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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTATATTGTGGATGAGGTCAAAGACAAAAGTGACCAACAGATTGATGCTCTCTCATGGAAGCAGGAAAGTGTCGAAAATCTTCCTTTGCAGGAGAATGGgtacttctcatctttgttcctagcaagcatagttgtacctttgtttttccttgtgcagttaatgaatcctttaaaaaaaaattgcacgcaattgccaacctgagaacatttagtttgcctaatgtacagcactattcccacttgttcttcagtttgcctaatgtactgagtctgtcacttag

Basic information

species Zea mays
transcript GRMZM2G012601_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G012601_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g25370.1 (Oryza sativa), 5'ss of exon 7
AGTATATTGTGGATGAGGTCAAAGACAAAAGTGACCAACAGATTGATGCTCTCTCATGGAAGCAGGAAAGTGTCGAAAATCTTCCTTTGCAGGAGAATGGgtacttctc---atctttgttcctagcaagcatagttgtacctttgtttttccttgtgcagttaatgaatcctttaaaaaaaaattgcacgcaattgccaacctgagaacatt---tagtttgcctaatgtacagcactattcccacttgttcttcagtttgcctaatgtactga----------gtctgtcacttag
 |||| |||| |||||||| ||||| || |||| |||||| ||||||||||| ||||||||||||||  ||||  |||| ||||||||||| ||||||||||| || ||   || ||| || |||| | |  ||   ||     |      | || | || |    |||    ||         ||  | | |  ||| |  || ||||||||   |||||  ||  | | | | | | ||| | |    |||   | ||||| ||||||||| |          | ||  || ||||
GGTATCTTGTAGATGAGGTGAAAGATAAGAGTGGCCAACATATTGATGCTCTTTCATGGAAGCAGGAGGGTGTAAAAAACCTTCCTTTGCAAGAGAATGGgtatttttctcaatttttttttctagtatgtgtatcagtcttgctaaccaacattatacaatagtagaacttgttttttcc---tttaaaggaggtgcaattctaagaacattatatagttcaccacaggcatatcgc-attactatgccttcgaaaatttgcgtaatgtactcattacttggttgccttccatttag
















