ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TACTGCAGCTGGTGCGGTGTATGATAGAGAATTCATTGTTTGTTCGTTGGACCTACTGTCTGGACTTGCAGAAGGTCTTGGCGCTGGTATTGAAAGTCTTgtaagttcttgcctttgcatatggtattgttttccctttcaagtacacaaacacaccactcacatacccacatgggtgcgtccggggtggagttagatta...

Basic information

species	Zea mays
transcript	GRMZM2G376731_T01
intron #	20
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G376731_T01 (Zea mays), 5'ss of exon 20
lower sequence: LOC_Os04g59494.1 (Oryza sativa), 5'ss of exon 20

TACTGCAGCTGGTGCGGTGTATGATAGAGAATTCATTGTTTGTTCGTTGGACCTACTGTCTGGACTTGCAGAAGGTCTTGGCGCTGGTATTGAAAGTCTTgtaagttcttgcct-ttgcatatggtattgttttccctttcaagtacacaaacacaccactcacatacccacatgggtgcgtccggggtggagttagatta
| |||||||||||||  | |||||||  ||||||||||| ||| | ||||| ||  |||| |||||||||||||| |||||||||||||||||||| || |||| |||     | | ||  ||| ||||   ||   |||       ||        | || || || | || |  ||   || |  |  ||   | |   
TGCTGCAGCTGGTGCATTATATGATAAGGAATTCATTGTGTGTGCATTGGATCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTGAAAGCCTGgtaaattcaactatatggccaatgatatttccttttttttgttaattactctttgttcccttacctatcgacctcagta-atctgtaggagatccatacct

upper sequence: GRMZM2G376731_T01 (Zea mays), 5'ss of exon 20
lower sequence: Vv18s0001g00910.t01 (Vitis vinifera), 5'ss of exon 20

TACTGCAGCTGGTGCGGTGTATGATAGAGAATTCATTGTTTGTTCGTTGGACCTACTGTCTGGACTTGCAGAAGGTCTTGGCGCTGGTATTGAAAGTCTTgtaagttcttgcctttgcatatggtattgttttccctttcaagtacacaaacacaccactcacatacccacatgggtgcgtccggggtggagttagatta
|    |||||| ||     ||||||| ||||||||||||||| || |||||| | || || || |||||||||||||||||   ||| ||||| ||  | ||| ||   |   ||| | |     | | || |        | ||   | |  ||    |   || |     |   |||   |  |     ||     | 
TCTGTCAGCTGCTGTTCAATATGATAAAGAATTCATTGTTTGCTCTTTGGACTTGCTCTCAGGGCTTGCAGAAGGTCTTGGTAGTGGAATTGAGAGCTTGgtacgtctctttttttcctttccaaaattttcttgagcgggaatatgtagattcaagcatttgatgcttttcttaatgcaaacatgtgattgtctatctg

upper sequence: GRMZM2G376731_T01 (Zea mays), 5'ss of exon 20
lower sequence: Vv03s0038g02830.t01 (Vitis vinifera), 5'ss of exon 20

TACTGCAGCTGGTGCGGTGTATGATAGAGAATTCATTGTTTGTTCGTTGGACCTACTGTCTGGACTTGCAGAAGGTCTTGGCGCTGGTATTGAAAGTCTTgtaagttcttgcctttgcatatggtattgttttccctttcaagtacac-aaacacaccactcacatacccacatgggtgcgtccggggtggagtt---agatta--
| || |||||||||    |||||||| ||| || ||||| || ||  | ||| | ||||||||||||||||||||||||||   ||| || || ||| | |||  | | |  ||   ||      ||| ||    ||   |  ||||  | |||      |   ||   || | |    |  || |     | ||   | |||   
TGCTTCAGCTGGTGTTCAGTATGATAAAGAGTTTATTGTATGCTCTCTCGACTTGCTGTCTGGACTTGCAGAAGGTCTTGGTAGTGGGATAGAGAGTTTGgtatttccctttctccaca------atttttggatctggaagttacattagacaaggtgtttttatgaacaaaagttatccgccagttcttatttttgaaattgta

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|91872776|gb|EB402733.1|EB402733

EST:     ACCTACTGTCTGGACTTGCAGAAGGTCTTGGCGCTGGTATTGAAAGTCTT                         GTTGCACAGAGCAGTTTGAGAGATCTGCTTTTGCAATGCTGCATGGATGAA
genomic: ACCTACTGTCTGGACTTGCAGAAGGTCTTGGCGCTGGTATTGAAAGTCTTgtaagttctt ... ttctttgtagGTTGCACAGAGCAGTTTGAGAGATCTGCTTTTGCAATGCTGCATGGATGAA

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: 235

TACTGCAGCTGGTGCGGTGTATGATAGAGAATTCATTGTTTGTTCGTTGGACCTACTGTCTGGACTTGCAGAAGGTCTTGGCGCTGGTATTGAAAGTCTTgtaagttctt ... ttctttgtagGTTGCACAGAGCAGTTTGAGAGATCTGCTTTTGCAATGCTGCATGGATGAAGCAGCTGATGTTCGACAAAGTGCCCTTGCCCTTCTTGGAGACCTTTCTA

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 203

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 241