ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtgcgccacacactatcttatcccccatcttcctgcgcgcgacccataaccaatcccaagtagacgctgcgcattgtgtcagcctgccatggcttgacattgatagcgtcgtcttctgatgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCATCATGCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAG

Basic information

species	Zea mays
transcript	GRMZM2G047143_T02
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G047143_T03 (Zea mays), 3'ss of exon 4
lower sequence: AT3G25980.1 (Arabidopsis thaliana), 3'ss of exon 4

gtgcgccacacactatcttatcccccatcttcctgcgcgcgacccataaccaatcccaagtagacgctgcgcattgtgtcagcctgccatggcttgacattgatagcgtcgtcttctgatgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCATCATGCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAG
                         ||  ||  ||            |  |  || |||||      ||    || | |  |  |  | | | || |   || || |      || ||    |  | || |     | ||||||||| || |||||||||||||||||||| || || || ||| | ||| | || ||  |  | || ||| | || || || || || 
-----------------------gtcagttttttgtttttagtgttgatactttcgcaagt-----ttgtttgttttctttgatt--ctttgtttcattatgttatc-----tttatggaactttttagTGTGTCGAGGGAGAAGAGTGATAAGGAGATCATGAGGGAGATTCAAGCTATTATGAGACAGGTTGCTTCAAGTGTTACTTACTTGCCTTGTCTTGATGAA

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|31406271|gb|CD485003.1|CD485003

EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT

EST: gi|76019513|gb|DT946683.1|DT946683

EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT

EST: gi|34391357|gb|CF384585.1|CF384585

EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT

EST: gi|101396573|gb|EB820212.1|EB820212

EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT

EST: gi|87155980|gb|DY400769.1|DY400769

EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGATAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT

EST: gi|31441067|gb|CD510498.1|CD510498

EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT

EST: gi|101396571|gb|EB820211.1|EB820211

EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT

EST: gi|211437588|gb|FL436643.1|FL436643

EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGATAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT

EST: gi|148946894|gb|EC892174.2|EC892174

EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT

EST: gi|78078551|gb|DV506963.1|DV506963

EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT

EST: gi|5713718|gb|AI943710.1|AI943710

EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGATAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT

EST: gi|60349178|gb|DN216151.1|DN216151

EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT

EST: gi|94475186|gb|EB704144.1|EB704144

EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT

EST: gi|78023687|gb|DV492074.1|DV492074

EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGATAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT

EST: gi|12969132|gb|BG266077.1|BG266077

EST:     CGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGATAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: CGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT

EST: gi|4966592|gb|AI691448.1|AI691448

EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGATAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT

EST: gi|32912163|gb|CF016975.1|CF016975

EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGATAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT

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: 195

TGCAGCGTATCGTGCTGGTCATAATGAGCAAAGCCACCAGCGAGGTGCTCGAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCATCATGCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAG

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 20

Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 21

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 18

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtcagcctgccatggcttgacattgatagcgtcgtcttctgatgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCATCATGCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAG