ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CAGCAGACGATGCTCTGAAACACAAATGGTTCTCTGAAGTTCCTCTGCCTAAATCAAAAGACTTCATGCCAACATTTCCTGCTCTTAATGAACTTGACAGgtatttttttaaccatctcctttcactctggtccaatgctacgttgttctatttcataaatgcaaaattgatttccatatataatttgaaattacacag

Basic information

species	Zea mays
transcript	GRMZM2G139038_T03
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G139038_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os04g41100.6 (Oryza sativa), 5'ss of exon 7

CAGCAGACGATGCTCTGAAACACAAATGGTTCTCTGAAGTTCCTCTGCCTAAATCAAAAGACTTCATGCCAACATTTCCTGCTCTTAATGAACTTGACAGgtattttttt--aaccatctcctttcactctggtccaatgctacgttgttctatttcataaatgcaaaattgatttccatatataatttgaaattacacag
||||||| | |||| || | ||  | ||||||  |||||||||||| ||||||||||| || |||||||||||||| |||||||| |||||| | |||||||| || ||   |||||| |  | |   | | ||       ||  |   | | ||||||  | |  ||||| |||| | ||         ||||| |||||
CAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCTCTACCTAAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttcgcaaccatttaatctacttgtagtgttgc-ttaaatatctttgtttcatgta-gtgaaatttattttccta---------aaattccacag

upper sequence: GRMZM2G139038_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv01s0010g02550.t01 (Vitis vinifera), 5'ss of exon 5

CAGCAGACGATGCTCTGAAACACAAATGGTTCTCTGAAGTTCCTCTGCCTAAATCAAAAGACTTCATGCCAACATTTCCTGCTCTTAATGAACTTGACAGgtatttttttaaccatctcctttcactctggtccaatgctacgttgt--tctatttcataaatgcaaaattgatttccatatataatttgaaattacacag-------
|||| || | |||||| || ||  | ||||||   ||||||||||| || ||||| ||||| |||||||| || ||||||||||   |||  |  |||||||||    || ||| | | | |  ||| |     |  | |  || |   |  | ||  ||  |   | |   ||||| | | |||| ||    | |            
CAGCTGAAGCTGCTCTTAACCATGATTGGTTCCGCGAAGTTCCTCTTCCCAAATCTAAAGATTTCATGCCTACTTTTCCTGCTCAGCATGCCCAGGACAGgtatc---ttgaccctatacatg-actttaaatgagagatgagtaggagtgcagtttttattttttatagcaatttcta-aaataaattttgttcatttgattatcag

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|67025629|gb|CO454378.1|CO454378

EST:     AAATCAAAAGACTTCATGCCAACATTTCCTGCTCTTAATGAACTTGACAG                         GCGTACCAAACGTTATCTGAAGAGTCCTGATCCTCTGGAAGAGCAACGTCT
genomic: AAATCAAAAGACTTCATGCCAACATTTCCTGCTCTTAATGAACTTGACAGgtattttttt ... aattacacagGCGTACCAAACGTTATCTGAAGAGTCCTGATCCTCTGGAAGAGCAACGTCT

EST: gi|5608154|gb|AI901821.1|AI901821

EST:     TCAAAAG-CTTCATGCCAACATTTCCTGCTCTTAATGAACTTGCCAG                         GCGTACCAAACGTTATCTGAAGAGTCCTGATCCTCTGGAAGAGCAACGTCT
genomic: TCAAAAGACTTCATGCCAACATTTCCTGCTCTTAATGAACTTGACAGgtattttttt ... aattacacagGCGTACCAAACGTTATCTGAAGAGTCCTGATCCTCTGGAAGAGCAACGTCT

EST: gi|67019152|gb|CO447901.1|CO447901

EST:     TAATCAAAAGACTTCATGCCAACATTCCCTGCTCTTAATGAACTTGACAG                         GCGTACCAAACGTTATCTGAAGAGTCCTGATCCTCTGGAAGAGCAACGTCT
genomic: AAATCAAAAGACTTCATGCCAACATTTCCTGCTCTTAATGAACTTGACAGgtattttttt ... aattacacagGCGTACCAAACGTTATCTGAAGAGTCCTGATCCTCTGGAAGAGCAACGTCT

EST: gi|13388885|gb|BG462452.1|BG462452

EST:     AAATCAAAAGACTTCATGCCAACATTTCCTGCTCTTAATGAACTTGACAG                         GCGTACCAAACGTTATCTGAAGAGTCCTGATCCTCTGGAAGAGCAACGTCT
genomic: AAATCAAAAGACTTCATGCCAACATTTCCTGCTCTTAATGAACTTGACAGgtattttttt ... aattacacagGCGTACCAAACGTTATCTGAAGAGTCCTGATCCTCTGGAAGAGCAACGTCT

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), 49 (downstream exon)
Score: 137

CAGCAGACGATGCTCTGAAACACAAATGGTTCTCTGAAGTTCCTCTGCCTAAATCAAAAGACTTCATGCCAACATTTCCTGCTCTTAATGAACTTGACAGgtattttttt ... aattacacagGCGTACCAAACGTTATCTGAAGAGTCCTGATCCTCTGGAAGAGCAACGTCTGAAAGAACTGCAAGGGAACATAGGCAACCGTGGGCTTTTTGGCTGAACT

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 90

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100