ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CAGGAGCAGAGTAAAATACTTCAGCATCGTGGATCCAACACAAATGGCATACTACATATCTGAAATATTAGACGCCGGACCACAGGGACCTCTGTTTATGgtaaatttcagccttttgtaccatctgtacatctgttctttccgtatcttgatatatgttgcttgatgcattacag

Basic information

species	Zea mays
transcript	GRMZM2G140524_T02
intron #	11
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G140524_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os05g10770.1 (Oryza sativa), 5'ss of exon 10

CAGGAGCAGAGTAAAATACTTCAGCATCGTGGATCCAACACAAATGGCATACTACATATCTGAAATATTAGACGCCGGACCACAGGGACCTCTGTTTATGgtaaatttcagccttttgtaccatctgtacatctgttctttccgtatcttgatatat-gttgcttgatgcattacag---
 || |||||||| |||||||||||||| ||||||||||  |||||||||||||||||||| |||||| | || || ||    ||||| |||||||||||||||||||| ||  | |    |  ||| ||  | |  | | |  | ||||  | ||||  |||||   | ||||   |   
TAGAAGCAGAGTGAAATACTTCAGCATTGTGGATCCAATCCAAATGGCATACTACATATCGGAAATACTGGATGCTGGGATGCAGGGGCCTCTGTTTATGgtaaatttaagtttctca-gctgtctttatgtat-ctgtcttagcatctgtacatattattgctcatttcatttttgcag

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|22819921|gb|BU500011.1|BU500011

EST:     ACTACATATCTGAAATATTAGACGCCGGACCACAGGGACCTCTGTTTATG                         GTGACTCTGGAAAACTGTCCAGGCGAACTTTTTATCAACGTCTCTCCTGCC
genomic: ACTACATATCTGAAATATTAGACGCCGGACCACAGGGACCTCTGTTTATGgtaaatttca ... tgcattacagGTGACTCTGGAAAACTGTCCAGGCGAACTTTTTATCAACGTCTCTCCTGCC

EST: gi|87156370|gb|DY401159.1|DY401159

EST:     ACTACATATCTGAAATATTAGACGCCGGACCACAGGGACCTCTGTTTATG                         GTGACTCTGGAAAACTGTCCAGGCGAACTTTTTATCAACGTCTCTCCTGCC
genomic: ACTACATATCTGAAATATTAGACGCCGGACCACAGGGACCTCTGTTTATGgtaaatttca ... tgcattacagGTGACTCTGGAAAACTGTCCAGGCGAACTTTTTATCAACGTCTCTCCTGCC

EST: gi|26560092|gb|CA832327.1|CA832327

EST:     ACTACATATCTGAAATATTAGACGCCGGACCACAGGGACCTCTGTTTATG                         GTGACTCTGGAAAACTGTCCAGGCGAACTTTTTATCAACGTCTCTCCTGCC
genomic: ACTACATATCTGAAATATTAGACGCCGGACCACAGGGACCTCTGTTTATGgtaaatttca ... tgcattacagGTGACTCTGGAAAACTGTCCAGGCGAACTTTTTATCAACGTCTCTCCTGCC

EST: gi|166437570|gb|EG164716.1|EG164716

EST:     ACTACATATCTGAAATATTAGACGCTGGACCACAGGGACCTCTGTTTATG                         GTGACTCTGGAAAACTGTCCAG
genomic: ACTACATATCTGAAATATTAGACGCCGGACCACAGGGACCTCTGTTTATGgtaaatttca ... tgcattacagGTGACTCTGGAAAACTGTCCAG

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 4 RNA-Seq libraries.

Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 102

CAGGAGCAGAGTAAAATACTTCAGCATCGTGGATCCAACACAAATGGCATACTACATATCTGAAATATTAGACGCCGGACCACAGGGACCTCTGTTTATGgtaaatttca ... tgcattacagGTGACTCTGGAAAACTGTCCAGGCGAACTTTTTATCAACGTCTCTCCTGCCAAGTGCTGGAGCATGGTCCGTGAGAGGCTGAATATGGAAATACGGAGGC

Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 67

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 84