ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gttcgttgccattttgaagtctgagtgcttatgtttgttgccgtagaaacattgagctgatcaatttccttttgcagCTACCTCAGACTAATCCTGGTCTAAACAATACTCCTTTCAAGTTCACTAAATATTCAAACGCATACATGCTTGTGTACATTCGCGAAAGTGACAAGGACA

Basic information

species	Oryza sativa
transcript	LOC_Os07g06950.1
intron #	13
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os07g06950.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G018508_T01 (Zea mays), 3'ss of exon 9

gttcgttgccattttgaagtctg-agtgcttatgtttgttgccgtagaaacattgagctgatcaatttccttttgcagCTACCTCAGACTAATCCTGGTCTAAACAATACTCCTTTCAAGTTCACTAAATATTCAAACGCATACATGCTTGTGTACATTCGCGAAAGTGACAAGGACA
||  ||| | ||||  ||| ||  |||  || | |||| |  | || ||||| ||| || | ||||| | ||||||||||||||||||| ||||||||  | ||||| ||||| |||||||| |||||||||||||| ||||||||||||||||||||||| ||||| ||||||||||
gtatgtttcaatttctaaggctacagttattgtctttggtatcttataaacactgaacttaccaattccattttgcagCTACCTCAGACAAATCCTGGCTTGAACAACACTCCCTTCAAGTTTACTAAATATTCAAATGCATACATGCTTGTGTACATTCGTGAAAGCGACAAGGACA

upper sequence: LOC_Os07g06950.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM5G864266_T01 (Zea mays), 3'ss of exon 15

gttcgttgccattttgaagtctga-gtgcttatgtttgttgccgtagaaacattgagctgatcaatttccttttgcagCTACCTCAGACTAATCCTGGTCTAAACAATACTCCTTTCAAGTTCACTAAATATTCAAACGCATACATGCTTGTGTACATTCGCGAAAGTGACAAGGACA
||  ||| |  |||  ||| ||    |  ||   |||| |  | || ||||||||| |  ||||||||| | ||||||||||||||||| ||||||||  ||||||| || || |||||||| |||||||||||||| ||||||||||||||||||||||| ||||||||||||||||
gtatgtttcactttctaaggctactattattgactttggtatcttataaacattgaacgtatcaatttcatgttgcagCTACCTCAGACAAATCCTGGCTTAAACAACACCCCATTCAAGTTTACTAAATATTCAAATGCATACATGCTTGTGTACATTCGTGAAAGTGACAAGGACA

upper sequence: LOC_Os07g06950.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G018508_T03 (Zea mays), 3'ss of exon 9

gttcgttgccattttgaagtctg-agtgcttatgtttgttgccgtagaaacattgagctgatcaatttccttttgcagCTACCTCAGACTAATCCTGGTCTAAACAATACTCCTTTCAAGTTCACTAAATATTCAAACGCATACATGCTTGTGTACATTCGCGAAAGTGACAAGGACA---------
||  ||| | ||||  ||| ||  |||  || | |||| |  | || ||||| ||| || | ||||| | ||||||||||||||||||| ||||||||  | ||||| ||||| |||||||| |||||||||||||| ||||||||||||||||||||||| ||||| ||||||||||         
gtatgtttcaatttctaaggctacagttattgtctttggtatcttataaacactgaacttaccaattccattttgcagctacctcagACAAATCCTGGCTTGAACAACACTCCCTTCAAGTTTACTAAATATTCAAATGCATACATGCTTGTGTACATTCGTGAAAGCGACAAGGACAAAATTATTT

upper sequence: LOC_Os07g06950.1 (Oryza sativa), 3'ss of exon 13
lower sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 12

