ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGTTGAGTCTCTAGCAAATGAGGTCCGAGCAGCTAGTTTTGTAAATATCGACGACGTTGTTGCATTTGTAAACTGGCTTGATGAGGAACTATCCTTCTTGgtaagcttatctatttttttttcaatgcaacacatgacaaaatagttagtactgaaaaagggtcaaataacgttttag

Basic information

species	Oryza sativa
transcript	LOC_Os12g01449.1
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os12g01449.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G396927_T01 (Zea mays), 5'ss of exon 2

TGTTGAGTCTCTAGCAAATGAGGTCCGAGCAGCTAGTTTTGTAAATATCGACGACGTTGTTGCATTTGTAAACTGGCTTGATGAGGAACTATCCTTCTTGgtaagcttatctatttttttttcaatgcaacac----atgacaaaatagttagtactgaaaaagggtcaaata---acgttttag
||||||||||||||||||||||||||||||||| || ||||||||||| || || ||||||||||||||||| ||| | ||||||||  |||| ||||||||||||    | |        || || | ||||     | ||||| ||     || || |     | || ||    || ||||||
TGTTGAGTCTCTAGCAAATGAGGTCCGAGCAGCAAGCTTTGTAAATATTGATGATGTTGTTGCATTTGTAAATTGGTTGGATGAGGAGTTATCTTTCTTGgtaagcagcccgaacaggccctccatactacacctttgttacaaagtaccagttattgtacttatgacacattttcacattttag

upper sequence: LOC_Os12g01449.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G062738_T01 (Zea mays), 5'ss of exon 5

TGTTGAGTCTCTAGCAAATGAGGTCCGAGCAGCTAGTTTTGTAAATATCGACGACGTTGTTGCATTTGTAAACTGGCTTGATGAGGAACTATCCTTCTTGgtaagcttatctatttttttttcaatgcaacac----atgacaaaatagttagtactgaaaaagggtcaaataacgttttag------------------------
|||||| |||||||||||||||||||||||||| || ||  ||||||| || |||||||||||||||||||| ||| | ||||||||  | || ||||||||||||    | |   |    |  || ||| ||     | |  || |||  | || || |     | || ||    |  ||                         
TGTTGAATCTCTAGCAAATGAGGTCCGAGCAGCAAGCTTCATAAATATTGATGACGTTGTTGCATTTGTAAATTGGTTGGATGAGGAGTTGTCTTTCTTGgtaagcagcccgaacatgcccttcatacaatacctctgtcatgaagtagcaattattgtacttatgacacatgttctagtactaaagaggatcaacaaaattttag

upper sequence: LOC_Os12g01449.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA01G22620.1 (Glycine max), 5'ss of exon 5

TGTTGAGTCTCTAGCAAATGAGGTCCGAGCAGCTAGTTTTGTAAATATCGACGACGTTGTTGCATTTGTAAACTGGCTTGATGAGGAACTATCCTTCTTGgtaagcttatctatttttttttcaatgcaacacatgacaaaatagttagtactgaaaaagggtcaaataacgttttag------------------------
|||   |||  | |||  ||| || ||||||||    ||   | ||||  | ||| | || || ||||| |||||||| ||||||||||| |||||||||||| || | |   | |  ||    || ||  |    | |   | || || |  | | |   |||||  | | || |                          
TGTCATGTCCTTGGCAGCTGAAGTTCGAGCAGCCTCCTTCTCAGATATTAATGACTTGGTGGCCTTTGTGAACTGGCTAGATGAGGAACTTTCCTTCTTGgtatgcctttaggtgtcattacatattcattagtaaagacttttgtgagcaa-gcacagaagtcaa-cacctttgtgctcgctaaaaaatttaaaccattcc

upper sequence: LOC_Os12g01449.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA20G32630.1 (Glycine max), 5'ss of exon 4

