ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGGTGGGTACATGGTAGCATTTGCCGGTAGGAAGTATGCAGCCCGGTCTGTTCCAACCTTTGTGTCCAATTCCTCATATACAGTCTCCAGCTTCACCCTGgtatggaaccaaagatgtaccactatgcccatcacctatcaacttgtgacacaaagaatattcttaatgttgtctccatctgatgatacttgtctag

Basic information

species	Oryza sativa
transcript	LOC_Os03g44560.1
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os03g44560.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G166109_T04 (Zea mays), 5'ss of exon 3

TGGTGGGTACATGGTAGCATTTGCCGGTAGGAAGTATGCAGCCCGGTCTGTTCCAACCTTTGTGTCCAATTCCTCATATACAGTCTCCAGCTTCACCCTGgtatggaaccaaagatgtaccactatgcccatcacctatcaacttgtgacacaaagaat---attcttaatgttgtctc-catctgatgatacttgtctag
|||||| |  |||||||||||||| |||||||||||||||||  | ||  | || |  || || |||||  |||||  |||||| |||||||||||||||||| | | | | | | | || || ||| ||  ||    | |||  ||  || |     |   | ||||| || |   |  |  | || ||| |||    ||
TGGTGGATTTATGGTAGCATTTGCTGGTAGGAAGTATGCAGCTAGATCAATCCCGATATTCGTATCCAACACCTCAGTTACAGTGTCCAGCTTCACCCTGgtacgaatcgataaacgcactaccatgtccgccatacctaaacacgtagcagacgagttccgaatcttactgctacttgacgacggacgattcttccgcag

upper sequence: LOC_Os03g44560.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G023392_T01 (Zea mays), 5'ss of exon 2

TGGTGGGTACATGGTAGCATTTGCCGGTAGGAAGTATGCAGCCCGGTCTGTTCCAACCTTTGTGTCCAATTCCTCATATACAGTCTCCAGCTTCACCCTGgtatggaaccaaa--gatgtaccactatgcccatcacctatcaacttgtgacacaaagaatattcttaatgttgtctccatctgatgatacttgtctag
|||||| | |||||||||||||||||| ||||||||||||||  | ||| |||| |  ||||| |||||  |||||   ||||| ||||||||||| |||||| |   | | |   |   || |  ||| ||| ||  | | |||  |  ||| | |     |||| ||| || |  | | |||| ||| ||| | |||
TGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCTAGATCTATTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcgagacaaacacactatcatgtccagcatatctaaacacgcaacagagaa---gttctgaatcttattgcgacctgacgattcttctgtag

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|87021476|gb|CI274083.1|CI274083

EST:     TTCCAACCTTTGTGTCCAATTCCTCATATACAGTCTCCAGCTTCA-CCTG                         GTTCTTGAGTTCAATAAAGGCAGGCTTCAAAACTTGCATTGGAAGAAGGAT
genomic: TTCCAACCTTTGTGTCCAATTCCTCATATACAGTCTCCAGCTTCACCCTGgtatggaacc ... acttgtctagGTTCTTGAGTTCAATAAAGGCAGGCTTCAAAACTTGCATTGGAAGAAGGAT

EST: gi|87021716|gb|CI276115.1|CI276115

EST:     TTCCAACCTTTGTGTCCAATTCCTCATATACAGTCTCCAGCTTCACNCTG                         GTTCTTGAGTTCAATAAAGGCGGGCTTCAACACTTGCATTGGAAGAAGGAT
genomic: TTCCAACCTTTGTGTCCAATTCCTCATATACAGTCTCCAGCTTCACCCTGgtatggaacc ... acttgtctagGTTCTTGAGTTCAATAAAGGCAGGCTTCAAAACTTGCATTGGAAGAAGGAT

EST: gi|58592962|gb|CF991270.1|CF991270

EST:     -TCCAACC-TTGTGTCCAATTCCTCATATACAGTCTCCAGCTGCACCCTG                         GTTCTTGAGTTCAATAAAGGCAGGCTTCAAAACTTGCATTGGAAGAAGGAT
genomic: TTCCAACCTTTGTGTCCAATTCCTCATATACAGTCTCCAGCTTCACCCTGgtatggaacc ... acttgtctagGTTCTTGAGTTCAATAAAGGCAGGCTTCAAAACTTGCATTGGAAGAAGGAT

EST: gi|89199038|gb|CI253112.1|CI253112

EST:     TTCCAACCTTTGTGTCCAATTCCTCATATACAGTCTCCAGCTTCACCCTG                         GTTCTTGAGTTCAATAAAGGCAGGCTTCAAAACTTGCATTGGAAGAAGGAT
genomic: TTCCAACCTTTGTGTCCAATTCCTCATATACAGTCTCCAGCTTCACCCTGgtatggaacc ... acttgtctagGTTCTTGAGTTCAATAAAGGCAGGCTTCAAAACTTGCATTGGAAGAAGGAT

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 1 RNA-Seqlibrary.

Block sizes: 75 (upstream exon), 49 (downstream exon)
Score: 10

TGGTGGGTACATGGTAGCATTTGCCGGTAGGAAGTATGCAGCCCGGTCTGTTCCAACCTTTGTGTCCAATTCCTCATATACAGTCTCCAGCTTCACCCTGgtatggaacc ... acttgtctagGTTCTTGAGTTCAATAAAGGCAGGCTTCAAAACTTGCATTGGAAGAAGGATGGCTGTGGTGCTTGCGCGAAATCTTCAAGCCTTGTTTGCATCGGCAAGC