ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AACATGACTTCACCCCAAAGGTGTCAGACTTTGGCTTAGCAAGGACAGCTTTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaatctgaaattactatctttacttcttcatagttgattcaataccatcaactcatattacaaaattctggtcaatttctcttag

Basic information

species	Zea mays
transcript	GRMZM2G330298_T01
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G330298_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g51290.1 (Oryza sativa), 5'ss of exon 12

AACATGACTTCACCCCAAAGGTGTCAGACTTTGGCTTAGCAAGGACAGCTTTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgcta-aatctgaaattactatctttacttcttcatagttgattcaataccatcaactcatattacaaaattctggtcaatttctcttag
|||||||||||||||| |||||||||||||||||| ||||||| |||||  | |||||||| || |||||||||||||||||||| ||||||||||| ||||| | |   ||||||||||| |||||| ||| | |  |||||| || || | | ||| || | |    || ||| ||   || |  | ||||
AACATGACTTCACCCCCAAGGTGTCAGACTTTGGCCTAGCAAGAACAGCCATAGGTGAGGGGAATGAGCATATTTCAACTCGTGTTATGGGAACTTTCGGgtaagttttgatctgaaattattatctt-actacct-gtagttggtt-aacatcctcaccttaaa----aagattatg---aactctttttag

upper sequence: GRMZM2G330298_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA13G16380.1 (Glycine max), 5'ss of exon 9

AACATGACTTCACCCCAAAGGTGTCAGACTTTGGCTTAGCAAGGACAGCTTTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaatctgaaattactatctttacttcttcatagttgattcaataccatcaact-catattacaaaattctggtc--aatttctcttag---------
|| |||| || || ||||| || || || |||||  | ||  | |||||   || ||||| |||| |||| || ||||| ||||||||||||||||||||||| |  || | |    |  || |||||  |   |  | |    ||  ||  | | | || | |   |  |  ||    ||  | ||   | ||          
AAGATGATTTTACACCAAAAGTATCTGATTTTGGACTGGCCCGAACAGCAACGGATGAGGAAAACAAGCACATATCAACACGTGTCATGGGAACTTTTGGgtagg--aagttttc--tccctttcttttttctgttttggaaatttttatctcttaagcttcctgccattagttttccttctgacttcaacataaaatgaacta

upper sequence: GRMZM2G330298_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA17G06250.1 (Glycine max), 5'ss of exon 3

-AACATGACTTCACCCCAAAGGTGTCAGACT-TTGGCTTAGCAAGGACAGCTTTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaatctgaaattactatctttacttcttcatagttgat---tcaataccat-caactca--tattacaaaattctggtcaatttctcttag--
 |    |||||||   | |  |   || | | |||| || ||  | || || | || || ||  ||| | || || ||||||||||||||||||| |||||||||||            || |  | | |  ||    | | || ||   |||    | | ||| | |  | |    | | |       |||   |||    
CATAGGGACTTCAAGTCTA--GCAACATATTGTTGGATTGGCTTGAACGGCATCGGATGGGGAGAACAAACACATATCAACTCGTGTCATGGGAAGTTTTGGgtatgaagttgtcttcctttcattttctgttttggaaaattttatctctcagcttcttgcaatttagttgtcctcagacttcaacatattaaacttgtgg

upper sequence: GRMZM2G330298_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv11s0016g02150.t01 (Vitis vinifera), 5'ss of exon 11

AACATGACTTCACCCCAAAGGTGTCAGACTTTGGCTTAGCAAGGACAGCTTTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaatc--tgaaattactatctttacttcttcatagttgattcaataccatcaactcatattacaa----aattctggtcaatttctcttag----
||||||| || || ||||| ||||| |||||||| || ||  | |||||  ||| ||||| ||||   || || ||||| ||||||||||||||||||||||||| |  |||  |   |||| |||  ||| |  || ||   || |||  |   |||| |  | ||||| |     | |||    |   |||  |      
AACATGATTTTACACCAAAAGTGTCCGACTTTGGTTTGGCTCGCACAGCCATGGATGAGGAAAACAGACACATCTCAACACGTGTCATGGGAACTTTTGGgtatgatttatcgttagtattattattattattatttaat--ctgcttccttttaatcaccctacattaccatgccgactctataaaccatcttctgagact

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|211520168|gb|FL238542.1|FL238542

EST:     TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGG                         GTATTTTGCTCCTGAATATGCAATGACTGGCCATC
genomic: TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaa ... tttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATC

EST: gi|101397928|gb|EB820841.1|EB820841

EST:     TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGG                         GTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA
genomic: TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaa ... tttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA

EST: gi|211132438|gb|FL443442.1|FL443442

EST:     TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGG                         GTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA
genomic: TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaa ... tttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA

EST: gi|211541315|gb|FL466512.1|FL466512

EST:     TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGG                         GTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA
genomic: TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaa ... tttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA

EST: gi|5268951|gb|AI770915.1|AI770915

EST:     TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGG                         GTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA
genomic: TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaa ... tttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA

EST: gi|211541314|gb|FL466511.1|FL466511

EST:     TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGG                         GTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA
genomic: TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaa ... tttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA

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: 40 (upstream exon), 47 (downstream exon)
Score: 81

AACATGACTTCACCCCAAAGGTGTCAGACTTTGGCTTAGCAAGGACAGCTTTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaa ... tttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA

Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 59

Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 110