TGTTGAGTCTCTAGCAAATGAGGTCCGAGCAGCTAGTTTTGTAAATATCGACGACGTTGTTGCATTTGTAAACTGGCTTGATGAGGAACTATCCTTCTTGgtaagcttatctat--ttttttttcaat-----gcaacacatgacaaaatagttagtactgaaaaagggtc---aaataacgttttag------------
|||    ||  | |||| ||| ||  |||||||    ||    || || || ||  | || || ||||| |||||||| ||||||||||| ||||||||||||||  |   | |  ||| |  || ||      |||      | |||  | ||  ||  ||     | ||     | || |  |               
TGTCATCTCCTTGGCAACTGAAGTTAGAGCAGCCTCGTTCTCTAAGATTGAAGATCTGGTGGCTTTTGTGAACTGGCTAGATGAGGAACTTTCCTTCTTGgtaagtgttagtgtcatttctcctccatcattaacaagcttctaaaaacaaattcatatagattgtagatcttgggagaaggcatggaagtgtatccttt

upper sequence: LOC_Os12g01449.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA02G11260.1 (Glycine max), 5'ss of exon 5

TGTTGAGTCTCTAGCAAATGAGGTCCGAGCAGCTAGTTTTGTAAATATCGACGACGTTGTTGCATTTGTAAACTGGCTTGATGAGGAACTATCCTTCTTGgtaagcttatctatttttttttcaatgcaacacatgacaaaatagttagtactgaaaaagggtcaaataacgttttag------------------------
|||   |||  | |||  ||| || ||||||||    ||   | ||||  | ||| | || || ||||| |||||||| ||||||||||| |||||||||||| || | |   | |  ||    ||  | ||    | |   | || || |  | | |   ||||   | | || |                          
TGTCATGTCCTTGGCAGCTGAAGTTCGAGCAGCCTCCTTCTCAGATATTAATGACTTGGTGGCCTTTGTGAACTGGCTAGATGAGGAACTTTCCTTCTTGgtatgcctttaggtgtcattacatattaatcagtgaagatttttgtgagcaa-gcacagaagtcag-cacctttgtgctctctaaaaaattcaaaccattcc

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|29625752|gb|CB630763.1|CB630763

EST:     GTAAACTGGCTTGATGAGGAACTATCCTTCTTG                         GTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACT
genomic: GTAAACTGGCTTGATGAGGAACTATCCTTCTTGgtaagcttat ... aacgttttagGTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACT

EST: gi|29665532|gb|CB661807.1|CB661807

EST:     GTTGTTGCATTTGTAAACTGGCTTGATGAGGAACTATCCTTCTTG                         GTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACT
genomic: GTTGTTGCATTTGTAAACTGGCTTGATGAGGAACTATCCTTCTTGgtaagcttat ... aacgttttagGTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACT

EST: gi|29675785|gb|CB672060.1|CB672060

EST:     TTGTTGCATTTGTAAACTGGCTTGATGAGGAACTATCTTTCTTG                         GTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACT
genomic: TTGTTGCATTTGTAAACTGGCTTGATGAGGAACTATCCTTCTTGgtaagcttat ... aacgttttagGTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACT

EST: gi|29674414|gb|CB670689.1|CB670689

EST:     ACGACGTTGTTGCATTTGTAAACTGGCTTGATGAGGAACTATCCTTCTTG                         GTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACT
genomic: ACGACGTTGTTGCATTTGTAAACTGGCTTGATGAGGAACTATCCTTCTTGgtaagcttat ... aacgttttagGTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACT

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: 72 (upstream exon), 74 (downstream exon)
Score: 42

TGTTGAGTCTCTAGCAAATGAGGTCCGAGCAGCTAGTTTTGTAAATATCGACGACGTTGTTGCATTTGTAAACTGGCTTGATGAGGAACTATCCTTCTTGgtaagcttat ... aacgttttagGTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACTGATGCACTAAGAGAGGCAGCCTTTGAGTATCAAGACCTGCTAAAATTAG