ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ATAATCGATGCTGTTGTTGCTGCACGCATTTTAAATGCCACACTTGTTGTTCCCAAACTAGACCAAGCATCCTTCTGGAAAGATTCAAGgttaatttggagcgcaaatcacttctatgccagaatcttctaaggcttcctgtttttctaagatgactttaatgcatttgggttgtacttaatataacttttcccgcag

Basic information

species	Zea mays
transcript	GRMZM2G131699_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G131699_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os08g44015.1 (Oryza sativa), 5'ss of exon 5

ATAATCGATGCTGTTGTTGCTGCACGCATTTTAAATGCCACACTTGTTGTTCCCAAACTAGACCAAGCATCCTTCTGGAAAGATTCAAGgttaatttggagcgcaaatcacttctatgccagaatcttctaaggcttcctgtttttctaagatgactttaatgcatttgggttgtacttaatataacttttcccgcag
||||| |||||||||||||||||||| || ||||||||||||||||||||||||||| | || ||| |||| |||||||||||| ||||||||||||| ||     | | ||||  | ||  ||| |||||||||| ||  | |||||| ||  ||||  ||   | ||   ||||||         |||  | ||||
ATAATTGATGCTGTTGTTGCTGCACGTATCTTAAATGCCACACTTGTTGTTCCCAAATTGGATCAAACATCTTTCTGGAAAGATGCAAGgttaatttg-agtattgagcgcttcc-taccctaatattctaaggctgcccatgtttctatgaacacttacatttgtatg---tgtactg--------tttctctgcag

upper sequence: GRMZM2G131699_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA06G02110.1 (Glycine max), 5'ss of exon 4

ATAATCGATGCTGTTGTTGCTGCACGCATTTTAAATGCCACACTTGTTGTTCCCAAACTAGACCAAGCATCCTTCTGGAAAGATTCAAGgttaatttggagcgcaaatcacttctatgccagaatcttctaaggcttcctgtttttctaagatgactttaatgcatttgggttgta----cttaatataactt--ttcccgcag
|| |  ||||||||||||||||| || ||||| ||||| || ||||| ||||| ||| | || |||  ||| ||||||||||| || |||| | ||   |  |     ||  |   |||| ||    | |  |   |  || | || |||  |||  |   |      |   |||     ||| | |||  ||  ||   ||||
ATTACAGATGCTGTTGTTGCTGCGCGAATTTTGAATGCTACTCTTGTAGTTCCAAAATTGGATCAACGATCTTTCTGGAAAGACTCTAGgtcagttacaatagttgcacagat---tgcctgagcggtgtctgcacttttgctattgtaatttgaggtggttatcagagtactgtgaaatcttgacatactttgctttttgcag

upper sequence: GRMZM2G131699_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA04G02010.1 (Glycine max), 5'ss of exon 5

ATAATCGATGCTGTTGTTGCTGCACGCATTTTAAATGCCACACTTGTTGTTCCCAAACTAGACCAAGCATCCTTCTGGAAAGATTCAAGgttaatttggagcgcaaatcacttctatgccagaatcttctaaggcttcctgtttttctaagatgactttaatgcatttgggttgtac----ttaatataactt--ttcccgcag
|| |  |||||||||||||||||||| ||||| ||||| || ||||| ||||| ||| | || |||  ||| |||||||||||||| |||| | |    |  |     ||  |   |||| ||    | |  |   |  || | ||  ||  | |  |   |   |  |  ||||      || | |||  ||  ||   ||||
ATTACGGATGCTGTTGTTGCTGCACGAATTTTGAATGCTACTCTTGTGGTTCCAAAATTGGATCAACGATCTTTCTGGAAAGATTCTAGgtcagtcacaacagtggcacagat---tgcctgagcggtgtctgcacttttgctattgcaattttatgtggttatctgagtattgtgaaatgttgacatactttgctttttgcag

upper sequence: GRMZM2G131699_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv18s0001g00100.t01 (Vitis vinifera), 5'ss of exon 5

ATAATCGATGCTGTTGTTGCTGCACGCATTTTAAATGCCACACTTGTTGTTCCCAAACTAGACCAAGCATCCTTCTGGAAAGATTCAAGgttaatt-tggagcgcaaatcacttctatgccagaatcttctaaggcttcctgtttttctaagatgactttaatgcatttgggttgtacttaatataacttttcccgcag----------------------------------
||||  ||||||||||| ||||| |||||||||||||| || ||||| ||||| ||||| || ||    ||||| ||||  ||| | |||||| |  | ||  |   | ||  |   | |    | ||| |     ||  | ||||  |  | ||  | | | | |||    |  ||   |    | |||     |                                     
ATAACTGATGCTGTTGTCGCTGCCCGCATTTTAAATGCTACTCTTGTCGTTCCAAAACTGGATCAGAAGTCCTTTTGGAGGGATGCTAGgttagtcattgaatg---agcatatgcgttctgctacctttttgcaatttatattttgtt--gttggttctta-gtattcaaatcttaaaaagagcatcttgctgtgatatcagttaacaaatttgttactctgtcttctgcag

upper sequence: GRMZM2G131699_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv03s0038g03240.t01 (Vitis vinifera), 5'ss of exon 5

ATAATCGATGCTGTTGTTGCTGCACGCATTTTAAATGCCACACTTGTTGTTCCCAAACTAGACCAAGCATCCTTCTGGAAAGATTCAAGgttaatttggagcgcaaatcacttctatgccagaatcttctaaggcttcctgtttttctaagatgactttaatgcatttgggttgtacttaatataacttttcccgcag
||||  ||||| |||||||| || || ||||| |||||||| ||||||||||||||  | |||||   ||| || ||||| |||   ||||   |||          |||| | |       ||  | | ||  || | |     || |||   |  |  |||   |    || ||  | || |    |||   ||||
ATAACAGATGCAGTTGTTGCAGCTCGTATTTTGAATGCCACTCTTGTTGTTCCCAAGTTGGACCAGAAATCTTTTTGGAAGGATAGCAGgtctgttt----------tcacatttgcatattaacttaccaa--ctgcttaaa--tcaaaggaaatatatatgttgtgcatttatatgtgatgtggtgtttggtgcag

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|76010763|gb|DT937933.1|DT937933

EST:     ACACTTGTTGTTCCCAAACTAGACCAAGCATCCTTCTGGAAAGATTCAAG                         CAATTTTTCGGATATTTTTTACGCCGACTGGTTCATCTCATCTCTATCAAA
genomic: ACACTTGTTGTTCCCAAACTAGACCAAGCATCCTTCTGGAAAGATTCAAGgttaatttgg ... tttcccgcagCAATTTTTCGGATATTTTTTACGCCGACTGGTTCATCTCATCTCTATCAAA

EST: gi|89249642|gb|DY621428.1|DY621428

EST:     ACACTTGTTGTTCCCAAACTAGACCAAGCATCCTTCTGGAAAGATTCAAG                         CAATTTTTCGGATATTTTTTACGCCGACTGGTTCATCTCATCTCTATCAAA
genomic: ACACTTGTTGTTCCCAAACTAGACCAAGCATCCTTCTGGAAAGATTCAAGgttaatttgg ... tttcccgcagCAATTTTTCGGATATTTTTTACGCCGACTGGTTCATCTCATCTCTATCAAA

EST: gi|149110252|gb|EE190310.2|EE190310

EST:     ACACTTGTTGTTCCCAAACTAGACCAAGCATCCTTCTGGAAAGATTCAAG                         CAATTTTTCGGATATTTTTTACGCCGACTGGTTCATCTCATCTCTATCAAA
genomic: ACACTTGTTGTTCCCAAACTAGACCAAGCATCCTTCTGGAAAGATTCAAGgttaatttgg ... tttcccgcagCAATTTTTCGGATATTTTTTACGCCGACTGGTTCATCTCATCTCTATCAAA

EST: gi|78111344|gb|DV529741.1|DV529741

EST:     CCACTTGTTGTTCCCAAACTAGACCAAGCATCCTTCTGGAAAGAT-CAAG                         CAATTTTTCGGATATTTTTTACGCCGACTGGTTCATCTCATCTCTATCAAA
genomic: ACACTTGTTGTTCCCAAACTAGACCAAGCATCCTTCTGGAAAGATTCAAGgttaatttgg ... tttcccgcagCAATTTTTCGGATATTTTTTACGCCGACTGGTTCATCTCATCTCTATCAAA

EST: gi|71322750|gb|DR798057.1|DR798057

EST:     ACACTTGTTGTTCCCAAACTAGACCAAGCATCCTTCTGGAAAGATTCAAG                         CAATTTTTCGGATATTTTTTACGCCGACTGGTTCATCTCATCTCTATCAAA
genomic: ACACTTGTTGTTCCCAAACTAGACCAAGCATCCTTCTGGAAAGATTCAAGgttaatttgg ... tttcccgcagCAATTTTTCGGATATTTTTTACGCCGACTGGTTCATCTCATCTCTATCAAA

EST: gi|71308473|gb|DR790475.1|DR790475

EST:     ACACTTGTTGTTCCCAAACTAGACCAAGCATCCTTCTGGAAAGATTCAAG                         CAATTTTTCGGATATTTTTTACGCCGACTGGTTCATCTCATCTCTATCAAA
genomic: ACACTTGTTGTTCCCAAACTAGACCAAGCATCCTTCTGGAAAGATTCAAGgttaatttgg ... tttcccgcagCAATTTTTCGGATATTTTTTACGCCGACTGGTTCATCTCATCTCTATCAAA

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), 49 (downstream exon)
Score: 55

ATAATCGATGCTGTTGTTGCTGCACGCATTTTAAATGCCACACTTGTTGTTCCCAAACTAGACCAAGCATCCTTCTGGAAAGATTCAAGgttaatttgg ... tttcccgcagCAATTTTTCGGATATTTTTTACGCCGACTGGTTCATCTCATCTCTATCAAAGGATGTAAAGATTGTGAAAGAGCTTCCACATATAGGAGGTAAACTTCGG

Block sizes: 38 (upstream exon), 47 (downstream exon)
Score: 28

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 38