ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GGCGTTGTCAAGCTCATCAGCGCCGAGGGCTTCGAATTCGTTGTTGACAGGAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAGgtagggtactcttcacctcttccattcccatcagcgcgccgtcctcgcatcacatccatccctctcgtcttccccacag

Basic information

species	Zea mays
transcript	GRMZM2G059282_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G059282_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os11g48030.1 (Oryza sativa), 5'ss of exon 1

GGCGTTGTCAAGCTCATCAGCGCCGAGGGCTTCGAATTCGTTGTTGACAGGAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAGgtagggtactcttcacctcttccattcccatcagcgcgccgtcctcgcatcacatccatccctctcgtcttccccacag---------------
||| | ||||||||||||||||||||||||||||| ||||| || |||| |||||||||||||||||||||||| ||||||||||||||||| ||||| |||  |   |  | | | |||  |  ||| ||  ||    | | |||  | |  |     || |    | | | ||| |                
GGCTTCGTCAAGCTCATCAGCGCCGAGGGCTTCGAGTTCGTCGTCGACAAGAAGGCCGCCATGGTCTCCAACACGCTCCGCAACATGCTCACCTCCCCCGgttcgtctccttccccatctatcgatccgattcgctttgctttctcaaaccctagattgccttgaattatccaccaaatccaaatccaacacag

upper sequence: GRMZM2G059282_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv06s0004g05560.t01 (Vitis vinifera), 5'ss of exon 1

GGCGTTGTCAAGCTCATCAGCGCCGAGGGCTTCGAATTCGTTGTTGACAGGAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAGgtagggtactcttcacctcttc-cattcccatcagcgcgccgt----cctcgcatcacatccatccctctcgtcttccccacag----------------
| |  ||| ||||| |||||||| |||||||||||||||||  | |||| || ||| |||||||| ||  | ||| |||| ||||||||||| || || ||||   | |  ||    | ||| |    | || ||    |       | | | |  |     |    |    |  |     | |                
GACACTGTGAAGCTGATCAGCGCAGAGGGCTTCGAATTCGTGATCGACAAGAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCGgtatatttccgtttttattttctcgagacgattaggctactagaaaacgtaggaaaaaggaaagaaattaaattcttgaatcggaggtttattttattta

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|211141709|gb|FL287346.1|FL287346

EST:     GAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAG                         GCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCA
genomic: GAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAGgtagggtact ... ttccccacagGCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCA

EST: gi|211468741|gb|FL385438.1|FL385438

EST:     GAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAG                         GCGGCTTCTCTGAGACGCGCCAKGGCGAGGTCCGCTTCCCAGAGATCCCCA
genomic: GAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAGgtagggtact ... ttccccacagGCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCA

EST: gi|13490768|gb|BG517532.1|BG517532

EST:     AAGGCCGCCATGGTCTCCAATATTCTTTCGCAACATGCTCACATCCCCAG                         GCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCA
genomic: AAGGCCGCCATGGTCTCCAACA-CCCTCCGCAACATGCTCACATCCCCAGgtagggtact ... ttccccacagGCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCA

EST: gi|61119394|gb|DN560355.1|DN560355

EST:     GAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAG                         GTGGCTTTTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCA
genomic: GAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAGgtagggtact ... ttccccacagGCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCA

EST: gi|211141707|gb|FL287344.1|FL287344

EST:     GAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAG                         GCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCA
genomic: GAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAGgtagggtact ... ttccccacagGCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCA

EST: gi|211491482|gb|FL425975.1|FL425975

EST:     GAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAG                         GCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCA
genomic: GAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAGgtagggtact ... ttccccacagGCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCA

EST: gi|18163997|gb|BM333836.1|BM333836

EST:     GAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAG                         GCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCA
genomic: GAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAGgtagggtact ... ttccccacagGCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCA

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: 48 (upstream exon), 49 (downstream exon)
Score: 178

GGCGTTGTCAAGCTCATCAGCGCCGAGGGCTTCGAATTCGTTGTTGACAGGAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAGgtagggtact ... ttccccacagGCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCACCAACATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 534

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 336