ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TCCAGCGCAGGCAGCATCATTGTTAATAGTGGGGCCTTTTGTGGACTTCTGGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACGgtatgtgatacttgttctcaatcatttatgtttatgtcttttgcaaaatcctcacaaggaagaggaacccatctgtttcactcaagttagtttagcactg...

Basic information

species	Zea mays
transcript	GRMZM5G823629_T03
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G823629_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g40090.4 (Oryza sativa), 5'ss of exon 5

TCCAGCGCAGGCAGCATCATTGTTAATAGTGGGGCCTTTTGTGGACTTCTGGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACGgtatgtgatacttgttctcaatca--tttatgtttatgtcttttgcaaaatcctcacaaggaagaggaacccatctgtttcactcaagttagtttagcactg---
|||||| |||||||||||  |||||||| |||||||||||||||||||||||||||| || | |||||||||| |||| || |||||| |||||||||||||||||||| |||||| | |||||  | | || |||| ||| |||  || |  |  ||    ||     ||||| ||  ||  |  || || ||  ||| |    
TCCAGCTCAGGCAGCATCCCTGTTAATACTGGGGCCTTTTGTGGACTTCTGGCTGACCAATAGAAGAGTTGATACTTTCAATTACACAACAATAGTTACGgtatgtgattcttgttttgaatcagttctctgcttat-tctcttgtgaacttgttgcattacagt----cccatttggctctatgcagctatttcggcattataa

upper sequence: GRMZM5G823629_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g12490.1 (Oryza sativa), 5'ss of exon 5

TCCAGCGCAGGCAGCATCATTGTTAATAGTGGGGCCTTTTGTGGACTTCTGGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACGgtatgtgatacttgttctcaatcatttatgtttatgtcttttgcaaaatcctcacaag---gaagaggaacccatctgtttcactcaagttagtttagcactg
|||||| ||||||||||| ||  || || |||||||||| ||||||||||||||||| ||||||||||||||| |||| || |||||| |||||||||||||||| | |  || |         ||  | |  |    |  |   ||| ||  | |        ||  |   || | | |  |    | |||   |   |   
TCCAGCTCAGGCAGCATCTTTACTAGTACTGGGGCCTTTCGTGGACTTCTGGCTGACCAACAAAAGAGTTGATACTTTCAATTACACAGCAATAGTTACGgtatgcggtgattctctgtttatcttgttataaactgatcattagaaacccatatagctctactgataatttcaccaggtaaatattaattaccatgaaa---

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|78079407|gb|DV507819.1|DV507819

EST:     GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACG                         TTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA
genomic: GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACGgtatgtgata ... tccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA

EST: gi|71445236|gb|DR826286.1|DR826286

EST:     GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACG                         TTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA
genomic: GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACGgtatgtgata ... tccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA

EST: gi|67020229|gb|CO448978.1|CO448978

EST:     GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACG                         TTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA
genomic: GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACGgtatgtgata ... tccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA

EST: gi|76015509|gb|DT942679.1|DT942679

EST:     GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACG                         TTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA
genomic: GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACGgtatgtgata ... tccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA

EST: gi|76281273|gb|DV020841.1|DV020841

EST:     GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACG                         TTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA
genomic: GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACGgtatgtgata ... tccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA

EST: gi|32941721|gb|CF046540.1|CF046540

EST:     ATGCTTTTAACTACACATCAATAGTTACG                         TTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA
genomic: ATGCTTTTAACTACACATCAATAGTTACGgtatgtgata ... tccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA

EST: gi|76280569|gb|DV020137.1|DV020137

EST:     GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACG                         TTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA
genomic: GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACGgtatgtgata ... tccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA

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: 108

TCCAGCGCAGGCAGCATCATTGTTAATAGTGGGGCCTTTTGTGGACTTCTGGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACGgtatgtgata ... tccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAATTCATATGCATCGGAAGATTCACAGCCGTCTCGTTCCAAGTCCTAGGCC

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 135

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 165