ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AGACTAAACCTCCCCCTGTTACACCTCAAGTTGTGGATCTTCTTGATGGTTTGTCCTCAAGCACATCTCTTCCTGgtgagctcctgatgcttgattatccaatataaggaaaagttgcaaatacccctaaaagtcactgagtttgatttctcttccatatcaaactcaaggtgactccaaaggagcttttgcattagtaaccttcccataatcaatgaatttacttttactcaatttgcctgttcgccag

Basic information

species	Zea mays
transcript	GRMZM2G017421_T02
intron #	16
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G017421_T02 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os06g07090.1 (Oryza sativa), 5'ss of exon 16

---AGACTAAACCTCCCCCTGTTACACCTCAAGTTGTGGATCTTCTTGATGGTTTGTCCTCAAGCACATCTCTTCCTGgtgagctcctgatgcttg---attatccaatataaggaaaagttgcaaatacccctaaaagtcactgagtttgatttctcttccatatcaaactcaaggtgactccaaaggagcttttgcattagtaaccttcccataatcaatgaatttacttttactcaatttgcctgttcgccag
   ||||||||  | | ||||||||||| ||||||||||||||||||||||||||||||||||||||||||||| ||||| || ||||  ||| |    |||||| || || | | |    | |||||     | | | | ||||    |    |  ||| |  | ||                                                                                        
CTGAGACTAAAGTTGCACCTGTTACACCCCAAGTTGTGGATCTTCTTGATGGTTTGTCCTCAAGCACATCTCTTTCTGgtcagatcctactgccttactattatctaacattatggagcactacaaatgattatgatatttactgttgctatgcttgcttgctcaccag---------------------------------------------------------------------------------------

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|32794473|gb|CD946709.1|CD946709

EST:     GATCTTCTTGATGGTTTGTCCTCAAGCACATCTCTTCCTG                         ATGAGAATGCAGCTTACCCGACAATCACAGCATTCCAGAGTGCAACCTTGA
genomic: GATCTTCTTGATGGTTTGTCCTCAAGCACATCTCTTCCTGgtgagctcct ... tgttcgccagATGAGAATGCAGCTTACCCGACAATCACAGCATTCCAGAGTGCAACCTTGA

EST: gi|67023698|gb|CO452447.1|CO452447

EST:     TCAAGTTGTGGATCTTCTTGCTGGTTTGTCCTCAAGCACATCTCTTCCTG                         ATGAGAATGCAGCTTACCCGACAATCACAGCATTCCAGAGTGCAACCTTGA
genomic: TCAAGTTGTGGATCTTCTTGATGGTTTGTCCTCAAGCACATCTCTTCCTGgtgagctcct ... tgttcgccagATGAGAATGCAGCTTACCCGACAATCACAGCATTCCAGAGTGCAACCTTGA

EST: gi|32907233|gb|CF012046.1|CF012046

EST:     GATCTTCTTGATGGTTTGTCCTCAAGCACATCTCTTTCTG                         ATGAGAATGCAGCTTACCCGACAATCACAGCATTTCAGAGTGCAACCTTGA
genomic: GATCTTCTTGATGGTTTGTCCTCAAGCACATCTCTTCCTGgtgagctcct ... tgttcgccagATGAGAATGCAGCTTACCCGACAATCACAGCATTCCAGAGTGCAACCTTGA

EST: gi|60354854|gb|DN221827.1|DN221827

EST:     TCAAGTTGTGGATCTTCTTGATGGTTTGTCCTCAAGCACATCTCTTCCTG                         ATGAGAATGCAGCTTACCCGACAATCACAGCATTCCAGAGTGCAACCTTGA
genomic: TCAAGTTGTGGATCTTCTTGATGGTTTGTCCTCAAGCACATCTCTTCCTGgtgagctcct ... tgttcgccagATGAGAATGCAGCTTACCCGACAATCACAGCATTCCAGAGTGCAACCTTGA

EST: gi|32907234|gb|CF012047.1|CF012047

EST:     GATCTTCTTGATGGTTTGTCCTCAAGCACATCTCTTCCTG                         ATGAGAATGCAGCTTACCCGACAATCACAGCATTCCAGAGTGCAACCTTGA
genomic: GATCTTCTTGATGGTTTGTCCTCAAGCACATCTCTTCCTGgtgagctcct ... tgttcgccagATGAGAATGCAGCTTACCCGACAATCACAGCATTCCAGAGTGCAACCTTGA

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), 45 (downstream exon)
Score: 205

AGACTAAACCTCCCCCTGTTACACCTCAAGTTGTGGATCTTCTTGATGGTTTGTCCTCAAGCACATCTCTTCCTGgtgagctcct ... tgttcgccagATGAGAATGCAGCTTACCCGACAATCACAGCATTCCAGAGTGCAACCTTGAGGATCACATTCAGTTTCAAAAAGCAACCTGGAAAACCTCAGGAGACTAC

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 159

Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 175