ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CTGACGGACGTGGGGTGCACAAAGGCTTTTGGATTTGATATTACAGCTGCTTGCAGTGGGTTTATAGTTGGCTTAATCACAGCTACTCGTTTTATCAAAGgtaattaaaatattaaatatttatctggttgatggtgaatggcttccacaaaaacaatatgccgcatgaataatataatgcatacttctgtag

Basic information

species	Zea mays
transcript	GRMZM2G003190_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G003190_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g55060.1 (Oryza sativa), 5'ss of exon 4

CTGACGGACGTGGGGTGCACAAAGGCTTTTGGATTTGATATTACAGCTGCTTGCAGTGGGTTTATAGTTGGCTTAATCACAGCTACTCGTTTTATCAAAGgtaa---ttaaaatattaaatatttatctggttgatggtgaatggcttccacaaaaacaatat-gccgcatgaataatataatgcat---acttctgtag
||| |||| ||||| ||| |||| || ||||| |||||||| || ||||| || |||||||||||  |||| ||||| || |||||||||||||||||||||||   ||    | ||   | |     | ||||    | ||   ||  ||  |      | | | | | |   |    ||||  ||   | ||  ||||
CTGGCGGAGGTGGGATGCGCAAATGCATTTGGCTTTGATATCACTGCTGCATGTAGTGGGTTTATTATTGGTTTAATTACGGCTACTCGTTTTATCAAAGgtaactcttttttttttccttgtgaggattgttggctatcaaacactcacaggaggttgttgttgtcaccttgttcgattaatatatgacaatttcgtag

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|76012942|gb|DT940112.1|DT940112

EST:     TTGCAGTGNGTTTATAGTTGGCTTAATCACAGCTACTCGTTTTATCAAAG                         GTGGAGGTTTTCAGAATATCCTAGTAGTTGGTGCTGATGCTCTTTCAAA-T
genomic: TTGCAGTGGGTTTATAGTTGGCTTAATCACAGCTACTCGTTTTATCAAAGgtaattaaaa ... acttctgtagGTGGAGGTTTTCAGAATATCCTAGTAGTTGGTGCTGATGCTCTTTCAAAAT

EST: gi|71429556|gb|DR810606.1|DR810606

EST:     TTGCAGTGGGTTTATAGTGGGCTTAATCACAGCTACTCGTTTTATCAAAG                         GTGGAGGTTTTCAGAATATCCTAGTAGTTGGTGCTGATGCTCTTTCAAAAT
genomic: TTGCAGTGGGTTTATAGTTGGCTTAATCACAGCTACTCGTTTTATCAAAGgtaattaaaa ... acttctgtagGTGGAGGTTTTCAGAATATCCTAGTAGTTGGTGCTGATGCTCTTTCAAAAT

EST: gi|67024943|gb|CO453692.1|CO453692

EST:     TTGCAGTGGGTTTATAGTTGGCTTAATCACAGCTACTCGTTTTATCAAAG                         GTGGAGGTTTTCAGAATATCTTAGTAGTTGGTGCTGATGCTCTTTCAAAAT
genomic: TTGCAGTGGGTTTATAGTTGGCTTAATCACAGCTACTCGTTTTATCAAAGgtaattaaaa ... acttctgtagGTGGAGGTTTTCAGAATATCCTAGTAGTTGGTGCTGATGCTCTTTCAAAAT

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: 141

CTGACGGACGTGGGGTGCACAAAGGCTTTTGGATTTGATATTACAGCTGCTTGCAGTGGGTTTATAGTTGGCTTAATCACAGCTACTCGTTTTATCAAAGgtaattaaaa ... acttctgtagGTGGAGGTTTTCAGAATATCCTAGTAGTTGGTGCTGATGCTCTTTCAAAATATGTGGATTGGACAGACAGAGGTACATGCATCCTTTTTGGTGATGCTGC

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 121

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 90