ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ATCGAGAAACAGGAATTTGGACTTAAGCCAATGAATTGTCCAGGACACTGTCTAATGTTTGCTAATAGGGTTCGGTCGTACAGAGgtgagtttcttcctaatttttgtattttaaattgctttgttttaagtgagcgagcgaaagggcctcaagctgagttggttaggtggtttgagtagcactt...

Basic information

species	Zea mays
transcript	GRMZM2G553314_T01
intron #	11
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G553314_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os08g19850.1 (Oryza sativa), 5'ss of exon 11

ATCGAGAAACAGGAATTTGGACTTAAGCCAATGAATTGTCCAGGACACTGTCTAATGTTTGCTAATAGGGTTCGGTCGTACAGAGgtgagt-ttcttcctaatt-----tttgtattttaaattgctttgttttaagtgagcgagcgaaagggcctcaagctgagttggttaggtggtttgagtagcactt
|| ||||||||||||||||| || ||||||||||||||||| || || || ||||||||||   | |||||||| || ||||||||| | | | |||| ||||       ||||||   ||| ||  |   ||| |   || ||        ||    |    | | | ||      | ||  |       
ATTGAGAAACAGGAATTTGGTCTCAAGCCAATGAATTGTCCTGGCCATTGCCTAATGTTTGAGCACAGGGTTCGTTCATACAGAGgtaaatctccttcataatggcatagttgtatcacaaaatgtatctcttttatcaagtgaaaattcctgctgtcaaagtaatcgcttcaaccttctgcctg------

upper sequence: GRMZM2G553314_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv19s0015g00470.t01 (Vitis vinifera), 5'ss of exon 11

ATCGAGAAACAGGAATTTGGACTTAAGCCAATGAATTGTCCAGGACACTGTCTAATGTTTGCTAATAGGGTTCGGTCGTACAGAGgtgagtttcttcctaatttttgtat-tttaaattgctttgttttaagtgagcgagcgaaagggcctcaagctgagttggttaggtggtttgagtagcactt--
 | || ||||| || ||||| ||||||||||||||||| ||||| || ||| | |||||||   |||| ||||| || || ||||||||||   ||   | ||||| ||| ||||  ||   | |  |||  ||      |         | | |||   |   |||| | |    | ||||  |   
GTTGAAAAACAAGAGTTTGGGCTTAAGCCAATGAATTGCCCAGGGCATTGTTTGATGTTTGAACATAGAGTTCGTTCATATAGAGgtgagtgcatttg-attttttatatatttatcttaaatagcattacatggtgctcctttgctctttgaggctccatc--ttagattgaggcaatagccttctt

upper sequence: GRMZM2G553314_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv01s0026g00340.t01 (Vitis vinifera), 5'ss of exon 11

ATCGAGAAACAGGAATTTGGACTTAAGCCAATGAATTGTCCAGGACACTGTCTAATGTTTGCTAATAGGGTTCGGTCGTACAGAGgtgagt-----ttcttcctaatttttgtattttaaattgctttgttttaag--tgagcgagcgaaagggcctcaagctgagttggttaggtggtttgagtagcactt
 | || ||||| || ||||| ||||||||||||||||| ||||| |||||| | |||||||   |||| ||||| || || ||||||||||     |  ||||| || | | ||| |||||| || |    |   |  |    |  |   | |||  ||  ||   |||   |||     | |     | ||
GTTGAAAAACAAGAGTTTGGGCTTAAGCCAATGAATTGCCCAGGGCACTGTTTGATGTTTGAACATAGAGTTCGTTCATATAGAGgtgagtgcatttggttccttatatatttatcttaaatagcataacatggtgcttttttgctcttcaaggctccatcctagattg---aggcaaactaaa----attt

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|211046688|gb|FL336954.1|FL336954

EST:     TCTAATGTTTGCTAATAGGGTTCGGTCGTACAGAG                         AGTTGCCTCTTCGCATGGCTGATTTTGGAGTGCTTCATAGAAATGAGCTTA
genomic: TCTAATGTTTGCTAATAGGGTTCGGTCGTACAGAGgtgagtttct ... tttgctacagAGTTGCCTCTTCGCATGGCTGATTTTGGAGTGCTTCATAGAAATGAGCTTA

EST: gi|67033102|gb|CO461851.1|CO461851

EST:     TTGTCCAGGACACTGTCTAATGTTTGCTAATAGGGTTCGGTCGTACAGAG                         AGTTGCCTCTTCGCATGGCTGATTTTGGAGTGCTTCATAGAAATGAGCTTA
genomic: TTGTCCAGGACACTGTCTAATGTTTGCTAATAGGGTTCGGTCGTACAGAGgtgagtttct ... tttgctacagAGTTGCCTCTTCGCATGGCTGATTTTGGAGTGCTTCATAGAAATGAGCTTA

EST: gi|211403724|gb|FL311348.1|FL311348

EST:     GCTAATAGGGTTCGGTCGTACASAG                         AGTTGCCTCTTCGCATGGCTGATTTTGGAGTGCTTCATAGAAATGAGCTTA
genomic: GCTAATAGGGTTCGGTCGTACAGAGgtgagtttct ... tttgctacagAGTTGCCTCTTCGCATGGCTGATTTTGGAGTGCTTCATAGAAATGAGCTTA

EST: gi|211181488|gb|FL345837.1|FL345837

EST:     TTGTCCAGGACACTGTCTAATGTTTGCTAATAGGGTTCGGTCGTACAGAG                         AGTTGCCTCTTCGCATGGCTGATTTTGGAGTGCTTCATAGAAATGAGCTTA
genomic: TTGTCCAGGACACTGTCTAATGTTTGCTAATAGGGTTCGGTCGTACAGAGgtgagtttct ... tttgctacagAGTTGCCTCTTCGCATGGCTGATTTTGGAGTGCTTCATAGAAATGAGCTTA

EST: gi|211197538|gb|FL314132.1|FL314132

EST:     TTGTCCAGGACACTGTCTAATGTTTGCTAATAGGGTTCGGTCGTACAGAG                         AGTTGCCTCTTCGCATGGCTGATTTTGGAGTGCTTCATAGAAATGAGCTTA
genomic: TTGTCCAGGACACTGTCTAATGTTTGCTAATAGGGTTCGGTCGTACAGAGgtgagtttct ... tttgctacagAGTTGCCTCTTCGCATGGCTGATTTTGGAGTGCTTCATAGAAATGAGCTTA

EST: gi|50324858|gb|CO519984.1|CO519984

EST:     TTGTCCAGGACACTGTCTAATGTTTGCTAATAGGGTTCGGTCGTACAGAG                         AGTTGCCTCTTCGCATGGCTGATTTTGGAGTGCTTCATAGAAATGAGCTTA
genomic: TTGTCCAGGACACTGTCTAATGTTTGCTAATAGGGTTCGGTCGTACAGAGgtgagtttct ... tttgctacagAGTTGCCTCTTCGCATGGCTGATTTTGGAGTGCTTCATAGAAATGAGCTTA

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), 48 (downstream exon)
Score: 421

ATCGAGAAACAGGAATTTGGACTTAAGCCAATGAATTGTCCAGGACACTGTCTAATGTTTGCTAATAGGGTTCGGTCGTACAGAGgtgagtttct ... tttgctacagAGTTGCCTCTTCGCATGGCTGATTTTGGAGTGCTTCATAGAAATGAGCTTAGTGGTGCTCTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAG

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 302

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 363