ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTGGTGTCAAGTGCTATCATTGATAAATACATTGGTGAAAGTGCACGCTTAATTCGTGAAATGTTTAACTATGCACGTGAGCATCAGgtaagctttgttttattttgttatctgtgtatgtatacctagctattctgatttatttatttatttatataaagcactagttttcacggttttcactgtc...

Basic information

species	Zea mays
transcript	GRMZM2G074037_T01
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G074037_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os06g40560.1 (Oryza sativa), 5'ss of exon 6

GTGGTGTCAAGTGCTATCATTGATAAATACATTGGTGAAAGTGCACGCTTAATTCGTGAAATGTTTAACTATGCACGTGAGCATCAGgtaagctttgttttattttgttatctgtgtatgtatacctagctattctgatttatttatttatttatataaagcactagttttcacggttttcactgtc---
 | |||||||||||||||||||| || ||||| ||||||||||||||  | ||  | || ||||||  ||||||||| |||||||| ||||| ||  |||| |||||||| |||||||  || |      |    || |  || ||| |   || |||        ||  | | ||              
ATTGTGTCAAGTGCTATCATTGACAAGTACATAGGTGAAAGTGCACGTCTCATAAGAGAGATGTTTTCCTATGCACGGGAGCATCAAgtaag-ttcattttgttttgtta-ctgtgtaccta-ataagttttaaatggtccatctatcttggtacatactcttaatgtagtgagggaagcaggaagttgc

upper sequence: GRMZM2G074037_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA06G01200.1 (Glycine max), 5'ss of exon 8

GTGGTGTCAAGTGCTATCATTGATAAATACATTGGTGAAAGTGCACGCTTAATTCGTGAAATGTTTAACTATGCACGTGAGCATCAGgtaagctttgttttattttgttatctgtgtatgtatacctagctattctgatttatttatttatttatataaagcactagttttcacggttttcactgtc---------
|| || || ||| |||| ||| ||||||  ||||||||||||||| | |||||| | ||||||||||| ||||| ||  | |||||||||              |||  | || || || |  | | |   |    |  || ||| || ||     |  || | |  |||| ||  ||| ||   |          
GTTGTATCTAGTACTATAATTCATAAATCTATTGGTGAAAGTGCAAGATTAATTAGGGAAATGTTTAAATATGCCCGCAATCATCAGgta--------------ttgagaact-tgcat-tgcatcaaaaca----ggatttttttttcatgcccttgtagaattgatttttactatttccatcctttttgtttag

upper sequence: GRMZM2G074037_T01 (Zea mays), 5'ss of exon 6
lower sequence: EFJ28962 (Selaginella moellendorffii), 5'ss of exon 6

GTGGTGTCAAGTGCTATCATTGATAAATACATTGGTGAAAGTGCACGCTTAATTCGTGAAATGTTTAACTATGCACGTGAGCATCAGgtaagctttgttttattttgttatctgtgtatgtatacctagctattctgatttatttatttatttatataaagcactagttttcacggttttcactgtc
|||||||| ||||||||| | || || ||||||||||| ||||| ||  |||| |||||||||||   |||||| ||||| || || |||     |||     |   |||||     ||  | |  |  || |||   |  |                                             
GTGGTGTCGAGTGCTATCGTCGACAAGTACATTGGTGAGAGTGCTCGGCTAATCCGTGAAATGTTCGGCTATGCTCGTGATCACCAAgta-----tgtcgcgctagcttatcaaaacattgacatttttcttttcctttgcag--------------------------------------------

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|211391774|gb|FL355250.1|FL355250

EST:     AAAGTS-ACGCTTAATTCGTGAAATGTTTAACTATGCACGTGAGCATCAG                         CCATGCATCATTTTCATGGATGARATTGATGCCATTGGTGGCCGAAGATTT
genomic: AAAGTGCACGCTTAATTCGTGAAATGTTTAACTATGCACGTGAGCATCAGgtaagctttg ... tgttgcctagCCATGCATCATTTTCATGGATGAAATTGATGCCATTGGTGGCCGAAGATTT

EST: gi|211075772|gb|FL462562.1|FL462562

EST:     AAAGTGCACGCTTAATTCGTGAAATGTTTAACTATGCACGTGAGCATCAG                         CCATGCATCATTTTC
genomic: AAAGTGCACGCTTAATTCGTGAAATGTTTAACTATGCACGTGAGCATCAGgtaagctttg ... tgttgcctagCCATGCATCATTTTC

EST: gi|211416916|gb|FL328808.1|FL328808

EST:     AAAGTGCACGCTTAATTCGTGAAATGTTTAACTATGCACGTGAGCATCAG                         CCATGCATCATTTTCATGGATGAAATTGATGCCATTGGTGGCCGAAGATTT
genomic: AAAGTGCACGCTTAATTCGTGAAATGTTTAACTATGCACGTGAGCATCAGgtaagctttg ... tgttgcctagCCATGCATCATTTTCATGGATGAAATTGATGCCATTGGTGGCCGAAGATTT

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: 47 (upstream exon), 47 (downstream exon)
Score: 61

GTGGTGTCAAGTGCTATCATTGATAAATACATTGGTGAAAGTGCACGCTTAATTCGTGAAATGTTTAACTATGCACGTGAGCATCAGgtaagctttg ... tgttgcctagCCATGCATCATTTTCATGGATGAAATTGATGCCATTGGTGGCCGAAGATTTAGTGAGGGCACAAGTGCAGATCGTGAGATTCAGAGGACATTGATGGAGC

Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 32

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 36