ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCAACAGCTTAATGAGCATGCTAAGCTCTCGATGCTGAGGAATGCCACATGGACACTATCAAACTTCTGCCGTGGGAAGCCACAACCGAACTTTGATCAGgtttctatctgggattatttgtttcagttgttttggccaaagttggtccttcaaatgatattggtttgttttgttcatgcttgagtag

Basic information

species	Zea mays
transcript	GRMZM2G009845_T02
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G009845_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g06350.1 (Oryza sativa), 5'ss of exon 5

GCAACAGCTTAATGAGCATGCTAAGCTCTCGATGCTGAGGAATGCCACATGGACACTATCAAACTTCTGCCGTGGGAAGCCACAACCGAACTTTGATCAGgtttctatctgggattatttgt-ttcagttgttttggccaaagttg--gtccttcaaatgatattggtttgttttgttcatgcttgagtag
|||||||||||||||||| || |||||||| ||||| |||||||||||||||||||| ||||||||||||||||||||||| || || || ||||| |||||||   |||||| |   || |  |  | ||   || || |||||    || ||   ||| | |||  ||| ||| ||  || | ||| ||
GCAACAGCTTAATGAGCACGCCAAGCTCTCAATGCTCAGGAATGCCACATGGACACTGTCAAACTTCTGCCGTGGGAAGCCTCAGCCTAATTTTGAGCAGgtttaattctgggctaccttctactttgatgcactgacctaagtttttatcattaggatggttttg--ttgattt-tttgtgttcgagcag

upper sequence: GRMZM2G009845_T02 (Zea mays), 5'ss of exon 5
lower sequence: PP1S63_171V6.1 (Physcomitrella patens), 5'ss of exon 5

-GCAACAGCTTAATGAGCATGCTAAGCTCTCGATGCTGAGGAATGCCACATGGACACTATCAAACTTCTGCCGTGGGAAGCCACAACCGAACTTTGATCAGgttt--ctatctgggattatttgtttcagttgttttggccaaagttggtccttcaaatgatattggtttgttt-----tgttcatgcttgagtag-------------------------------------------------------------------------------------------------------
 ||  |||||||  ||   ||| ||| | || |||||  | |||||||| ||||| || ||||||||||||||||| ||||| || ||    ||||| |||||    | ||      ||    | | | ||  |  |||| ||| |   | |||        |     ||||       ||||  |  ||||  |                                                                                                        
CGCT-CAGCTTACCGATACTGCGAAGTTGTCAATGCTTCGAAATGCCACCTGGACGCTCTCAAACTTCTGCCGTGGAAAGCCCCAGCCACCTTTTGAGCAGgtgagacgattcccagttgacgggtgctgtc-tgctggcgaaattctcttctttgtggagcagctcattgtacaacactgtttgttattgaccatcatcgatctgtgttgtttcttgagtttgaatctttcgattcgtatattcacaggttctttgccaaatttcccacattgcagtctaataatttttggtttgcag

upper sequence: GRMZM2G009845_T02 (Zea mays), 5'ss of exon 5
lower sequence: EFJ31557 (Selaginella moellendorffii), 5'ss of exon 5

GCAACAGCTTAATGAGCATGCTAAGCTCTCGATGCTGAGGAATGCCACATGGACACTATCAAACTTCTGCCGTGGGAAGCCACAACCGAACTTTGATCAGgtttctatctgggattatttgtttcagttgttttggccaaagttggtccttcaaatgatattggtttgttttgttcatgcttgagtag
   |||||| || ||| |||| ||||| || |||||| | || || || ||||| ||||||||||| || ||||| ||||| || ||||||||||| ||||| | |     || | ||||||   ||   | | |    || || |  | |     | | ||| ||  |   |               
AGCACAGCTGAACGAGAATGCGAAGCTGTCTATGCTGCGCAACGCAACGTGGACGCTATCAAACTTTTGTCGTGGCAAGCCGCAGCCGAACTTTGAGCAGgtatgt-----gggtcatttgt---aggcatgtcgatacaaatttgatcgttggtcggtgttgtttcttgcag---------------

