ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ACATGTCTTGCTTCCAAGGATTGTTCTTCTGTCCGGAGGCTGCGTCCCTGTTGCTTCACAGTTTCTGCGTGTACCACATCACACCTCAAGGACACGAGgtcacttatgctgtctttttttttctctccattgttgcattgattaattcaggcagccaaccactaaccattcttttcatgttaggtcaggttcttagttcttacatggttgtgtatgttaagtattgcag

Basic information

species	Zea mays
transcript	GRMZM2G413857_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G413857_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g09670.1 (Oryza sativa), 5'ss of exon 3

ACATGTCTTGCTTCCAAGGATTGTTCTTCTGTCCGGAGGCTGCGTCCCTGTTGCTTCACAGTTTCTGCGTGTACCACATCACACCTCAAGGACACGAGgtcacttatgctgtctttttttttctctccattgttgcattgattaattcaggcagccaaccactaaccattcttttcatgttaggtcaggttcttagttcttacatggttgtgtatgttaagtattgcag
| ||||||||||| ||||||||||||||||| || ||||| ||||| ||||||||||||| ||| ||  | ||||||||||| |||||||| || ||||||| | ||| || || ||| || |   ||| | ||   |      |||||     |      |      ||  | | ||  |       ||| ||   || ||||                         
ATATGTCTTGCTTTCAAGGATTGTTCTTCTGCCCAGAGGCCGCGTCGCTGTTGCTTCACAATTTTTGTATTTACCACATCACTCCTCAAGGTCATGAGgtcagtcatgatggctctttcttac---ccaatattatgtaagc--attca-----ctgtttgcccgtatttgctctgatacttacatgtgttattttgtcctacag------------------------

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|89761919|gb|DY689741.1|DY689741

EST:     TGTTGCTTCACAGTTTCTGCGTGTACCACATCACACCTCAAGGACACGAG                         TTGGGAGCAGCTCCGATTTCAGCTGATGTGCCTGTGCCATCTGTCGACGAC
genomic: TGTTGCTTCACAGTTTCTGCGTGTACCACATCACACCTCAAGGACACGAGgtcacttatg ... agtattgcagTTGGGAGCAGCTCCGATTTCAGCTGATGTGCCTGTGCCATCTGTCGACGAC

EST: gi|211370584|gb|FL353380.1|FL353380

EST:     TGTTGCTTCACAGTTTCTGCGTGTACCACATCACACCTCAAGGACACGAG                         TTGGGAGCAGCTCCGATTTCAGCTGATGTGCCTGTRGCCATCTGTCGACGA
genomic: TGTTGCTTCACAGTTTCTGCGTGTACCACATCACACCTCAAGGACACGAGgtcacttatg ... agtattgcagTTGGGAGCAGCTCCGATTTCAGCTGATGTGCCTGT-GCCATCTGTCGACGA

EST: gi|71443344|gb|DR824394.1|DR824394

EST:     TGTTGCTTCACAGTTTCTGCGTGTACCACATCACACCTCAAGGACACGAG                         TTGGGAGCAGCTCCGATTTCAGCTGATGTGCCTGTGCCATCTGTCGACGAC
genomic: TGTTGCTTCACAGTTTCTGCGTGTACCACATCACACCTCAAGGACACGAGgtcacttatg ... agtattgcagTTGGGAGCAGCTCCGATTTCAGCTGATGTGCCTGTGCCATCTGTCGACGAC

EST: gi|211436829|gb|FL403332.1|FL403332

EST:     TGTTGCTTCACAGTTTCTGCGTGTACCACATCACACCTCAAGGACACGAG                         TTGGGAGCAGCTCCGATTTCAGCTGATGTGCCTGTGCCATCTGTCGACGAC
genomic: TGTTGCTTCACAGTTTCTGCGTGTACCACATCACACCTCAAGGACACGAGgtcacttatg ... agtattgcagTTGGGAGCAGCTCCGATTTCAGCTGATGTGCCTGTGCCATCTGTCGACGAC

EST: gi|71443847|gb|DR824897.1|DR824897

EST:     TGTTGCTTCACAGTTTCTGCGTGTACCACATCACACCTCAAGGACACGAG                         TTGGGAGCAGCTCCGATTTCAGCTGATGTGCCTGTGCCATCTGTCGACGAC
genomic: TGTTGCTTCACAGTTTCTGCGTGTACCACATCACACCTCAAGGACACGAGgtcacttatg ... agtattgcagTTGGGAGCAGCTCCGATTTCAGCTGATGTGCCTGTGCCATCTGTCGACGAC

EST: gi|67011356|gb|CO440105.1|CO440105

EST:     ACACCTTAAGGAC-CGAG                         TTGGGAGCAGCTCCCATTTCAGCTGATGTGCCTGTGCCATCTGTCGACGAC
genomic: ACACCTCAAGGACACGAGgtcacttatg ... agtattgcagTTGGGAGCAGCTCCGATTTCAGCTGATGTGCCTGTGCCATCTGTCGACGAC

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: 37

ACATGTCTTGCTTCCAAGGATTGTTCTTCTGTCCGGAGGCTGCGTCCCTGTTGCTTCACAGTTTCTGCGTGTACCACATCACACCTCAAGGACACGAGgtcacttatg ... agtattgcagTTGGGAGCAGCTCCGATTTCAGCTGATGTGCCTGTGCCATCTGTCGACGACCTTGCAGATCAGGTTGCTGATGTCCTCGATTTTTTCAG

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

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 13