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|13558577|gb|BG549933.1|BG549933
EST:     TTGCAGGAGAATGG                         ATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGA
genomic: TTGCAGGAGAATGGgtacttctca ... tgtcacttagATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGA
EST: gi|87157176|gb|DY401965.1|DY401965
EST:     CTCTCATGGAAGCAGGAAAGTGTCGAAAATCTTCCTTTGCAGGAGAATGG                         ATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGA
genomic: CTCTCATGGAAGCAGGAAAGTGTCGAAAATCTTCCTTTGCAGGAGAATGGgtacttctca ... tgtcacttagATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGA
EST: gi|13558246|gb|BG549602.1|BG549602
EST:     TTGCAGGAGAATGG                         ATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGA
genomic: TTGCAGGAGAATGGgtacttctca ... tgtcacttagATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGA
EST: gi|211396604|gb|FL446415.1|FL446415
EST:     CTCTCATGGAAGCAGGAAAGTGTCGAAAATCTTCCTTTGCAGGAGAATGG                         ATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGA
genomic: CTCTCATGGAAGCAGGAAAGTGTCGAAAATCTTCCTTTGCAGGAGAATGGgtacttctca ... tgtcacttagATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGA
EST: gi|211220526|gb|FL333428.1|FL333428
EST:     CTCTCATGGAAGCAGGAAAGTGTCGAAAATCTTCCTTTGCAGGAGAATGG                         ATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGA
genomic: CTCTCATGGAAGCAGGAAAGTGTCGAAAATCTTCCTTTGCAGGAGAATGGgtacttctca ... tgtcacttagATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGA
EST: gi|32827453|gb|CD967131.1|CD967131
EST:     CTCTCATGGAAGCAGGAAAGTGTCGAAAATCTTCCTTTGCAGGAGAATGG                         ATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGA
genomic: CTCTCATGGAAGCAGGAAAGTGTCGAAAATCTTCCTTTGCAGGAGAATGGgtacttctca ... tgtcacttagATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGA
EST: gi|22542734|gb|BU093172.1|BU093172
EST:     CTCTCATGGAAGCAGGAAAGTGTCGAAAATCTTCCTTTGCAGGAGAATGG                         ATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGA
genomic: CTCTCATGGAAGCAGGAAAGTGTCGAAAATCTTCCTTTGCAGGAGAATGGgtacttctca ... tgtcacttagATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGA
EST: gi|211414363|gb|FL328793.1|FL328793
EST:     CTCTCATGGAAGCAGGAAAGTGTCGAAAATCTTCCTTTGCAGGAGAATGG                         ATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGA
genomic: CTCTCATGGAAGCAGGAAAGTGTCGAAAATCTTCCTTTGCAGGAGAATGGgtacttctca ... tgtcacttagATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGA
EST: gi|211288878|gb|FL323799.1|FL323799
EST:     CTCTCATGGAAGCAGGAAAGTGTCGAAAATCTTCCTTTGCAGGAGAATGG                         ATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGA
genomic: CTCTCATGGAAGCAGGAAAGTGTCGAAAATCTTCCTTTGCAGGAGAATGGgtacttctca ... tgtcacttagATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGA
EST: gi|21809632|gb|BQ667950.1|BQ667950
EST:     CTCTCATGGAAGCAGGAAAGTGTCGAAAATCTTCCTTTGCAGGAGAATGG                         ATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGA
genomic: CTCTCATGGAAGCAGGAAAGTGTCGAAAATCTTCCTTTGCAGGAGAATGGgtacttctca ... tgtcacttagATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGA
EST: gi|211396603|gb|FL446414.1|FL446414
EST:     CTCTCATGGAAGCAGGAAAGTGTCGAAAATCTTCCTTTGCAGGAGAATGG                         ATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGA
genomic: CTCTCATGGAAGCAGGAAAGTGTCGAAAATCTTCCTTTGCAGGAGAATGGgtacttctca ... tgtcacttagATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGA
EST: gi|211027850|gb|FL309697.1|FL309697
EST:     CTCTCATGGAAGCAGGAAAGTGTCGAAAATCTTCCTTTGCAGGAGAATGG                         ATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAKA
genomic: CTCTCATGGAAGCAGGAAAGTGTCGAAAATCTTCCTTTGCAGGAGAATGGgtacttctca ... tgtcacttagATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGA

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), 45 (downstream exon)
Score: 69

AGTATATTGTGGATGAGGTCAAAGACAAAAGTGACCAACAGATTGATGCTCTCTCATGGAAGCAGGAAAGTGTCGAAAATCTTCCTTTGCAGGAGAATGGgtacttctca ... tgtcacttagATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 45

AGTATATTGTGGATGAGGTCAAAGACAAAAGTGACCAACAGATTGATGCTCTCTCATGGAAGCAGGAAAGTGTCGAAAATCTTCCTTTGCAGGAGAATGGgtacttctca ... tgtcacttagATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 68

AGTATATTGTGGATGAGGTCAAAGACAAAAGTGACCAACAGATTGATGCTCTCTCATGGAAGCAGGAAAGTGTCGAAAATCTTCCTTTGCAGGAGAATGGgtacttctca ... tgtcacttagATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 49

AGTATATTGTGGATGAGGTCAAAGACAAAAGTGACCAACAGATTGATGCTCTCTCATGGAAGCAGGAAAGTGTCGAAAATCTTCCTTTGCAGGAGAATGGgtacttctca ... tgtcacttagATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTATATTGTGGATGAGGTCAAAGACAAAAGTGACCAACAGATTGATGCTCTCTCATGGAAGCAGGAAAGTGTCGAAAATCTTCCTTTGCAGGAGAATGGgtacttctcatctttgttcctagcaagcatagttgtacctttgtttttccttgtgcagttaatgaatcctttaaaaaaaaattgcacgcaattgccaacctgagaacatttagtttgcctaatgtacagcactattcccacttgttcttcagtttgcctaatgtactgagtctgtcacttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA