ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ATCTGTATACCAAGCTAACAGAATTAATGTCAGGACACCTCTCGGAAAATCAGTTGCAGAGGTTGGGTGTGAGCCTATTCTGCATATGCGGCATTTCCAGgtctctcccatcgtattgctctatatttttacccttgatgttcaattgtcataatttctctcttcactgcactaaagtactgatttcttttttttcctca...

Basic information

species	Zea mays
transcript	GRMZM2G142836_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G142836_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os12g19304.2 (Oryza sativa), 5'ss of exon 6

ATCTGTATACCAAGCTAACAGAATTAATGTCAGGACACCTCTCGGAAAATCAGTTGCAGAGGTTGGGTGTGAGCCTATTCTGCATATGCGGCATTTCCAGgtctctcccatcgtattgctctatatttttacccttgatgttcaattgtca---taatttctctcttcactgcactaaagtactgatttcttttttttcctca
|  ||  || || |||| | || | ||||  | ||| ||||| |||||||  ||||||||||||||||||||||| ||| |||||||||| ||||||||||| |  | |    | ||    |  | | |   | |   |    || |   |    | |   |  ||||  | ||||  | | |  |||   ||||| | | | 
AGTTGCCTATCAGGCTAGCCGATTCAATGCTAAGACTCCTCTGGGAAAATTGGTTGCAGAGGTTGGGTGTGAGCCCATTTTGCATATGCGACATTTCCAGgtttgccaccctct-ttatcttgaactctggacataattaactaactactagttcactcattggcttccgtccactgcaatgc--attggctttttgttcact

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|13515706|gb|BG517982.1|BG517982

EST:     CAGTTGCAGAGGTTGGGTGTGAGCCTATTCTGCATATGCGGCATTTCCAG                         AAAACAAGGAGGTTACCCAACAAGCTTGTTCACCAGGTTGTCCATGGTAAT
genomic: CAGTTGCAGAGGTTGGGTGTGAGCCTATTCTGCATATGCGGCATTTCCAGgtctctccca ... catctttcagAAAACAAGGAGGTTACCCAACAAGCTTGTTCACCAGGTTGTCCATGGTAAT

EST: gi|211331145|gb|FL454096.1|FL454096

EST:     CAGTTGCAGAGGTTGGGTGTGAGCCTATTYTGCATATGCGGCATTTCCAG                         AAAACAAGGAGGTTACCCAACAAGCTTGTTCACCAGGTTGTCCATGGTAAT
genomic: CAGTTGCAGAGGTTGGGTGTGAGCCTATTCTGCATATGCGGCATTTCCAGgtctctccca ... catctttcagAAAACAAGGAGGTTACCCAACAAGCTTGTTCACCAGGTTGTCCATGGTAAT

EST: gi|211425343|gb|FL007530.1|FL007530

EST:     CAGTTGCAGAGGTTGGGTGTGAGCCTATTCTGCATATGCGGCATTTCCAG                         AAAACAAGGAGGTTACCCAACAAGCCTGTTCACCAGGTTGTCCATGGTAAG
genomic: CAGTTGCAGAGGTTGGGTGTGAGCCTATTCTGCATATGCGGCATTTCCAGgtctctccca ... catctttcagAAAACAAGGAGGTTACCCAACAAGCTTGTTCACCAGGTTGTCCATGGTAAT

EST: gi|211425342|gb|FL007529.1|FL007529

EST:     CAGTTGCAGAAGTTGGGTGTGAGCCTATTCTGCATATGCGGCATTTCCAG                         AAAACAAGGAGGTTACCCAACAAGCTTGTTCACCAGGTTGTCCATGGTAAT
genomic: CAGTTGCAGAGGTTGGGTGTGAGCCTATTCTGCATATGCGGCATTTCCAGgtctctccca ... catctttcagAAAACAAGGAGGTTACCCAACAAGCTTGTTCACCAGGTTGTCCATGGTAAT

EST: gi|16379668|gb|BI993084.1|BI993084

EST:     CAGTTGCAGAGGTTGGGTGTGAGCCTATTCTGCATATGCGGCATTTCCAG                         AAAACAAGGAGGTTACCCAACAAGCTTGTTCACCAGGTTGTCCATGGTAAT
genomic: CAGTTGCAGAGGTTGGGTGTGAGCCTATTCTGCATATGCGGCATTTCCAGgtctctccca ... catctttcagAAAACAAGGAGGTTACCCAACAAGCTTGTTCACCAGGTTGTCCATGGTAAT

EST: gi|13515717|gb|BG517993.1|BG517993

EST:     CAGTTGCAGAGGTTGGGTGTGAGCCTATTCTGCATATGCGGCATTTCCAG                         AAAACAAGGAGGTTACCCAACAAGCTTGTTCACCAGGTTGTCCATGGTAAT
genomic: CAGTTGCAGAGGTTGGGTGTGAGCCTATTCTGCATATGCGGCATTTCCAGgtctctccca ... catctttcagAAAACAAGGAGGTTACCCAACAAGCTTGTTCACCAGGTTGTCCATGGTAAT

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), 48 (downstream exon)
Score: 66

ATCTGTATACCAAGCTAACAGAATTAATGTCAGGACACCTCTCGGAAAATCAGTTGCAGAGGTTGGGTGTGAGCCTATTCTGCATATGCGGCATTTCCAGgtctctccca ... catctttcagAAAACAAGGAGGTTACCCAACAAGCTTGTTCACCAGGTTGTCCATGGTAATGGTGACAAACCCTTGCAATAGCTGTTCATCAATACTTGTATTTATTTTA

Block sizes: 45 (upstream exon), 42 (downstream exon)
Score: 50

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 51