ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TTGACCAGCAGTGGAACGCTAGAGTATCCGATTTTGGGCTTGCAAAGCTATTGTGGTCAGAGAAAAGCTATGTTACAACCCGTGTTATGGGAACATTTGGgttagtagtgagaacccttccatcctcatcgctactcagtctactacaaacggagctagatcgatcttgtcgttactgagctattggtgctgttgcag

Basic information

species	Zea mays
transcript	GRMZM2G176604_T04
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G014366_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g03410.1 (Oryza sativa), 5'ss of exon 4

TTGACCAGCAGTGGAACGCTAGAGTATCCGATTTTGGGCTTGCAAAGCTATTGTGGTCAGAGAAAAGCTATGTTACAACCCGTGTTATGGGAACATTTGGgttagtagtgagaacccttccatcctcatcgctactcagtctactacaaacggagctagatcgatcttgtcgttactgagctattggtgctgttgcag
|||||||||| ||||| |||| ||| || |||||||| ||||| ||||||||||| ||||||| ||| |||||||| ||||||||||||||||| |||||||||||| ||| || ||   ||    |            | ||||  | |   |  |   |  ||||| || | |||||   |||||   ||||||||
TTGACCAGCAATGGAATGCTAAAGTGTCAGATTTTGGTCTTGCGAAGCTATTGTGCTCAGAGAGAAGTTATGTTACTACCCGTGTTATGGGAACCTTTGGgttagtattgacaatccacacacaacc------------tttactgtacataaaagttagtacatcttatcatgactgaa--attggctatgttgcag

upper sequence: GRMZM2G014366_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA09G39160.1 (Glycine max), 5'ss of exon 4

TTGACCAGCAGTGGAACGCTAGAGTATCCGATTTTGGGCTTGCAAAGCTATTGTGGTCAGAGAAAAGCTATGTTACAACCCGTGTTATGGGAACATTTGGgttagtagtgagaacccttccatcctcatcgcta-ctcagtctactacaaacggagctagatcgatcttgtcgttactgagctattggtgc----tgttgcag------------------------------------------
|||| |  || |||||| | |  || ||||||||||| ||||| ||||| ||||| || ||||| || || || ||||| || || ||||| |||||||||||||||     || |    ||| ||| |  ||  || |    | || ||   |  | || ||     ||     | || |  | |||| |    ||||  |                                           
TTGATCGCCAATGGAACTCCAAGGTTTCCGATTTTGGACTTGCTAAGCTTTTGTGTTCTGAGAATAGTTACGTCACAACTCGAGTGATGGGGACATTTGGgttagtatgattaagctaagcattctcctatctctcttaccaaattataattagttcaagttcctgtatgattgcaatgtgtaagtggtccctaatgtttaaaggtcaaaagatattgattctctccttttttctttttctgtag

upper sequence: GRMZM2G014366_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA18G47170.1 (Glycine max), 5'ss of exon 4

TTGACCAGCAGTGGAACGCTAGAGTATCCGATTTTGGGCTTGCAAAGCTATTGTGGTCAGAGAAAAGCTATGTTACAACCCGTGTTATGGGAACATTTGGgttagtagtgagaacccttccatcctc--atcgcta-ctcagtctactacaaacggagctagatcgatcttgtcgttactgagctattggtgctgttgcag---------------------------------------------------
 ||| |  || |||||| | |  || || |||||||||||||| ||||| || || || ||||| || ||||| ||||| || || |||||||||||||||||||||     || |    |||  ||  ||| ||  || |    | || ||   |   ||  |   || |||  | | ||   | |    |  ||| ||                                                    
-TGATCGCCAATGGAACTCCAAGGTTTCTGATTTTGGGCTTGCTAAGCTTTTATGTTCTGAGAATAGTTATGTCACAACTCGAGTGATGGGAACATTTGGGttagtatgattaagctaagcattatcctatctctctcttaccaaattataattagttttaagt---tcctgt-atgattgcaatgtgtaagtggttccaaatttttaaaggtaaaatgatattgattctctcctttttctttttctgtagt

upper sequence: GRMZM2G014366_T03 (Zea mays), 5'ss of exon 4
lower sequence: Vv15s0046g02030.t01 (Vitis vinifera), 5'ss of exon 4

TTGACCAGCAGTGGAACGCTAGAGTATCCGATTTTGGGCTTGCAAAGCTATTGTGGTCAGAGAAAAGCTATGTTACAACCCGTGTTATGGGAACATTTGGgttagtagtgagaacccttccatcctcatcgctactcagtctactacaaacggagctagatcgatcttgtcgttactgagctattggtgctgttgcag
|||| |  || |||||| |||  || || ||||||||||| |||||||| || || || |||| ||| ||||| || || ||||| ||||||||||| ||||||||        || || | |  |  |    | ||   || | ||| |    |  | || ||     |   |  | |  |     ||   || |||
TTGATCGCCAATGGAACTCTAAGGTGTCTGATTTTGGGCTGGCAAAGCTCTTATGTTCTGAGATAAGTTATGTAACGACTCGTGTGATGGGAACATTCGGgttagt--------ccatttccttttggtaatgaatcgaccttc-acataaaatggcatattgagaagatttctgat-atttcccaatggctttccag

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|60352497|gb|DN219470.1|DN219470

EST:     TTGTGGTCAGAGAAAAGCTATGTTACAACCCGTGTTATGGGAACATTTGG                         GTACGTGGCGCCTGAATATGCCAGCACCGGAATGCTGAACGAGAGGAGTGA
genomic: TTGTGGTCAGAGAAAAGCTATGTTACAACCCGTGTTATGGGAACATTTGGgttagtagtg ... gctgttgcagGTACGTGGCGCCTGAATATGCCAGCACCGGAATGCTGAACGAGAGGAGTGA

EST: gi|60352421|gb|DN219394.1|DN219394

EST:     TTGTGGTCAGAGAAAAGCTATGTTACAACCCGTGTTATGGGAACATTTGG                         GTACGTGGCGCCTGAATATGCCAGCACCGGAATGCTGAACGAGAGGAGTGA
genomic: TTGTGGTCAGAGAAAAGCTATGTTACAACCCGTGTTATGGGAACATTTGGgttagtagtg ... gctgttgcagGTACGTGGCGCCTGAATATGCCAGCACCGGAATGCTGAACGAGAGGAGTGA

EST: gi|60394580|gb|DN227450.1|DN227450

EST:     TTGTGGTCAGAGAAAAGCTATGTTACAACCCGTGTTATGGGAACATTTGG                         GTACGTGGCGCCTGAATATGCCAGCACCGGAATGCTGAACGAGAGGAGTGA
genomic: TTGTGGTCAGAGAAAAGCTATGTTACAACCCGTGTTATGGGAACATTTGGgttagtagtg ... gctgttgcagGTACGTGGCGCCTGAATATGCCAGCACCGGAATGCTGAACGAGAGGAGTGA

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: 45 (upstream exon), 48 (downstream exon)
Score: 216

TTGACCAGCAGTGGAACGCTAGAGTATCCGATTTTGGGCTTGCAAAGCTATTGTGGTCAGAGAAAAGCTATGTTACAACCCGTGTTATGGGAACATTTGGgttagtagtg ... gctgttgcagGTACGTGGCGCCTGAATATGCCAGCACCGGAATGCTGAACGAGAGGAGTGATGTATATAGCTTTGGCGTACTCATAATGGAGATCATCACTGGTAGATCT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 272

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 194