ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAGgttagttttactttaagtatggtgtattttgggtggcattttgacttctcttgacatctgatctgtatattctatgttaaag

Basic information

species	Zea mays
transcript	GRMZM2G017089_T01
intron #	8
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G017089_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os03g21990.1 (Oryza sativa), 5'ss of exon 10

GACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAGgttagttt-tactttaa-gtatggtgtattttgggtggcattttgac-ttctcttgacatctgatctgtatattctatgttaaag
| |||||||| |||||||| ||||| ||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| || || ||  | |||   || | | |    ||||| ||| | || || | |||| |  | | |   ||  || || |||
GGCTTGCTGTGAGCCAACGGCACACATATTTATTTTCTGCTGGTGATGACAAACAAGTAAAGTGTTGGGATCTTGAACAAAACAAGgttagcttatagttcgatgtagattgcagtatacagggcatattggcattatcgtaacattttgtttct---tttcatttttaag

upper sequence: GRMZM2G017089_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA09G04910.1 (Glycine max), 5'ss of exon 9

GACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAGgttagttttactttaagtatggtgtattttgggtggcattttgacttctcttgacatctgatctgtatattctatgttaaag-------------------
| |||||||| ||| |  | || |||||  | || ||||||||||| || |||||||| |||||||||||||||||||| || ||||| || | | | ||   | |  ||| ||         ||||   |   |  ||  |    |||    |      |  ||||                    
GTCTTGCTGTTAGCAACAGACATACTTACATGTTCTCTGCTGGTGACGATAAACAAGTTAAATGTTGGGATCTTGAACAGAATAAGgtcagatctccatttcatttattgttttggactgaatatttcagcagttactggaactccatcaaattgcaggctactaaaatacatgatattgtatttag

upper sequence: GRMZM2G017089_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA15G15960.2 (Glycine max), 5'ss of exon 8

GACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAGgttagttttac-tttaagtatggtgtattttgggtggcat-------------tttgacttctcttgacatctgatctgtatattctatgttaaag-------
| |||||||| ||| |  | || |||||  | || |||||||||||||| |||||||| ||||||||||| |||||||| || ||||| |  | | | ||| | ||     | || |||   | ||              |||||| |     | | | |     || | |  ||| ||  |       
GTCTTGCTGTTAGCAACAGACATACTTACATGTTCTCTGCTGGTGATGATAAACAAGTTAAATGTTGGGACCTTGAACAGAATAAGgtcaaatctccgtttcattagtaatttttctggactgaatatttcagcagttacttgactccatcaaataacaggctactaaaatacatgatattgtatttag

upper sequence: GRMZM2G017089_T02 (Zea mays), 5'ss of exon 8
lower sequence: AT3G16650.1 (Arabidopsis thaliana), 5'ss of exon 9

GACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAGgtt--agttttactttaagtatggtgtattttgggtggcattttgacttctcttgacatctgatctgtatattctatgttaaag-----------------
| || ||||| ||| |  | || || ||| | |||||||||||||||||||| ||||| ||||| ||||| ||||| || || ||||||  |  |  |   |   | |  | |  | ||  |   | ||   |||||| |||  |    | |  || | | ||||    |                 
GCCTCGCTGTAAGCAATAGACATACCTATATGTTTTCTGCTGGTGATGACAAGCAAGTCAAATGCTGGGACCTTGAGCAGAATAAGgtttaaactcgatgatggatttcatctcatctgtatattaattactcttctcctgatctgaacttttcatgtccaatgtctttggaatttgtctttgatag

upper sequence: GRMZM2G017089_T02 (Zea mays), 5'ss of exon 8
lower sequence: AT4G15900.1 (Arabidopsis thaliana), 5'ss of exon 9

GACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAGgttagttttactttaagtatggtgtattttgggtggcattttgacttctcttgacatctgatctgtatattctatgttaaag
| || ||||| ||| | || || || ||| | || ||||||||||||||||| ||||| ||||| ||||| ||||| || || |||||||     ||| ||    |  | |   ||   |||  || | |  |||  ||   |  ||  | |  |||  ||       
GCCTCGCTGTAAGCAATCGACATACCTATATGTTCTCTGCTGGTGATGACAAGCAAGTCAAATGCTGGGACCTTGAGCAGAATAAGgtta---caactcta----ttctcttcattatctggatttctcatatctaatgctcttggaatttttgatttgatag-----

upper sequence: GRMZM2G017089_T02 (Zea mays), 5'ss of exon 8
lower sequence: Vv05s0077g02310.t01 (Vitis vinifera), 5'ss of exon 9

GACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAGgttagt-tttactttaagtat---ggtgtattttgggtggcattttgacttctcttgacatctgatctgtatattctatgttaaag
| |||||||| ||| |    || || ||| | || || |||||||||||||||||||| ||||| ||||| |||||||| || ||||||||    |  |||||       | || ||  ||     ||  | ||||    || | ||   || | | | |||| |||| |  
GCCTTGCTGTTAGCAACAAACATACATATATGTTCTCAGCTGGTGATGACAAACAAGTTAAATGCTGGGACCTTGAACAGAATAAGgttagaaccttttttaaactcaccgctgaatcctgtactacaagt-gactaaa-ttcatatgctatatattt-ttctttgttcag-

upper sequence: GRMZM2G017089_T02 (Zea mays), 5'ss of exon 8
lower sequence: PP1S402_49V6.1 (Physcomitrella patens), 5'ss of exon 8

GACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAGgttagttttactttaagtatggtgtattttgggtggcattttgacttctcttgacatctgatctgtatattc-tatgttaaag----------------------------------------------
| ||||| || |||   || ||  |||||||||| || ||||||||||||||||| || |||||||||||||||||| | || |||||  ||      ||       |  | ||    || ||||    | ||   |    |     ||| |  || | | |  || |                                               
GCCTTGCAGTGAGCGCCCGGCATCCTTATTTATTCTCAGCTGGTGATGACAAACAGGTCAAATGTTGGGATCTTGAATACAATAAGgtgtgtccaggcttttacgacgcttgttggttgtagcatccgtaattagttcatgaatgtgtctatgaatccatgtactatatgtatttatcgctgaggatctttgctctggtgtattggtttgtgcag

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|78085590|gb|DV513983.1|DV513983

EST:     CTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAG                         GTTATTAGGTCCTACCATGGGCATCTGAGTGGTGTTTACTGCCT
genomic: CTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAGgttagtttta ... tatgttaaagGTTATTAGGTCCTACCATGGGCATCTGAGTGGTGTTTACTGCCT

EST: gi|71432304|gb|DR813354.1|DR813354

EST:     CTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAG                         GTTATTAGGTCCTACCATGGGCATCTGAGTGGTGTTTACTGCCTAGCTCTC
genomic: CTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAGgttagtttta ... tatgttaaagGTTATTAGGTCCTACCATGGGCATCTGAGTGGTGTTTACTGCCTAGCTCTC

EST: gi|6021220|gb|AW066148.1|AW066148

EST:     CTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAG                         GTTATTAGGTCCTACCATGGGCATCTGAGTGGTGTTTACTGCCTAGCTCTC
genomic: CTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAGgttagtttta ... tatgttaaagGTTATTAGGTCCTACCATGGGCATCTGAGTGGTGTTTACTGCCTAGCTCTC

EST: gi|32933221|gb|CF038033.1|CF038033

EST:     CTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAG                         GTTATTAGGTCCTACCATGGGCATCTGAGTGGTGTTTACTGCCTAGCTCTC
genomic: CTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAGgttagtttta ... tatgttaaagGTTATTAGGTCCTACCATGGGCATCTGAGTGGTGTTTACTGCCTAGCTCTC

EST: gi|211016045|gb|FL237689.1|FL237689

EST:     CTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAG                         GTTATTAGGTCCTACCATGGGCATCTGAGTGGTGTTTACTGCCTAGCTCTC
genomic: CTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAGgttagtttta ... tatgttaaagGTTATTAGGTCCTACCATGGGCATCTGAGTGGTGTTTACTGCCTAGCTCTC

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: 46 (upstream exon), 49 (downstream exon)
Score: 183

GACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAGgttagtttta ... tatgttaaagGTTATTAGGTCCTACCATGGGCATCTGAGTGGTGTTTACTGCCTAGCTCTCCATCCAACAATTGATATCTTACTGACTGGTGGCCGGGATTCAGTTTGCA

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 117

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 112