ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GACCATCAAAATCCAACACAAATTGTTACAGAGATGTGTGGCTTCATGACTATCCTATCTGGGACGTTTCTTCTTCACAAGACAAAAGATATGACTGATAgtatgtcacgattcatgcacttttacacaccccatgagaacgtttgattttgtcttttgatattttcttctcaaacag

Basic information

species	Zea mays
transcript	GRMZM2G129268_T01
intron #	8
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G129268_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os11g09140.2 (Oryza sativa), 5'ss of exon 8

GACCATCAAAATCCAACACAAATTGTTACAGAGATGTGTGGCTTCATGACTATCCTATCTGGGACGTTTCTTCTTCACAAGACAAAAGATATGACTGATAgtatgtcacgattcatgcacttttacacaccccatgagaacgtttgattttgtcttttgatattttcttctcaaacag
|| |  |||||||||||||||||||| || ||| ||||||| ||  |||| ||||| |||||||| ||||| || ||||||||||| || |||||||| |||||| ||| ||   |    ||  |||    |   || |    |   |  |    | | ||    | ||  |||| ||
GATCGACAAAATCCAACACAAATTGTCACGGAGCTGTGTGGTTTTGTGACCATCCTTTCTGGGACATTTCTCCTCCACAAGACAAAGGACATGACTGACAgtatgccacaatctgtcattttacacattttcatagatactactatgtcatcatgtctaatgagatttttccaaatag

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|32832980|gb|CD972658.1|CD972658

EST:     TATCCTATCTGGGACGTTTCTTCTTCACAAGACAAAAGATATGACTGATA                         GTCCTGGAAAATCTTTGTTGACACGACGGCCAAAGCATGCTAGTCAGAATG
genomic: TATCCTATCTGGGACGTTTCTTCTTCACAAGACAAAAGATATGACTGATAgtatgtcacg ... tctcaaacagGTCCTGGACAATCTTTGTTGACACGACGGCCAAAGCATGCTAGTCAGAATG

EST: gi|5296256|gb|AI782936.1|AI782936

EST:     TATCCTATCTGGGACGTTTCTTCTTCACAAGACAAAAGATATGACTGATA                         GTCCTGGACAATCTTTGTTGACACGACGGCCAAAGCATGCTAGTCAGAACG
genomic: TATCCTATCTGGGACGTTTCTTCTTCACAAGACAAAAGATATGACTGATAgtatgtcacg ... tctcaaacagGTCCTGGACAATCTTTGTTGACACGACGGCCAAAGCATGCTAGTCAGAATG

EST: gi|32834213|gb|CD973891.1|CD973891

EST:     AAAGATATGACTGATA                         GTCCTGGAAAATCTTTGTTGACACGACGGCCAAAGCATGCTAGTCAGAATG
genomic: AAAGATATGACTGATAgtatgtcacg ... tctcaaacagGTCCTGGACAATCTTTGTTGACACGACGGCCAAAGCATGCTAGTCAGAATG

EST: gi|32832507|gb|CD972185.1|CD972185

EST:     TATCCTATCTGGGACGTTTCTTCTTCACAAGACAAAAGATATGACTGATA                         GTCCTGGAAAATCTTTGTTGACACGACGGCCAAAGCATGCTAGTCAGAATG
genomic: TATCCTATCTGGGACGTTTCTTCTTCACAAGACAAAAGATATGACTGATAgtatgtcacg ... tctcaaacagGTCCTGGACAATCTTTGTTGACACGACGGCCAAAGCATGCTAGTCAGAATG

EST: gi|32833802|gb|CD973480.1|CD973480

EST:     TATCCTATCTGGGACGTTTCTTCTTCACAAGACAAAAGATATGACTGATA                         GTCCTGGAAAATCTTTGTTGACACGACGGCCAAAGCATGCTAGTCAGAATG
genomic: TATCCTATCTGGGACGTTTCTTCTTCACAAGACAAAAGATATGACTGATAgtatgtcacg ... tctcaaacagGTCCTGGACAATCTTTGTTGACACGACGGCCAAAGCATGCTAGTCAGAATG

