ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaaaagacagagcctctcactgcctgacatcttcctacatctttagatatagttaatttgaatgtttttcctgttttttttttctttcagGTACAAGGTTTTTATAAATCCAAGCATTAGTGATGTCCTTTGCACTGCGACCGCTGAGGCATTAGCAATGGGTAAGTTTGTTGTCTGCGCAGACCACCCA

Basic information

species	Oryza sativa
transcript	LOC_Os11g05990.1
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os11g05990.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G175453_T02 (Zea mays), 3'ss of exon 7

-------------------------------------gtaaaagacagagcctctcactgcctgacatcttcctacatctttagatatagttaatttgaatgtttttcctgttttttttttctttcagGTACAAGGTTTTTATAAATCCAAGCATTAGTGATGTCCTTTGCACTGCGACCGCTGAGGCATTAGCAATGGGTAAGTTTGTTGTCTGCGCAGACCACCCA
                                      ||||   | |     ||  ||   || ||   |  || ||| ||   | | ||  |||||| ||| | |||   | ||   ||  | ||||||||||||||| ||||| |||||||| || || ||||| ||||| |||||||| |||||  |||| ||||| ||||| || || ||||| |||||||| 
gtacaaaccagaactactcagctcagttgccgttttcttaaacatctgtctgcctgcctatatggcacggtgttatatcatt--gtcttgtcgatttgattgtctgtccccatgttccgtt--tccagGTACAAGGTTTTCATAAACCCAAGCATCAGCGACGTCCTCTGCACCGCGACCGCGGAGGCGCTAGCGATGGGCAAGTTCGTGGTGTGCGCCGACCACCCG

upper sequence: LOC_Os11g05990.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA19G38720.1 (Glycine max), 3'ss of exon 6

gtaaaagacagagcctctcactgcctgacatcttcctacatctt---tagatatagttaatttgaa---tgttttt------cctgttttttttttctttcagGTACAAGGTTTTTATAAATCCAAGCATTAGTGATGTCCTTTGCACTGCGACCGCTGAGGCATTAGCAATGGGTAAGTTTGTTGTCTGCGCAGACCACCCA
   |||  || |  | |  ||  | |||    |||  |    ||   ||   | | |  || || |   ||||||         || || || ||| ||  |||||||| || ||||||||||| |||||||| ||||| || ||||| || || ||||||||| | || ||||| || ||||| || || || || || |||
--taaatgcacattcacctac-acatgattctttctcatgctttacatacccagactccatctggaacttgttttgattaaatttggttcttatttattgtagGTACAAAGTCTTTATAAATCCCAGCATTAGCGATGTGCTATGCACAGCTACAGCTGAGGCACTTGCCATGGGCAAATTTGTAGTTTGTGCTGATCATCCA

upper sequence: LOC_Os11g05990.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA03G36050.1 (Glycine max), 3'ss of exon 6

gtaaaagacagagcctctcactgcctgacatcttcctac---atct----ttagatatagttaatttgaatgtttttcctg-----ttttttttttctttcagGTACAAGGTTTTTATAAATCCAAGCATTAGTGATGTCCTTTGCACTGCGACCGCTGAGGCATTAGCAATGGGTAAGTTTGTTGTCTGCGCAGACCACCCA
   | | |     | |     | | | ||||   |  ||   ||||    || | | |  |||| ||   |  || |  ||      ||| |  || ||  |||||||| || ||||||||||| |||||||||||||| || ||||| || || ||||||||  | || ||||| || ||||| || || || || || |||
---acacatgattctttctcatcctttacatgcccagactcaatctggaatttgtttttattaagtttggttcttattttgacacactttatccttattgtagGTACAAAGTCTTTATAAATCCTAGCATTAGTGATGTGCTATGCACAGCTACAGCTGAGGCGCTTGCCATGGGCAAATTTGTAGTTTGTGCTGATCATCCA

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|27576595|gb|CA999289.1|CA999289

EST:     AACCTTAACTTTCATAAAGGCCGGGATCATGCGGATGATTCTCTTCATGG                         GTACAAGGTTTTTATAAATCCAAGCATTAGTGATGTCCTTTGCACTGCGAC
genomic: AACCTTAACTTTCATAAAGGCCGGGATCATGCGGATGATTCTCTTCATGGgtaaaagaca ... tttctttcagGTACAAGGTTTTTATAAATCCAAGCATTAGTGATGTCCTTTGCACTGCGAC

EST: gi|58596381|gb|CK006909.1|CK006909

EST:     AACCTTAACTTTCATAAAGGCCGGGATCATGCGGATGATTCTCTTCATGG                         GTACAAGGTTTTTATAAATCCAAGCATTAGTGATGTCCTTTGCACTGCGAC
genomic: AACCTTAACTTTCATAAAGGCCGGGATCATGCGGATGATTCTCTTCATGGgtaaaagaca ... tttctttcagGTACAAGGTTTTTATAAATCCAAGCATTAGTGATGTCCTTTGCACTGCGAC

EST: gi|27578026|gb|CB000721.1|CB000721

EST:     AACCTTAACTTTCATAAAGGCCGGGATCATGCGGATGATTCTCTTCATGG                         GTACAAGGTTTTTATAAATCCAAGCATTAGTGATGTCCTTTGCACTGCGAC
genomic: AACCTTAACTTTCATAAAGGCCGGGATCATGCGGATGATTCTCTTCATGGgtaaaagaca ... tttctttcagGTACAAGGTTTTTATAAATCCAAGCATTAGTGATGTCCTTTGCACTGCGAC

EST: gi|29686800|gb|CB683075.1|CB683075

EST:     AACCTTAACTTTCATAAAGGCCGGGATCATGCGGATGATTCTCTTCATGG                         GTACAAGGTTTTTATAAATCCAAGCATTAGTGATGTCCTTTGCACTG
genomic: AACCTTAACTTTCATAAAGGCCGGGATCATGCGGATGATTCTCTTCATGGgtaaaagaca ... tttctttcagGTACAAGGTTTTTATAAATCCAAGCATTAGTGATGTCCTTTGCACTG

EST: gi|86899383|gb|CI298181.1|CI298181

EST:     AACCTTAACTTTCATAAAGGCCGGGATCATGCGGATGATTCTCTTCATGG                         GTACAAGGTTTTTATAAATCCAAGCATTAGTGATGTCCTTTGCACTGCGAC
genomic: AACCTTAACTTTCATAAAGGCCGGGATCATGCGGATGATTCTCTTCATGGgtaaaagaca ... tttctttcagGTACAAGGTTTTTATAAATCCAAGCATTAGTGATGTCCTTTGCACTGCGAC

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: 58 (upstream exon), 66 (downstream exon)
Score: 43

ATGGTGAAGATTCACATGAGGTGCAATCAGCGGCTATGAAGTTGAACCTAAACCTTAACTTTCATAAAGGCCGGGATCATGCGGATGATTCTCTTCATGGgtaaaagaca ... tttctttcagGTACAAGGTTTTTATAAATCCAAGCATTAGTGATGTCCTTTGCACTGCGACCGCTGAGGCATTAGCAATGGGTAAGTTTGTTGTCTGCGCAGACCACCCA

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tacatctttagatatagttaatttgaatgtttttcctgttttttttttctttcagGTACAAGGTTTTTATAAATCCAAGCATTAGTGATGTCCTTTGCACTGCGACCGCTGAGGCATTAGCAATGGGTAAGTTTGTTGTCTGCGCAGACCACCCA