ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGGTGATCTCTTGATGGAGTTAGGAGCTGGGATAGAATTAGCTACTGCAGCTTTCCCACAGCTTTTCCTACCAATGGCATGCATAGCAAATGTTGTTAAGgtttgtcctactgatttgttgcaacttgcaacaggttcttgctatagtatgttactaatatttttaacttgccttgcaaaatgggtgatgaaatgtattctacttgtttgatgcattttctcctatcag

Basic information

species	Zea mays
transcript	GRMZM5G833124_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G833124_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g34650.1 (Oryza sativa), 5'ss of exon 5

TGGTGATCTCTTGATGGAGTTAGGAGCTGGGATAGAATTAGCTACTGCAGCTTTCCCACAGCTTTTCCTACCAATGGCATGCATAGCAAATGTTGTTAAGgtttgtcctactgatttgttgcaacttgcaacaggttcttgctatagtatgtt-actaatatttttaacttg----ccttgcaaaatgggtgatgaaatgtattctact-tgtttgatgcattttctcctatcag
||| |||||||||||||||||||||||||||||||| |||||||| ||||||||||| || ||||||||||| ||||| ||||| |||||||||||||||||||| ||||  | |||  ||  ||  |    |     ||  ||| |  ||||   |||  ||  |    ||    | ||    |   |   ||| | || |   |  | |  |||||| | ||  | |  ||||
TGGCGATCTCTTGATGGAGTTAGGAGCTGGGATAGAGTTAGCTACGGCAGCTTTCCCTCAACTTTTCCTACCTATGGCTTGCATCGCAAATGTTGTTAAGgtttgacctagcggtttactgtgacgagtcctaa--cattaatatggcttgtttgataaagttactgtaatgaaccctttttgtacctgcaaatgtactgaagattgttctacttgatgaaattgttacattcag

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|32931635|gb|CF036447.1|CF036447

EST:     CTTTCCCACAGCTTTTCCTACCAATGGCATGCATAGCAAATGTTGTTAAG                         AATGTTGCTGCTGTCACTTCCACCTCTACTCGAACACCAATTTACAAGGCG
genomic: CTTTCCCACAGCTTTTCCTACCAATGGCATGCATAGCAAATGTTGTTAAGgtttgtccta ... ctcctatcagAATGTTGCTGCTGTCACTTCCACCTCTACTCGAACACCAATTTACAAGGCG

EST: gi|60356183|gb|DN223156.1|DN223156

EST:     CTTTCCCACAGCTTTTCCTACCAATGGCATGCATAGCAAATGTTGTTAAG                         AATGTTGCTGCTGTCACTTCCACCTCTACTCGAACACCAATTTACAAGGCG
genomic: CTTTCCCACAGCTTTTCCTACCAATGGCATGCATAGCAAATGTTGTTAAGgtttgtccta ... ctcctatcagAATGTTGCTGCTGTCACTTCCACCTCTACTCGAACACCAATTTACAAGGCG

EST: gi|71440154|gb|DR821204.1|DR821204

EST:     CTTTCCCACAGCTTTTTCTACCA-TGGCATGCATAGCAAATGTTGTTAAG                         AATGTTGCTGCTGTCACTTCCACCTCTACTCGAACACCAATTT
genomic: CTTTCCCACAGCTTTTCCTACCAATGGCATGCATAGCAAATGTTGTTAAGgtttgtccta ... ctcctatcagAATGTTGCTGCTGTCACTTCCACCTCTACTCGAACACCAATTT

EST: gi|32932638|gb|CF037450.1|CF037450

EST:     CTTTCCCACAGCTTTTCCTACCAATGGCATGCATAGCAAATGTTGTTAAG                         AATGTTGCTGCTGTCACTTCCACCTCTACTCGAACACCAATTTACAAGGCG
genomic: CTTTCCCACAGCTTTTCCTACCAATGGCATGCATAGCAAATGTTGTTAAGgtttgtccta ... ctcctatcagAATGTTGCTGCTGTCACTTCCACCTCTACTCGAACACCAATTTACAAGGCG

EST: gi|93281685|gb|EB673949.1|EB673949

EST:     CTTTCCCA-AGCTTTTCCTACCAATGGCATGCATAGCAAATGTTGTTAAG                         AATGTTGCTGCTG
genomic: CTTTCCCACAGCTTTTCCTACCAATGGCATGCATAGCAAATGTTGTTAAGgtttgtccta ... ctcctatcagAATGTTGCTGCTG

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: 48 (upstream exon), 49 (downstream exon)
Score: 98

TGGTGATCTCTTGATGGAGTTAGGAGCTGGGATAGAATTAGCTACTGCAGCTTTCCCACAGCTTTTCCTACCAATGGCATGCATAGCAAATGTTGTTAAGgtttgtccta ... ctcctatcagAATGTTGCTGCTGTCACTTCCACCTCTACTCGAACACCAATTTACAAGGCGTATGCAAAAGGAGAAAACATCGGTGATGTTACTGCTAAAGGAGAAAGTG

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 211

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 197