ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GATTTACTGCAAAAATCAAATGCAACTGACGCTTCAGGAAATGTGATACTTAGTGACTTTGGTGTCCACATGCAGCAGAAGgtatctcttgttaaatcccttgtgaaatagattttgtacatagcatctttgaaggtctgtataagggtataaactatatagtacatatgaaattatagac...

Basic information

species	Zea mays
transcript	GRMZM2G127717_T01
intron #	12
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G127717_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os09g24910.2 (Oryza sativa), 5'ss of exon 12

GATTTACTGCAAAAATCAAATGCAACTGACGCTTCAGGAAATGTGATACTTAGTGACTTTGGTGTCCACATGCAGCAGAAGgtatctcttg---ttaaatcccttgtg--aaatagattttgtacatagcatctttgaaggtctgtat-aagggtataaactatatagtacatatgaaattatagac
||||||||||||||||||||||||||||| || ||||||||||| ||||||||||||||||||||||||||||| |||||||||| | ||    ||||| ||| |  |  ||| |||||||| |  |||||||||  |   |   ||| |    | | |   | | | |||| | | |         
GATTTACTGCAAAAATCAAATGCAACTGATGCATCAGGAAATGTAATACTTAGTGACTTTGGTGTCCACATGCAACAGAAGgtatgttttcatcttaaaccccctcgggcaaacagattttgcatttagcatcttctattattattattattatttttagaaacacaatacaaacgcaggc------

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|56382617|gb|CV985286.1|CV985286

EST:     CTTCAGGAAATGTGATACTTAGTGACTTTGGTGTCCACATGCAGCAGAAG                         ATCAAGAAGCATTTCAAGGACATCGGTGTTCCCGCTGATCTAAAATACATT
genomic: CTTCAGGAAATGTGATACTTAGTGACTTTGGTGTCCACATGCAGCAGAAGgtatctcttg ... caccttacagATCAAGAAGCATTTCAAGGACATCGGTGTTCCCGCTGATCTAAAATACATT

EST: gi|76283550|gb|DV023118.1|DV023118

EST:     AATGTGATACTTAGTGACTTTGGTGTCCACATGCAGCAGAAG                         ATCAAGAAGCATTTCAAGGACATCGGTGTTCCCGCTGATCTAAAATACATT
genomic: AATGTGATACTTAGTGACTTTGGTGTCCACATGCAGCAGAAGgtatctcttg ... caccttacagATCAAGAAGCATTTCAAGGACATCGGTGTTCCCGCTGATCTAAAATACATT

EST: gi|78021223|gb|DV489610.1|DV489610

EST:     CTTCAGGAAATGTGATACTTAGTGACTTTTGTGTCCACATGCAGCAGAAG                         ATCAAGAAGCATTTCAAGGACATCGGTGTTCCTGCTGATCTAAAATACATT
genomic: CTTCAGGAAATGTGATACTTAGTGACTTTGGTGTCCACATGCAGCAGAAGgtatctcttg ... caccttacagATCAAGAAGCATTTCAAGGACATCGGTGTTCCCGCTGATCTAAAATACATT

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), 44 (downstream exon)
Score: 20

GATTTACTGCAAAAATCAAATGCAACTGACGCTTCAGGAAATGTGATACTTAGTGACTTTGGTGTCCACATGCAGCAGAAGgtatctcttg ... caccttacagATCAAGAAGCATTTCAAGGACATCGGTGTTCCCGCTGATCTAAAATACATTGATCCAACATATATGGTTCGGGCCTGCCGGGCAAATGCATCTGATGCTA

Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 13

Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 23