Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAACCTCGGGGCATGCCCATGATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGGgtaaggatggccatgttctccttctccctgcatgattgtactgtactgtttaaactttgtgtttgaattttgtgcag

Basic information

species Zea mays
transcript GRMZM2G138125_T01
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138125_T01 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os04g59624.2 (Oryza sativa), 5'ss of exon 18
CAAACCTCGGGGCATGCCCATGATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGGgtaag-gatggccatg---ttctccttctccctgcatgattgtactgtactgtt-taaactttg-tgtttgaattttgtgcag
    | ||| |  ||||| |||    || |||| || ||||||||| |||||||||||||||| ||||| ||||||| |  |  ||||    |       |  ||    |  || |   |   ||| |  ||  || || |||  ||||||| ||
---TCGTCGAGCTATGCCAATGG---CCAAGCACTACTACAAGGGAGCCTCATCTGACTATGTTGCCAATGGgtaagaggagttcatgggacttaatcaatggcttttgggctgcataattaagttgtgtaccgtgctgcttg--ttttgtgtag

upper sequence: GRMZM2G138125_T01 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os04g59624.3 (Oryza sativa), 5'ss of exon 17
CAAACCTCGGGGCATGCCCATGATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGGgtaag-gatggccatg---ttctccttctccctgcatgattgtactgtactgtt-taaactttg-tgtttgaattttgtgcag
||  | ||| |  ||||| |||    || |||| || ||||||||| |||||||||||||||| ||||| ||||||| |  |  ||||    |       |  ||    |  || |   |   ||| |  ||  || || |||  ||||||| ||
CAGTCGTCGAGCTATGCCAATGG---CCAAGCACTACTACAAGGGAGCCTCATCTGACTATGTTGCCAATGGgtaagaggagttcatgggacttaatcaatggcttttgggctgcataattaagttgtgtaccgtgctgcttg--ttttgtgtag
















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|5525254|gb|AI861093.1|AI861093
EST:     ATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGG                         GGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTA
genomic: ATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGGgtaaggatgg ... ttttgtgcagGGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTA
EST: gi|32943511|gb|CF048330.1|CF048330
EST:     ATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGG                         GGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTA
genomic: ATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGGgtaaggatgg ... ttttgtgcagGGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTA
EST: gi|67034321|gb|CO462871.1|CO462871
EST:     ATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGG                         GGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTA
genomic: ATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGGgtaaggatgg ... ttttgtgcagGGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTA
EST: gi|29130029|gb|CB380733.1|CB380733
EST:     ATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGG                         GGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTA
genomic: ATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGGgtaaggatgg ... ttttgtgcagGGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTA
EST: gi|28873895|gb|CB329824.1|CB329824
EST:     GGATCCTCATCTGACTATGTCGCCAACGG                         GGCATTTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTA
genomic: GGATCCTCATCTGACTATGTCGCCAACGGgtaaggatgg ... ttttgtgcagGGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTA
EST: gi|33091324|gb|CF051318.1|CF051318
EST:     ATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGG                         GGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTA
genomic: ATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGGgtaaggatgg ... ttttgtgcagGGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTA
EST: gi|67020146|gb|CO448895.1|CO448895
EST:     TGTCGCC-TCGG                         GGCATCTTTTGCGCTGAAGCCACAGGATGAAAGTTTCACTGTTCGAAACTA
genomic: TGTCGCCAACGGgtaaggatgg ... ttttgtgcagGGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTA
EST: gi|32937325|gb|CF042144.1|CF042144
EST:     ATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGG                         GGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCCCTGTTCGAAACTA
genomic: ATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGGgtaaggatgg ... ttttgtgcagGGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTA
EST: gi|71419756|gb|DR804887.1|DR804887
EST:     ATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGG                         GGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTA
genomic: ATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGGgtaaggatgg ... ttttgtgcagGGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTA
EST: gi|71419751|gb|DR804886.1|DR804886
EST:     ATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGG                         GGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTA
genomic: ATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGGgtaaggatgg ... ttttgtgcagGGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTA
EST: gi|31909601|gb|CD651000.1|CD651000
EST:     ATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGG                         GGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTA
genomic: ATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGGgtaaggatgg ... ttttgtgcagGGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTA
EST: gi|60355698|gb|DN222671.1|DN222671
EST:     ATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGG                         GGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTA
genomic: ATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGGgtaaggatgg ... ttttgtgcagGGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTA
EST: gi|32930746|gb|CF035558.1|CF035558
EST:     CTATGTCGCCAACGG                         GGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTA
genomic: CTATGTCGCCAACGGgtaaggatgg ... ttttgtgcagGGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTA
EST: gi|60394842|gb|DN227711.1|DN227711
EST:     ATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGG                         GGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTA
genomic: ATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGGgtaaggatgg ... ttttgtgcagGGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTA

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: 48 (upstream exon), 48 (downstream exon)
Score: 94

CAAACCTCGGGGCATGCCCATGATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGGgtaaggatgg ... ttttgtgcagGGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTACATTCCAAGTAACAGAAGCGCAGAGAGTCCTGAAGAGATAAAGGCAAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 28

CAAACCTCGGGGCATGCCCATGATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGGgtaaggatgg ... ttttgtgcagGGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTACATTCCAAGTAACAGAAGCGCAGAGAGTCCTGAAGAGATAAAGGCAAGA


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 18

CAAACCTCGGGGCATGCCCATGATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGGgtaaggatgg ... ttttgtgcagGGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTACATTCCAAGTAACAGAAGCGCAGAGAGTCCTGAAGAGATAAAGGCAAGA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 14

CAAACCTCGGGGCATGCCCATGATGCCCCAGCAATATTACAAGGGATCCTCATCTGACTATGTCGCCAACGGgtaaggatgg ... ttttgtgcagGGCATCTTTTGCGCTGAAGCCAAAGGATGAAAGTTTCACTGTTCGAAACTACATTCCAAGTAACAGAAGCGCAGAGAGTCCTGAAGAGATAAAGGCAAGA