EST: gi|78093188|gb|DV521562.1|DV521562

EST:     AAGACAAAAGATATGACTGATA                         GTCCTGGACAATCTTTGTTGACACGACGGCCAAAGCATGCTAGTCAGAATG
genomic: AAGACAAAAGATATGACTGATAgtatgtcacg ... tctcaaacagGTCCTGGACAATCTTTGTTGACACGACGGCCAAAGCATGCTAGTCAGAATG

EST: gi|60355925|gb|DN222898.1|DN222898

EST:     TATCCTATCTGGGACGTTTCTTCTTCACAAGACAAAAGATATGACTGATA                         GTCCTGGACAATCTTTGTTGACACGACGGCCAAAGCATGCTAGTCAGAATG
genomic: TATCCTATCTGGGACGTTTCTTCTTCACAAGACAAAAGATATGACTGATAgtatgtcacg ... tctcaaacagGTCCTGGACAATCTTTGTTGACACGACGGCCAAAGCATGCTAGTCAGAATG

EST: gi|60355918|gb|DN222891.1|DN222891

EST:     TATCCTATCTGGGACGTTTCTTCTTCACAAGACAAAAGATATGACTGATA                         GTCCTGGACAATCTTTGTTGACACGACGGCCAAAGCATGCTAGTCAGAATG
genomic: TATCCTATCTGGGACGTTTCTTCTTCACAAGACAAAAGATATGACTGATAgtatgtcacg ... tctcaaacagGTCCTGGACAATCTTTGTTGACACGACGGCCAAAGCATGCTAGTCAGAATG

EST: gi|32835880|gb|CD975558.1|CD975558

EST:     TATCCTATCTGGGACGTTTCTTCTTCACAAGACAAAAGATATGACTGATA                         GTCCTGGAAAATCTTTGTTGACACGACGGCCAAAGCATGCTAGTCAGAATG
genomic: TATCCTATCTGGGACGTTTCTTCTTCACAAGACAAAAGATATGACTGATAgtatgtcacg ... tctcaaacagGTCCTGGACAATCTTTGTTGACACGACGGCCAAAGCATGCTAGTCAGAATG

EST: gi|5762112|gb|AI967160.1|AI967160

EST:     AAAAGATATGACTGATA                         GTCCTGGACAATCTTTGTTGACACGACGGCCAAAGCATGCTAGTCAGAACG
genomic: AAAAGATATGACTGATAgtatgtcacg ... tctcaaacagGTCCTGGACAATCTTTGTTGACACGACGGCCAAAGCATGCTAGTCAGAATG

EST: gi|5846795|gb|AI999878.1|AI999878

EST:     TATCCTATCTGGGACGTTTCTTCTTCACAAGACAAAAGATATGACTGATA                         GTCCTGGACAATCTTTGTTGACACGACGGCCAAAGCATGCTAGTCAGAACG
genomic: TATCCTATCTGGGACGTTTCTTCTTCACAAGACAAAAGATATGACTGATAgtatgtcacg ... tctcaaacagGTCCTGGACAATCTTTGTTGACACGACGGCCAAAGCATGCTAGTCAGAATG

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: 47 (upstream exon), 47 (downstream exon)
Score: 75

GACCATCAAAATCCAACACAAATTGTTACAGAGATGTGTGGCTTCATGACTATCCTATCTGGGACGTTTCTTCTTCACAAGACAAAAGATATGACTGATAgtatgtcacg ... tctcaaacagGTCCTGGACAATCTTTGTTGACACGACGGCCAAAGCATGCTAGTCAGAATGCGTTTGCAATTGAAGTGATGCCACTAAAATGTCAAGATTATATAGATGA

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 82

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 98