ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCTTTGGGAGCCTACTTATGAAGACTGCTTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttgttcagatatatgcttcaatttttaatgcaattactggaggtcgcatcacttgaattttgtgaagttaaagttgtttacagattttagaattaatgattaatattctttcatttgttgtttgaag

Basic information

species	Zea mays
transcript	GRMZM2G063909_T02
intron #	10
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G063909_T03 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 11

GCTTTGGGAGCCTACTTATGAAGACTGCTTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttgtt-cagatatatgcttcaatttttaatgcaattactggaggtcgcatcacttgaatt-ttgtgaagttaaagttgtttacagattttagaattaatgattaatattctttcatttgttgtttgaag
| | ||||||||||| |||||||| |||||||||||||| ||||| ||||||||||||||||| ||||||||||||||||||||||| || |  ||  || |  || | |||| |    || | ||   ||   | | ||   |   ||  |   |||   | ||| | | ||     | | | |                             
GTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCCACCAGTGGCTTCGTATGTTTACCGGAGgtagctttttttaccaatgcatccaaca-tctttact----ttccaggcaatcctgtaaattttgtaactgcaatagtaaccctattttctggttc----actgaag-----------------------------

upper sequence: GRMZM2G063909_T03 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 11

GCTTTGGGAGCCTACTTATGAAGACTGCTTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttgttcagatatatgcttcaatttttaatgcaattactggaggtcgcatcacttgaattttgtgaagttaaagttgtttacagattttagaattaatgattaatattctttcatttgttgtttgaag
| | ||||||||||| |||||||| |||||||||||||| ||||| |||||| |||||||||| |||||||||||||||||||||||  ||| ||  || |  ||  |||   | | |   |     ||   |    |  | |    |     ||| |  |||| | | || |   |                                   
GTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCCAGCAGTGGCTTCATATGTTTACCGGAGgtagctttttatca-attcattcaccatctttacttaccag-gcaatctgtaaaaattttcaactgcaatagcaataatgccgttttctggttctctgaag---------------------------------

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|60345083|gb|DN212056.1|DN212056

EST:     TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG                         AATTTTCAAGGATGGGAAATCAATAGAAGCTGATGATTCTCTGGATTATGC
genomic: TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttgtttgaagAATTTTCAAGGATGGGAAATCAATAGAAGCTGATGATTCTCTGGATTATGC

EST: gi|60354991|gb|DN221964.1|DN221964

EST:     TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG                         AATTTTCAAGGATGGGAAATCAATAGAAGCTGATGATTCTCTGGATTATGC
genomic: TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttgtttgaagAATTTTCAAGGATGGGAAATCAATAGAAGCTGATGATTCTCTGGATTATGC

EST: gi|78088374|gb|DV516767.1|DV516767

EST:     TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG                         AATTTTCAAGGATGGGAAATCAATAGAAGCTGATGATTCTCTGGATTATGC
genomic: TTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttgtttgaagAATTTTCAAGGATGGGAAATCAATAGAAGCTGATGATTCTCTGGATTATGC

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: 49 (upstream exon), 49 (downstream exon)
Score: 204

GCTTTGGGAGCCTACTTATGAAGACTGCTTAAATTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttgtttgaagAATTTTCAAGGATGGGAAATCAATAGAAGCTGATGATTCTCTGGATTATGCGGCAAATTTATCACATATGCTTGGTTTTGACGACCCCAGGATGCTGGAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 370

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 123