ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtatgtttccttcaaaactctgggaggtgaataaatgtgtgacctaaatacagttagatcattaaaaatggcataaattcaaaccatgtttaaaacggttgcaccatggagcatgactaccaacacatttccatttcgttaccagGAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGACCTCAAAGGATACCTAATGAATGCCTACATCCACCCGGTGTTCAAAGGTG

Basic information

species	Zea mays
transcript	GRMZM2G064189_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G064189_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g35050.4 (Oryza sativa), 3'ss of exon 11

gtatgtttccttcaaaactctgggaggtgaataaatgtgtgacctaaatacagttagatcattaaaaatggcataaattcaaacca-tgtttaaaacggttgcaccatggagcatgactaccaacacatttccatttcgtta-ccagGAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGACCTCAAAGGATACCTAATGAATGCCTACATCCACCCGGTGTTCAAAGGTG
                                               ||      ||   | |    ||    | ||||  |   | |||  ||  |         |  ||     || |  |||   |   |||| | ||  |||||| || |||  |||||||||||| ||||| || ||||||||||| || ||||||||||||||||| |||||||||||||||||||||||||||||||| |
-----------------------------------------------atgtcaaaaggagaatgtgcatcttgtgaattagagaaactgtggaattcaaccttcaaactgaaatcaaccaataacgtctcatcattcccttttccagGATGCAATGCGGAAGGATACCCTAGAACGCGCAAGAGAGCCAGGGTTCGACCTCAAAGGATACCTGATGAATGCCTACATCCACCCGGTGTTCAAAGGCG

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|78021094|gb|DV489481.1|DV489481

EST:     AGTACTGCAACAACCGCTACAAGCCGACTTTTGTGAAATGCCCATTGCAG                         GAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGAC
genomic: AGTACTGCAACAACCGCTACAAGCCGACTTTTGTGAAATGCCCATTGCAGgtatgtttcc ... tcgttaccagGAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGAC

EST: gi|5846752|gb|AI999835.1|AI999835

EST:     AGTACTGCAACAACCGCTACAAGCCGACTTTTGTGAAATGCCCATTGCAG                         GAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAG
genomic: AGTACTGCAACAACCGCTACAAGCCGACTTTTGTGAAATGCCCATTGCAGgtatgtttcc ... tcgttaccagGAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAG

EST: gi|5847484|gb|AW000563.1|AW000563

EST:     AGTACTGCAACAACCGCTACAAGCCGACTTTTGTGAAATGCCCATTGCAG                         GAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGAC
genomic: AGTACTGCAACAACCGCTACAAGCCGACTTTTGTGAAATGCCCATTGCAGgtatgtttcc ... tcgttaccagGAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGAC

EST: gi|40336310|gb|CK370380.1|CK370380

EST:     AGTACTGCAACAACCGCTACAAGCCGACTTTTGTGAAATGCCCATTGCAG                         GAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGAC
genomic: AGTACTGCAACAACCGCTACAAGCCGACTTTTGTGAAATGCCCATTGCAGgtatgtttcc ... tcgttaccagGAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGAC

EST: gi|5055562|gb|AI734449.1|AI734449

EST:     AGTACTGCAACAACCGCTACAAGCCGACTTTTGTGAAATGCCCATTGCAG                         GAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGAC
genomic: AGTACTGCAACAACCGCTACAAGCCGACTTTTGTGAAATGCCCATTGCAGgtatgtttcc ... tcgttaccagGAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGAC

EST: gi|37392989|gb|CF633749.1|CF633749

EST:     AGTACTGCAACAACCGCTACAAGCCGACTTTTGTGAAATGCCCATTGCAG                         GAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGAC
genomic: AGTACTGCAACAACCGCTACAAGCCGACTTTTGTGAAATGCCCATTGCAGgtatgtttcc ... tcgttaccagGAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGAC

EST: gi|213167976|gb|FM187628.1|FM187628

EST:     AGTACTGCAACAACCGCTACAAACCGACTTTTGTGAAATGCCCATTGCAG                         GAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGAC
genomic: AGTACTGCAACAACCGCTACAAGCCGACTTTTGTGAAATGCCCATTGCAGgtatgtttcc ... tcgttaccagGAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGAC

EST: gi|74035115|gb|DT535605.1|DT535605

EST:     AGTACTGCAACAACCGCTACAAGCCGACTTTTGTGAAATGCCCATTGCAG                         GAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGAC
genomic: AGTACTGCAACAACCGCTACAAGCCGACTTTTGTGAAATGCCCATTGCAGgtatgtttcc ... tcgttaccagGAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGAC

EST: gi|60338400|gb|DN205373.1|DN205373

EST:     AGTACTGCAACAACCGCTACAAACCGACTTTTGTGAAATGCCCATTGCAG                         GAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGAC
genomic: AGTACTGCAACAACCGCTACAAGCCGACTTTTGTGAAATGCCCATTGCAGgtatgtttcc ... tcgttaccagGAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGAC

EST: gi|37379442|gb|CF626465.1|CF626465

EST:     AGTACTGCAACAACCGCTACAAGCCGACTTTTGTGAAATGCCCATTGCAG                         GAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGAC
genomic: AGTACTGCAACAACCGCTACAAGCCGACTTTTGTGAAATGCCCATTGCAGgtatgtttcc ... tcgttaccagGAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGAC

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: 46 (upstream exon), 47 (downstream exon)
Score: 66

GTCAACACCTGTGCTCCTTGTTCTTCCTGTAGTGACCTTCTATTTCCACAAGTACTGCAACAACCGCTACAAGCCGACTTTTGTGAAATGCCCATTGCAGgtatgtttcc ... tcgttaccagGAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGACCTCAAAGGATACCTAATGAATGCCTACATCCACCCGGTGTTCAAAGGTG

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 88

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

Block sizes: 28 (upstream exon), 45 (downstream exon)
Score: 48

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

taaaacggttgcaccatggagcatgactaccaacacatttccatttcgttaccagGAGGCGATGAAGAAGGATACCCTGGAACGTGCCAGAGAGCCAGGATTTGACCTCAAAGGATACCTAATGAATGCCTACATCCACCCGGTGTTCAAAGGTG