ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtatgctctaactcttgggactacttctgttagaaaattctgggcatctttaacttatctactgacatatttcttatgcagGGATCGATGATACCTTACCAATAGAACCATGGTTTATTGGTGGACCTGTGATTAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATTCCAACAG

Basic information

species	Oryza sativa
transcript	LOC_Os10g32730.2
intron #	7
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os10g32730.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G027115_T02 (Zea mays), 3'ss of exon 8

gtatgctctaactcttgggact------acttctgtt----------agaaaattctgggcatctttaacttatctactgacatatttcttatgcagGGATCGATGATACCTTACCAATAGAACCATGGTTTATTGGTGGACCTGTGATTAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATTCCAACAG----
||||| || || ||||| |  |      |||| ||||          |||| ||| || |  | || | |||||||   || | || |  | ||||||||| || | ||||||||||||||||||||||||||||||||| |||||||| ||||||||||||||||||||||||||||||||||| |||||||    
gtatgttcaaagtcttgagcttctctatacttttgttcattgagaagagaacattatgtgggttttaagcttatctgtcgataaatgtgctgtgcagGGATTGAAGGTACCTTACCAATAGAACCATGGTTTATTGGTGGGCCTGTGATCAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATACCAACAGGTAT

upper sequence: LOC_Os10g32730.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G027115_T01 (Zea mays), 3'ss of exon 8

gtatgctctaactcttgggact------acttctgtt----------agaaaattctgggcatctttaacttatctactgacatatttcttatgcagGGATCGATGATACCTTACCAATAGAACCATGGTTTATTGGTGGACCTGTGATTAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATTCCAACAG
||||| || || ||||| |  |      |||| ||||          |||| ||| || |  | || | |||||||   || | || |  | ||||||||| || | ||||||||||||||||||||||||||||||||| |||||||| ||||||||||||||||||||||||||||||||||| |||||||
gtatgttcaaagtcttgagcttctctatacttttgttcattgagaagagaacattatgtgggttttaagcttatctgtcgataaatgtgctgtgcagGGATTGAAGGTACCTTACCAATAGAACCATGGTTTATTGGTGGGCCTGTGATCAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATACCAACAG

upper sequence: LOC_Os10g32730.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT4G21470.1 (Arabidopsis thaliana), 3'ss of exon 6

--------gtatgctctaactcttgggactacttctgttagaaaat--tctgggcatcttta-------acttatctactgacatatttct-tatgcagGGATCGATGATACCTTACCAATAGAACCATGGTTTATTGGTGGACCTGTGATTAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATTCCAACAG
          |  |   ||||||    | |||| || ||     ||    ||  |||||          |||| | |||      |||| | | ||||||||| ||  | || |||||||| || ||||||  |||||| || || || || ||||||||||||||||| ||||||||||| ||||| || || |
gtaaaaattcactcatgaactctgttcaatactcctcttccttgataacatgttcatctcggtaatgagacttttataccttgtaatttgtatttgcagGGATAGAGAACACTTTACCAATTGATCCATGGCATATTGGAGGTCCAGTCATCAAAGGATTTGGCCGTGGCTCTAAAGTACTCGGAATCCCCACCG

upper sequence: LOC_Os10g32730.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv00s0181g00140.t01 (Vitis vinifera), 3'ss of exon 7

-------------gtatgctctaac---tcttgggactacttctgttagaaaattctgggcatctttaactt--atct-actgacatatttctta-tgcagGGATCGATGATACCTTACCAATAGAACCATGGTTTATTGGTGGACCTGTGATTAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATTCCAACAG
              ||     || |   |  |   ||   | ||  ||      ||| || ||   | | ||  |||| |   |   |||| | | ||||||| |||| |||||||||||| |||| || |||| ||| ||||| ||||| ||||| |||||||| ||||| || || ||||| ||| | |||||||
gtaaacctctcagatacttcttatcatattctcaaacatttcctagtaaggttctcttggtattacttattttcatctgaactattgatttgtaactgcagGGGTCGAGGATACCTTACCAGTAGAGCCTTGGTATATAGGTGGGCCTGTCATTAAGGGATTTGGTCGTGGGTCAAAGGTACTTGGAGTCCCAACAG

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|29671819|gb|CB668094.1|CB668094

EST:     CCTCCTTGACGTAAAGCCTGAAAAATGGGGATTGCCACCATTTAGTGATT                         GGATCGATGATACCTTACCAATAGAACCATGGTTTATTGGTGGACCTGTGA
genomic: CCTCCTTGACGTAAAGCCTGAAAAATGGGGATTGCCACCATTTAGTGATTgtatgctcta ... tcttatgcagGGATCGATGATACCTTACCAATAGAACCATGGTTTATTGGTGGACCTGTGA

EST: gi|29629324|gb|CB634335.1|CB634335

EST:     CCTCCTTGACGTAAAGCCTGAAAAATGGGGATTGCCACCATTTAGTGATT                         GGATTGATGATACCTTACCAATAGAACCATGGTTTATTGGTGGACCTGTGA
genomic: CCTCCTTGACGTAAAGCCTGAAAAATGGGGATTGCCACCATTTAGTGATTgtatgctcta ... tcttatgcagGGATCGATGATACCTTACCAATAGAACCATGGTTTATTGGTGGACCTGTGA

EST: gi|29684882|gb|CB681157.1|CB681157

EST:     CCTCCTTGACGTAAAGCCTGAAAAATGGGGATTGCCACCATTTAATGATT                         GGATCGATGATACCTTACCAATAGAACCATGGTTTATTGGTGGACCTGTGA
genomic: CCTCCTTGACGTAAAGCCTGAAAAATGGGGATTGCCACCATTTAGTGATTgtatgctcta ... tcttatgcagGGATCGATGATACCTTACCAATAGAACCATGGTTTATTGGTGGACCTGTGA

EST: gi|29623338|gb|CB628349.1|CB628349

EST:     CCTCCTTGACGTAAAGCCTGAAAAATGGGGATTGCCACCATTTAGTGATT                         GGATTGATGATACCTTACCAATAGAACCATGGTTTATTGGTGGACCTGTGA
genomic: CCTCCTTGACGTAAAGCCTGAAAAATGGGGATTGCCACCATTTAGTGATTgtatgctcta ... tcttatgcagGGATCGATGATACCTTACCAATAGAACCATGGTTTATTGGTGGACCTGTGA

EST: gi|33680484|gb|CF308723.1|CF308723

EST:     CCTCCTTGACGTAAAGCCTGAAAAATGGGGATTGCCACCATTTAGTGATT                         GGATCGATGATACCTTACCAATAGAACCATGGTTTATTGGTGGACCTGTGA
genomic: CCTCCTTGACGTAAAGCCTGAAAAATGGGGATTGCCACCATTTAGTGATTgtatgctcta ... tcttatgcagGGATCGATGATACCTTACCAATAGAACCATGGTTTATTGGTGGACCTGTGA

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: 55 (upstream exon), 63 (downstream exon)
Score: 33

GTCCCCAAAAGGACTGCTGAATTCAGTTCTGCTGATGAGGTGATCAATTCCCTCCTTGACGTAAAGCCTGAAAAATGGGGATTGCCACCATTTAGTGATTgtatgctcta ... tcttatgcagGGATCGATGATACCTTACCAATAGAACCATGGTTTATTGGTGGACCTGTGATTAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATTCCAACAG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ctgttagaaaattctgggcatctttaacttatctactgacatatttcttatgcagGGATCGATGATACCTTACCAATAGAACCATGGTTTATTGGTGGACCTGTGATTAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATTCCAACAG