACTTCCTATGGGTCGGAGAGCGCACTCGCCAGCTTGATGGTGCTCACGTTGAGTTCCTTCGAGGCATTGCCAACCCTCTTGGTATCAAGgtaaatctaatgctcaacatttagcaagtcctgtttgacctctgcatttgtaaagctcaaggtttaggcattgtctgagaaatttctcctcacccaacaatgtaatacag
 |||||||| ||| | || ||||| ||||| || |||||||| |||||||||||||| |||||||| ||  | || || || ||||| || || |||||||||  |     | ||| ||  |  |  |   || || |       |   ||||   |||  | || |    | |   | |||   ||         ||     ||     
TTGCTCTGCGCACATGCTTTGGGTTGGAGAACGAACTCGCCAACTTGATGGTGCTCATGTTGAGTTTCTGAGGGGAATCGCTAACCCCCTCGGAATCAAGgtatgt-----gatcatcaagtctcttggtttggttaattggaataggagtaagtttcatagctttgttcgtatagaaaaaaacactgagatgtagactcaagaa-----

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|61119679|gb|DN560640.1|DN560640

EST:     GTGCTCACGTTGAGTTCCTTCGAGGCATTGCCAACCCTCTTGGTATCAAG                         GTTAGTGACAAGATGGACCCAGCAGAACTTGTGCGGTTGATTGATATATTG
genomic: GTGCTCACGTTGAGTTCCTTCGAGGCATTGCCAACCCTCTTGGTATCAAGgtaaatctaa ... tgtaatacagGTTAGTGACAAGATGGACCCAGCAGAACTTGTGCGGTTGATTGATATATTG

EST: gi|211427349|gb|FL101762.1|FL101762

EST:     CGTTGAGTTCCTTCGAGGCATTGCCAACCCTCTTGGTATCAAG                         GTTAGTGACAAGATGGACCCAGCAGAACTTGTGCGGTTGATTGATATATTG
genomic: CGTTGAGTTCCTTCGAGGCATTGCCAACCCTCTTGGTATCAAGgtaaatctaa ... tgtaatacagGTTAGTGACAAGATGGACCCAGCAGAACTTGTGCGGTTGATTGATATATTG

EST: gi|211368059|gb|FL471721.1|FL471721

EST:     GTGCTCACGTTGAGTTCCTTCGAGGCATTGCCAACCCTCTTGGTATCAAG                         GTTAGTGACAAGATGGACCCAGCAGAACTTGTGCGGTTGATTGATATATTG
genomic: GTGCTCACGTTGAGTTCCTTCGAGGCATTGCCAACCCTCTTGGTATCAAGgtaaatctaa ... tgtaatacagGTTAGTGACAAGATGGACCCAGCAGAACTTGTGCGGTTGATTGATATATTG

EST: gi|211427348|gb|FL101761.1|FL101761

EST:     GTGCTCACGTTGAGTTCCTTCGAGGCATTGCCAACCCTCTTGGTATCAAG                         GTTAGTGACAAGATGGACCCAGCAGAACTTGTGCGGTTGATTGATATATTG
genomic: GTGCTCACGTTGAGTTCCTTCGAGGCATTGCCAACCCTCTTGGTATCAAGgtaaatctaa ... tgtaatacagGTTAGTGACAAGATGGACCCAGCAGAACTTGTGCGGTTGATTGATATATTG

EST: gi|74237450|gb|DT645364.1|DT645364

EST:     GTGCTCACGTTGAGTTCCTTCGAGGCATTGCCAACCCTCTTGGTATCAAG                         GTTAGTGACAAGATGGACCCAGCAGAACTTGTGCGGTTGATTGATATATTG
genomic: GTGCTCACGTTGAGTTCCTTCGAGGCATTGCCAACCCTCTTGGTATCAAGgtaaatctaa ... tgtaatacagGTTAGTGACAAGATGGACCCAGCAGAACTTGTGCGGTTGATTGATATATTG

EST: gi|78091973|gb|DV520347.1|DV520347

EST:     CCTCTTGGTATCAAG                         GTTAGTGACAAGATGGACCCAGCAGAACTTGTGCGGTTGATTGATATATTG
genomic: CCTCTTGGTATCAAGgtaaatctaa ... tgtaatacagGTTAGTGACAAGATGGACCCAGCAGAACTTGTGCGGTTGATTGATATATTG

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), 47 (downstream exon)
Score: 73

CTGCTCTGCCCACTTCCTATGGGTCGGAGAGCGCACTCGCCAGCTTGATGGTGCTCACGTTGAGTTCCTTCGAGGCATTGCCAACCCTCTTGGTATCAAGgtaaatctaa ... tgtaatacagGTTAGTGACAAGATGGACCCAGCAGAACTTGTGCGGTTGATTGATATATTGAATCCCGAAAACAGGGCTGGGAGAATAACCATCATCACAAGAATGGGAC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 127

Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 31