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|148966362|gb|EE017351.2|EE017351

EST:     GGACACTATCAAACTTCTGCCGTGGGAAGCCACAACCGAACTTTGATCAG                         GTCAAACCAGCATTGCCAGCACTTCAGCAACTTATCCACTCTCAGGATGAG
genomic: GGACACTATCAAACTTCTGCCGTGGGAAGCCACAACCGAACTTTGATCAGgtttctatct ... gcttgagtagGTCAAACCAGCATTGCCAGCACTTCAGCAACTTATCCACTCTCAGGATGAG

EST: gi|31350199|gb|CD434556.1|CD434556

EST:     GCTCACTATCAAACTTCTGCCGTGGGAAGCCACAACCGAACTTTGATCAG                         GTCAAACCAGCATTGCCAGCACTTCAGCCACTTATCCACTCTCAGGATGAG
genomic: G-ACACTATCAAACTTCTGCCGTGGGAAGCCACAACCGAACTTTGATCAGgtttctatct ... gcttgagtagGTCAAACCAGCATTGCCAGCACTTCAGCAACTTATCCACTCTCAGGATGAG

EST: gi|32929275|gb|CF034087.1|CF034087

EST:     GGACACTATCAAACTTCTGCCGTGGGAAGCCACAACCGAACTTTGATCAG                         GTCAAACCAGCATTGCCAGCACTTCAGCAACTTATCCACTCTCAGGATGAG
genomic: GGACACTATCAAACTTCTGCCGTGGGAAGCCACAACCGAACTTTGATCAGgtttctatct ... gcttgagtagGTCAAACCAGCATTGCCAGCACTTCAGCAACTTATCCACTCTCAGGATGAG

EST: gi|211010951|gb|FL253544.1|FL253544

EST:     ACACTATCAAACTTTCTGC-GTGGGGAAGCCACACCCGA-CTTTGATCAG                         GTCAAACCAGCATTGCCAGCACTTCA
genomic: ACACTATCAAACTT-CTGCCGTGGG-AAGCCACAACCGAACTTTGATCAGgtttctatct ... gcttgagtagGTCAAACCAGCATTGCCAGCACTTCA

EST: gi|148994071|gb|EE033948.2|EE033948

EST:     GGACACTATCAAACTTCTGCCGTGGGAAGCCACAACCAAACTTTGATCAG                         GTCAAACCAGCATTGCCAGC
genomic: GGACACTATCAAACTTCTGCCGTGGGAAGCCACAACCGAACTTTGATCAGgtttctatct ... gcttgagtagGTCAAACCAGCATTGCCAGC

EST: gi|32928651|gb|CF033463.1|CF033463

EST:     GGACACTATCAAACTTCTGCCGTGGGAAGCCACAACCGAACTTTGATCAG                         GTCAAACCAGCATTGCCAGCACTTCAGCAACTTATCCACTCTCAGGATGAG
genomic: GGACACTATCAAACTTCTGCCGTGGGAAGCCACAACCGAACTTTGATCAGgtttctatct ... gcttgagtagGTCAAACCAGCATTGCCAGCACTTCAGCAACTTATCCACTCTCAGGATGAG

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: 45 (upstream exon), 49 (downstream exon)
Score: 207

GCAACAGCTTAATGAGCATGCTAAGCTCTCGATGCTGAGGAATGCCACATGGACACTATCAAACTTCTGCCGTGGGAAGCCACAACCGAACTTTGATCAGgtttctatct ... gcttgagtagGTCAAACCAGCATTGCCAGCACTTCAGCAACTTATCCACTCTCAGGATGAGGAGGTCCTAACTGATGCCTGTTGGGCTCTATCATACCTATCTGATGGGA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 216

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 212