--------gttcgttgccattttgaagtctga--gtgcttatgtttgttgccgtaga-aacattgagctg---------atcaatttcctt---ttgcagCTACCTCAGACTAATCCTGGTCTAAACAATACTCCTTTCAAGTTCACTAAATATTCAAACGCATACATGCTTGTGTACATTCGCGAAAGTGACAAGGACA
          | ||||  ||| | | |  | |   || || | | |   |  | |   || ||  ||| |             || | |||   |||||||| || || || ||||| ||| | || || ||||| ||||||||||| ||||| ||||||||||||||| | ||||| ||  | ||    ||||||||||
ttcagagtactagttgatattattatgctttatgatggttttttctagcgttgcaactaaaatccagccgtatttgtgcggtgatgttcttatcttgcagCTTCCACAAACAAATCCAGGTTTTAATAACACTCCCTTCAAGTTCACAAAATACTCAAACGCATACATGTTGGTGTATATCAGAGAGGCCGACAAGGACA

upper sequence: LOC_Os07g06950.1 (Oryza sativa), 3'ss of exon 13
lower sequence: PP1S42_181V6.1 (Physcomitrella patens), 3'ss of exon 12

------gttcgttgccattttgaagtctgag--tgcttatgttt-----------gttgccgtagaaac--attgagctgatcaatttcctttt---gcagCTACCTCAGACTAATCCTGGTCTAAACAATACTCCTTTCAAGTTCACTAAATATTCAAACGCATACATGCTTGTGTACATTCGCGAAAGTGACAAGGACA
      | | || |  | || ||||| ||||  ||||   | ||           |||  | ||   |   || ||    || || ||  ||||   |||||| || || || |||||  || | || || || || ||||||||||| |||||||| |||||||||||| | ||||| ||  | ||   ||| || ||||
tcttgcgattgtcgtaagtt-gaagtatgagaatgctccagctttcacttatgcggttatcttatctatttatggaagaaataaaattatttttctcgcagCTTCCACAAACGAATCCGTGTTTCAATAACACGCCCTTCAAGTTCACGAAATATTCGAACGCATACATGTTGGTGTATATCAGAGAGGCTGATAAAGACA

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|29630971|gb|CB635980.1|CB635980

EST:     AAGAGGATGCAAAGAGGGCATTGGAAGAGCAATATGGTGGTGAGGAGGAG                         CTACCTCAGACTAATCCTGGTCTAAACAATACTCCTTTCAAGTTCACTAAA
genomic: AAGAGGATGCAAAGAGGGCATTGGAAGAGCAATATGGTGGTGAGGAGGAGgttcgttgcc ... ccttttgcagCTACCTCAGACTAATCCTGGTCTAAACAATACTCCTTTCAAGTTCACTAAA

EST: gi|58668120|gb|CK056806.1|CK056806

EST:     AAGAGGATGCAAAGAGGGCATTGGAAGAGCAATATGGTGGTGAGGAGGAG                         CTACCTCAGACTAATCCTGGTCTAAACAATACTCCTTTCAAGTTCACTAAA
genomic: AAGAGGATGCAAAGAGGGCATTGGAAGAGCAATATGGTGGTGAGGAGGAGgttcgttgcc ... ccttttgcagCTACCTCAGACTAATCCTGGTCTAAACAATACTCCTTTCAAGTTCACTAAA

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: 73 (upstream exon), 75 (downstream exon)
Score: 26

GTTTAAGTTTGATGATGAGCGTGTAACAAAAGAGGATGCAAAGAGGGCATTGGAAGAGCAATATGGTGGTGAGGAGGAGgttcgttgcc ... ccttttgcagCTACCTCAGACTAATCCTGGTCTAAACAATACTCCTTTCAAGTTCACTAAATATTCAAACGCATACATGCTTGTGTACATTCGCGAAAGTGACAAGGACA

<

<

<

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gagtgcttatgtttgttgccgtagaaacattgagctgatcaatttccttttgcagCTACCTCAGACTAATCCTGGTCTAAACAATACTCCTTTCAAGTTCACTAAATATTCAAACGCATACATGCTTGTGTACATTCGCGAAAGTGACAAGGACA