ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CGGCCGCCGATGCCTTTGCCATCGACGACGTCAACATATTCGAGTACCTCGGCGGCACTCCGCAGCCATTCGTCGACCTCTCCACCAATTTCTACACCAGgtccgtccatcggctacctgtccctctcttgttctcgtctgcgttgaaccattccgatctagaatgttttcgtccgtctcctgttgaatttcttgtttcatggccgtgtcttgattggttggattttatag

Basic information

species	Zea mays
transcript	GRMZM2G155868_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G155868_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os06g39140.2 (Oryza sativa), 5'ss of exon 1

CGGCCGCCGATGCCTTTGCCATCGACGACGTCAACATATTCGAGTACCTCGGCGGCACTCCGCAGCCATTCGTCGACCTCTCCACCAATTTCTACACCAGgtccgtccatcggctacctgtccctctcttgttctcgtctgcgttgaaccattccgatctagaatgttttcgtccgtctcctgttgaatttcttgtttcatggccgtgtcttgattggttggattttatag
|||| |  ||||| || ||||||||||| |  ||| | ||||||   || ||||||||  ||||||| |||||||||||||||||||| ||||||||||||||   |   |     |  |  |  | |  | ||| ||  |   |      |  |||| | |   | | |  | | |       | ||                                           
CGGCGGGGGATGCGTTCGCCATCGACGATGGGAACGTCTTCGAGGCGCTGGGCGGCACCACGCAGCCGTTCGTCGACCTCTCCACCAACTTCTACACCAGgtctcgcttgctttcgctcgctcgccgcc-gatctggttcgttcttcttgctcgcgatttcgggggctctgattcttgggggagtcaacag----------------------------------------

upper sequence: GRMZM2G155868_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv04s0008g04210.t01 (Vitis vinifera), 5'ss of exon 1

------CGGCCGCCGATGCCTTTGCCATCGACGACGTCAACATATTCGAGTACCTCGGCGGCACTCCGCAGCCATTCGTCGACCTCTCCACCAATTTCTACACCAGgtccgtccatcggctacctgtccctctcttgttctcgtctgcgttgaaccattccgatctagaatgttttcgtccgtctcctgttgaatttcttgtttcatggccgtgtcttgattggttggattttatag
      |      ||| |||||||  |||||| ||  |||  | ||  || |  | |||      |  ||| | ||| || ||||||||||||||||||||||||||| | |  | |  | |     |  | | ||||| |        || ||   ||   || |    | | || |   |      |  | |  ||         ||     | ||                   
GAGTCTCCCAAAACGACGCCTTTGAAATCGACAACACCAATCTCTTTCAGAAATTGGGC------CTTCAGACCTTCATCAACCTCTCCACCAATTTCTACACCAGgttc-tttaccaacaattacacaattttttgtttt--------ttaaattgttttaatttgacgtctgtttgattga---tgggaggaagtcggaaaatgggggaaaatttt-------------------

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|13382017|gb|BG458692.1|BG458692

EST:     GGCGGCACTCCGCAGCCATTCGTCGACCTCTCCACCAATTTCTACACCAG                         GGTTTATGAGGACGAAGAGGAGTGGTTTCGGGAGATATTCGGGGGGTCGAA
genomic: GGCGGCACTCCGCAGCCATTCGTCGACCTCTCCACCAATTTCTACACCAGgtccgtccat ... gattttatagGGTTTATGAGGACGAAGAGGAGTGGTTTCGGGAGATATTCGGGGGGTCGAA

EST: gi|211371422|gb|FL053367.1|FL053367

EST:     GGCGGCACTCCGCAGCCATTCGTCGACCTTTCCACCAATTTCTACACCAG                         GGTTTATGAGGACGAGGAGGAGTGGTTTCGAGAGATATTCGGGGGGTCCAA
genomic: GGCGGCACTCCGCAGCCATTCGTCGACCTCTCCACCAATTTCTACACCAGgtccgtccat ... gattttatagGGTTTATGAGGACGAAGAGGAGTGGTTTCGGGAGATATTCGGGGGGTCGAA

EST: gi|211485044|gb|FL285977.1|FL285977

EST:     GGCGGCACTCCGCAGCCATTCGTCGACCTCTCCACCAATTTCTACACCAG                         GGTTTATGAGGACGAGGAGGAGTGGTTTCGGGAGATATTCGGGGGGTCCAA
genomic: GGCGGCACTCCGCAGCCATTCGTCGACCTCTCCACCAATTTCTACACCAGgtccgtccat ... gattttatagGGTTTATGAGGACGAAGAGGAGTGGTTTCGGGAGATATTCGGGGGGTCGAA

EST: gi|15053287|gb|BI358832.1|BI358832

EST:     GGCGGCACTCCGCAGCCATTCGTTGACCTCTCCACCAATTTCTACACCAG                         GGTTTATGAGGACGAAGAGGAGTGGTTTCGGGAGATATTCGGGGGGTCGAA
genomic: GGCGGCACTCCGCAGCCATTCGTCGACCTCTCCACCAATTTCTACACCAGgtccgtccat ... gattttatagGGTTTATGAGGACGAAGAGGAGTGGTTTCGGGAGATATTCGGGGGGTCGAA

EST: gi|9733638|gb|BE512390.1|BE512390

EST:     GGCGGCACTCCGCAGCCATTCGTCGACCTTTCCACCAATTTCTACACCAG                         GGTTTATGAGGACGAGGAGGAGTGGTTTCGGGAGATATTCGGGGGGTCCAA
genomic: GGCGGCACTCCGCAGCCATTCGTCGACCTCTCCACCAATTTCTACACCAGgtccgtccat ... gattttatagGGTTTATGAGGACGAAGAGGAGTGGTTTCGGGAGATATTCGGGGGGTCGAA

EST: gi|149099397|gb|EE185437.2|EE185437

EST:     GGCGGCACTCCGCAGCCATTCGTCGACCTCTCCACCAATTTCTACACCAG                         GGTTTATGAGGACGAAGAGGAGTGGTTTCGGGAGATATTCGGGGGGTCGAA
genomic: GGCGGCACTCCGCAGCCATTCGTCGACCTCTCCACCAATTTCTACACCAGgtccgtccat ... gattttatagGGTTTATGAGGACGAAGAGGAGTGGTTTCGGGAGATATTCGGGGGGTCGAA

EST: gi|211371423|gb|FL053368.1|FL053368

EST:     GGCGGCACTCCGCAGCCATTCGTCGACCTTTCCACCAATTTCTACACCAG                         GGTTTATGAGGACGAGGAGGAGTGGTTTCGAGAGATATTCGGGGGGTCCAA
genomic: GGCGGCACTCCGCAGCCATTCGTCGACCTCTCCACCAATTTCTACACCAGgtccgtccat ... gattttatagGGTTTATGAGGACGAAGAGGAGTGGTTTCGGGAGATATTCGGGGGGTCGAA

EST: gi|211485043|gb|FL285976.1|FL285976

EST:     GGCGGCACTCCGCAGCCATTCGTCGACCTCTCCACCAATTTCTACACCAG                         GGTTTATGAGGACGAGGAGGAGTGGYTTCGGGAGATATTCGGGGGGYCCAA
genomic: GGCGGCACTCCGCAGCCATTCGTCGACCTCTCCACCAATTTCTACACCAGgtccgtccat ... gattttatagGGTTTATGAGGACGAAGAGGAGTGGTTTCGGGAGATATTCGGGGGGTCGAA

EST: gi|15053297|gb|BI358842.1|BI358842

EST:     GGCGGCACTCCGCAGCCATTCGTTGACCTCTCCACCAATTTCTACACCAG                         GGTTTATGAGGACGAAGAGGAGTGGTTTCGGGAGATATTCGGGGGGTCGAA
genomic: GGCGGCACTCCGCAGCCATTCGTCGACCTCTCCACCAATTTCTACACCAGgtccgtccat ... gattttatagGGTTTATGAGGACGAAGAGGAGTGGTTTCGGGAGATATTCGGGGGGTCGAA

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), 46 (downstream exon)
Score: 140

CGGCCGCCGATGCCTTTGCCATCGACGACGTCAACATATTCGAGTACCTCGGCGGCACTCCGCAGCCATTCGTCGACCTCTCCACCAATTTCTACACCAGgtccgtccat ... gattttatagGGTTTATGAGGACGAAGAGGAGTGGTTTCGGGAGATATTCGGGGGGTCGAAGAAGGAGGATGCCATCCAGAACCAGTATGAGTTCCTGATCCAGCGCATG

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 299

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 342