ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCTGCTTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCAAAGgtaattcagttattaaatatttatgtggttgttggtgaatcatactctcaaaattaatatgtcacttgaataatatatgcatacttttgtag

Basic information

species	Zea mays
transcript	GRMZM2G022563_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G022563_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g55060.1 (Oryza sativa), 5'ss of exon 4

CTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCTGCTTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCAAAGgtaattcagttattaaatatttatgtggttgttggtgaatcatactctca----aaattaatat-gtcac-----ttgaataatatatgcatacttttgtag
||| | || ||||| ||| |||| || ||||| |||||||| || ||||| |||||||||||| |  | || ||||| || |||||||| |||||||||||||| ||  || ||     ||     | |||||||  | ||| || ||||    |  ||  | | |||||     | || ||||||||| | | ||| ||||
CTGGCGGAGGTGGGATGCGCAAATGCATTTGGCTTTGATATCACTGCTGCATGTAGTGGGTTTATTATTGGTTTAATTACGGCTACTCGTTTTATCAAAGgtaactcttttttttttccttgtgaggattgttggcta-tcaaacactcacaggaggttgttgttgtcaccttgttcgattaatatatg-acaatttcgtag

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|71429948|gb|DR810998.1|DR810998

EST:     TTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCAAAG                         GCGGAGGTTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAA
genomic: TTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCAAAGgtaattcagt ... acttttgtagGCGGAGG-TTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAA

EST: gi|71429949|gb|DR810999.1|DR810999

EST:     TTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCAGAG                         GCGGAGGTTTTCAGAATGTCTTAGTAAGTGGTGCAGATGCTCTTTCAAAAT
genomic: TTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCAAAGgtaattcagt ... acttttgtagGCGGAGGTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAAT

EST: gi|76291106|gb|DV030674.1|DV030674

EST:     TTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCAAAG                         GCGGAGGTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAAT
genomic: TTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCAAAGgtaattcagt ... acttttgtagGCGGAGGTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAAT

EST: gi|149095842|gb|EE181493.2|EE181493

EST:     TTGTAGTGNGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCAAAG                         GCGGAGGTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAAT
genomic: TTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCAAAGgtaattcagt ... acttttgtagGCGGAGGTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAAT

EST: gi|148935022|gb|EC879064.2|EC879064

EST:     TTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCAAAG                         GCGGAGGTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAAT
genomic: TTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCAAAGgtaattcagt ... acttttgtagGCGGAGGTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAAT

EST: gi|101397488|gb|EB820667.1|EB820667

EST:     TTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCCCTTTATCAAAG                         GCGGAAGGTTT
genomic: TTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCAAAGgtaattcagt ... acttttgtagGCGGA-GGTTT

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), 47 (downstream exon)
Score: 165

CTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCTGCTTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCAAAGgtaattcagt ... acttttgtagGCGGAGGTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAATACGTGGATTGGACAGACAGAGGTACATGCATTCTTTTTGGTGATGCTGC

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 134

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 149