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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAACGTGCGCAAACAACAAGAGCTTGATAAGAATCAGGTAGTTGACAAAACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgccttcccctcccatccccatgttgtctttaagaataaagggcatgtgagtatggctaggttgatagattctactcctatatatgatacatt...

Basic information

species Zea mays
transcript GRMZM2G484880_T04
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G484880_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os11g34300.2 (Oryza sativa), 5'ss of exon 4
GAAAACGTGCGCAAACAACAAGAGCTTGATAAGAATCAGGTAGTTGACAAAACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgccttcccctcccatccccatgttgtctttaagaataaagggcatgtgagtatggctaggttgatagattctactcctatatatgatacatt-------
|||||  | |||||||||||||||||||| ||||  || |||||||||||||   | || |||||||||||| | |||||||| ||||||| ||| ||||||||||||      |||||   |  ||||  ||   || |  | |     ||||    | |  || |||  |||| || |||| ||||  |||| |   |       
GAAAATATCCGCAAACAACAAGAGCTTGAAAAGAGCCAAGTAGTTGACAAAAGCGTAAAATCTGGACGGTCAGCGCAGCATAAGCCAAAAGGCTCTAATGgttagcttatgcctccctcttctttccat--tggaattgatgaca-----catgctttttttactgggtcaatagtttttacttctatccatgacaagctagatgta

upper sequence: GRMZM2G484880_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g01130.1 (Oryza sativa), 5'ss of exon 3
GAAAACGTGCGCAAACAACAAGAGCTTGATAAGAATCAGGTAGTTGACAAAACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgccttcccctcccatccccatgttgtctttaagaataaagggcatgtgagtatg-gctaggttgatagattctactcctatatatgatacatt
|||||  | |||||||||||||||||||| ||||  || | |||||||||||   | || |||||||||||| | |||||||| |||||||  || ||||||||||||      |||||   |||  ||  | ||  |  ||||  |   |   ||  | |   || ||| ||||| || |||| ||||   ||| |    
GAAAATATCCGCAAACAACAAGAGCTTGAAAAGAGCCAAGCAGTTGACAAAAGTGTAAAATCTGGACGGTCAGCGCAGCATAAGCCAAAAGGTTCTAATGgttagcttattcctccctcttctccgtattgtttccattggaattgattacgcatgcttttttactgggtcgatagtttttacttctatccgtgacaagc-
















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|76912438|gb|DV164732.1|DV164732
EST:     AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
genomic: AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
EST: gi|71434326|gb|DR815376.1|DR815376
EST:     AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
genomic: AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
EST: gi|6031476|gb|AW076378.1|AW076378
EST:     AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
genomic: AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
EST: gi|211058545|gb|FK994410.1|FK994410
EST:     AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCAT
genomic: AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCAT
EST: gi|93284203|gb|EB676467.1|EB676467
EST:     AACAATGAAGTCTGGACGGTCAACACAGCATAAACCCAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAAAGTCTCA
genomic: AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
EST: gi|13178287|gb|BG349545.1|BG349545
EST:     AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
genomic: AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
EST: gi|211058547|gb|FK994412.1|FK994412
EST:     AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
genomic: AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
EST: gi|32913308|gb|CF018120.1|CF018120
EST:     AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
genomic: AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
EST: gi|26456042|gb|CA827625.1|CA827625
EST:     AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
genomic: AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
EST: gi|71438521|gb|DR819571.1|DR819571
EST:     AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
genomic: AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
EST: gi|166482492|gb|EG041825.1|EG041825
EST:     GGTCAACACAGCATAAACCAAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
genomic: GGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
EST: gi|71331879|gb|DR802817.1|DR802817
EST:     AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
genomic: AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
EST: gi|32865668|gb|CF005350.1|CF005350
EST:     AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
genomic: AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
EST: gi|31997934|gb|CD661839.1|CD661839
EST:     AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATG                         CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
genomic: AACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA
EST: gi|211058548|gb|FK994413.1|FK994413
EST:     ACAATGAAGTCTGGACGGGTCA-CACAGCATAAACCCAAAGTCTCCAATG                         CGGATGCAAAAGCTGA
genomic: ACAATGAAGTCTGGACGG-TCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGA

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: 49 (upstream exon), 49 (downstream exon)
Score: 393

GAAAACGTGCGCAAACAACAAGAGCTTGATAAGAATCAGGTAGTTGACAAAACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA


Block sizes: 48 (upstream exon), 39 (downstream exon)
Score: 199

GAAAACGTGCGCAAACAACAAGAGCTTGATAAGAATCAGGTAGTTGACAAAACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 199

GAAAACGTGCGCAAACAACAAGAGCTTGATAAGAATCAGGTAGTTGACAAAACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 211

GAAAACGTGCGCAAACAACAAGAGCTTGATAAGAATCAGGTAGTTGACAAAACAATGAAGTCTGGACGGTCAACACAGCATAAACCAAAAGTCTCCAATGgttagcttgc ... cattgttcagCGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA