ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCCCTCATGCTCCTTCGATGAGTGAAGAAGAAATAAATGCTCTTCCTGTATTCAAATACAAGGTTCAGGCACATCAGGGAAGTGCCTCTTTCCGAAAAAGgtaagatgtattatccttttggctacattttttagctggcatagcaaacgcatgataagtctacaactgccttccatctctgataagtaaccaaccatataattccgaatttgtctactttgtatgggatgtaactaaccatttaattcttttgattctatag

Basic information

species	Oryza sativa
transcript	LOC_Os03g16570.3
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os03g16570.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G337425_T03 (Zea mays), 5'ss of exon 5

GCCCTCATGCTCCTTCGATGAGTGAAGAAGAAATAAATGCTCTTCCTGTATTCAAATACAAGGTTCAGGCACATCAGGGAAGTGCCTCTTTCCGAAAAAGgtaagat-gtattatccttttggctacattttttagctggcatagcaaacgcatgataagtctacaactgccttccatctctgataagtaaccaaccatataattccgaatttgtctactttgtatgggatgtaactaaccatttaattcttttgattctatag
|||| |||||||| || ||||||||||||||||||||| |||||||||| |||||||| || ||||||||||| ||| |   | || ||  |||||||||||||    | ||| |||||| || |  |||| ||      |||| ||    |||    |||      | |  || |   ||  | |  | |||||| || |||||| ||| | |          |   || |||| |     | ||||  || |  | | ||||
GCCCACATGCTCCATCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGTTCAGGCACAACAGAGGCATCCCCCTGCCCGAAAAAGgtaaagccgaattgtcctttgggttg-atttgtt------catatcac---catatcgagttggttccagtatttcccatc-aacacatgaccaac-atttaattctgaaatgg--------agacatgaagtaatt--ttttctaatgtttgttttccaatag

upper sequence: LOC_Os03g16570.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G492252_T02 (Zea mays), 5'ss of exon 5

GCCCTCATGCTCCTTCGATGAGTGAAGAAGAAATAAATGCTCTTCCTGTATTCAAATACAAGGTTCAGGCACATCAGGGAAGTGCCTCTTTCCGAAAAAGgtaagatgtattatccttttggctacattttttagctggcatagcaaacgcatgataagtcta--caactgccttccatctctgataagtaaccaaccatataattccgaatttgtctactttgtatgggatgtaactaaccatttaattcttttgattctatag------
|||  |||| |||||| ||||||||||||||||||||| |||||||||| |||||||| || || |||||||| ||||||| |||| ||  ||||||||||||||| | |||||||||| ||     || || |  ||||          |||   |||| |   | | |  || |||||    | || | ||||| ||| |||||| ||||| |   || | |  |    |||  |||   || |  ||||   || | | |        
GCCTGCATGTTCCTTCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGTCCAGGCACAGCAGGGAAATGCCCCTGCCCGAAAAAGgtaagacgaattatcctttgggtcgatttgttcatatggc----------cataccaagtttgttccagtatctcccatcatcaacaaatgaccaaacatttaattctgaattggag-acatggattaatttgtctcta-tgatgtgtttctaacgaatgtttttcaacag

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|86499240|gb|CI141873.1|CI141873

EST:     GGAAGTGCCTCTTTCCGAAAAAG                         TGATGGACCATCTCAACCATCTGTTTCTTCTACTGAATCTGGCAATGAG
genomic: GGAAGTGCCTCTTTCCGAAAAAGgtaagatgta ... gattctatagTGATGGACCATCTCAACCATCTGTTTCTTCTACTGAATCTGGCAATGAG

EST: gi|218498707|gb|FG952314.1|FG952314

EST:     TTCAAATACAAGGTTCAGGCACATCAGGGAAGTGCCTCTTTCCGAAAAAG                         TGATGGACCATCTCAACCATCTGTTTCTTCTACTGAATCTGGCAATGAGAA
genomic: TTCAAATACAAGGTTCAGGCACATCAGGGAAGTGCCTCTTTCCGAAAAAGgtaagatgta ... gattctatagTGATGGACCATCTCAACCATCTGTTTCTTCTACTGAATCTGGCAATGAGAA

EST: gi|87009256|gb|CI276570.1|CI276570

EST:     TCAGGGAAGTGCCTCTTTCCGAAAAAG                         TGATGGACCATCTCAACCATCTGTTTCTTCTACTGAATCTGGCAATGAG
genomic: TCAGGGAAGTGCCTCTTTCCGAAAAAGgtaagatgta ... gattctatagTGATGGACCATCTCAACCATCTGTTTCTTCTACTGAATCTGGCAATGAG

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: 49 (upstream exon), 69 (downstream exon)
Score: 17

GCCCTCATGCTCCTTCGATGAGTGAAGAAGAAATAAATGCTCTTCCTGTATTCAAATACAAGGTTCAGGCACATCAGGGAAGTGCCTCTTTCCGAAAAAGgtaagatgta ... gattctatagTGATGGACCATCTCAACCATCTGTTTCTTCTACTGAATCTGGCAATGAG