Skip to another splice site:
1  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCAGCGGAAGCTGGAGTTCGCGGCGAGGTCTCAGTTGCTCGGCTACTTCCTCTGGACCGTCGGCTTCGACGATTCGAACAGCACAATCTCCAGGAAAGgtcagtagctagctactgagacatgacagcgtatgtaaaatctcatcttgatatataatcctgaatccatgtaaactaatgcaagatgcaatggttgactcatgcag

Basic information

species Zea mays
transcript GRMZM2G141456_T01
intron # 1
splice site 5'
intron type U2

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|50329785|gb|CO524911.1|CO524911
EST:     CCTCTGGACCGTCGGCTTCGACGATTCGAACAGCACAATCTCCAGGAAAG                         CATCGGAGTCATGGCACCAGTATGCTCAGGGTGGTTTTGGAATCATGCACG
genomic: CCTCTGGACCGTCGGCTTCGACGATTCGAACAGCACAATCTCCAGGAAAGgtcagtagct ... actcatgcagCATCGGAGTCATGGCACCAGTATGCTCAGGGTGGTTTTGGAATCATGCACG
EST: gi|71763906|gb|DR961843.1|DR961843
EST:     CCTTTGGACCGTCGGCTTCGACGATTCGAACAGCACAATCTCCAGGAAAG                         CATCGGAGTCATGGCACCAGTATGCTCAGGGTGGTTTTGGAATCATGCACG
genomic: CCTCTGGACCGTCGGCTTCGACGATTCGAACAGCACAATCTCCAGGAAAGgtcagtagct ... actcatgcagCATCGGAGTCATGGCACCAGTATGCTCAGGGTGGTTTTGGAATCATGCACG
EST: gi|50330224|gb|CO525350.1|CO525350
EST:     CCTCTGGACCGTCGGCTTCGACGATTCGAACAGCACAATCTCCAGGAAAG                         CATCGGAGTCATGGCACCAGTATGCTCAGGGTGGTTTTGGAATCATGCACG
genomic: CCTCTGGACCGTCGGCTTCGACGATTCGAACAGCACAATCTCCAGGAAAGgtcagtagct ... actcatgcagCATCGGAGTCATGGCACCAGTATGCTCAGGGTGGTTTTGGAATCATGCACG
EST: gi|50330237|gb|CO525363.1|CO525363
EST:     CCTCTGGACCGTCGGCTTCGACGATTCGAACAGCCCAATCTCCAGGAAAG                         CATCGGAGTCATGGCACCAGTATGCTCAGGGTGGTTTTGGAATCATGCACG
genomic: CCTCTGGACCGTCGGCTTCGACGATTCGAACAGCACAATCTCCAGGAAAGgtcagtagct ... actcatgcagCATCGGAGTCATGGCACCAGTATGCTCAGGGTGGTTTTGGAATCATGCACG
EST: gi|74240817|gb|DT648731.1|DT648731
EST:     CCTCTGGACCGTCGGCTTCGACGATTCGAACAGCACAATCTCCAGGAAAG                         CATCGGAGTCATGGCACCAGTATGCTCAGGGTGGTTTTGGAATCATGCACG
genomic: CCTCTGGACCGTCGGCTTCGACGATTCGAACAGCACAATCTCCAGGAAAGgtcagtagct ... actcatgcagCATCGGAGTCATGGCACCAGTATGCTCAGGGTGGTTTTGGAATCATGCACG
EST: gi|50329820|gb|CO524946.1|CO524946
EST:     CCTCTGGACCGTCGGCTTCGACGATTCGAACAGCACAATCTCCAGGAAAG                         CATCGGAGTCATGGCACCAGTATGCTCAGGGTGGTTTTGGAATCATGCACG
genomic: CCTCTGGACCGTCGGCTTCGACGATTCGAACAGCACAATCTCCAGGAAAGgtcagtagct ... actcatgcagCATCGGAGTCATGGCACCAGTATGCTCAGGGTGGTTTTGGAATCATGCACG
EST: gi|211121128|gb|FL435128.1|FL435128
EST:     CCTCTGGACCGTCGGCTTCGACGATTCGAACAGCACAATCTCCAGGAAAG                         CATCGGAGTCATGGCACCAGTATGCTCAGGGTGGTTTTGGAATCATGCACG
genomic: CCTCTGGACCGTCGGCTTCGACGATTCGAACAGCACAATCTCCAGGAAAGgtcagtagct ... actcatgcagCATCGGAGTCATGGCACCAGTATGCTCAGGGTGGTTTTGGAATCATGCACG
EST: gi|50329923|gb|CO525049.1|CO525049
EST:     CCTCTGGACCGTCGGCTTCGACGATTCGAACAGCACAATCTCCAGGAAAG                         CATCGGAGTCATGGCACCAGTATGCTCAGGGTGGTTTTGGAATCATGCACG
genomic: CCTCTGGACCGTCGGCTTCGACGATTCGAACAGCACAATCTCCAGGAAAGgtcagtagct ... actcatgcagCATCGGAGTCATGGCACCAGTATGCTCAGGGTGGTTTTGGAATCATGCACG
EST: gi|78090290|gb|DV518664.1|DV518664
EST:     CCTCTGGACCGTCGGCTTGGACGATTCGAACAGCACAATCTCCAGGAAAG                         CATCGGAGTCATGGCACCAGTATGCTCAGGGTGGTTTTGGAATCATGCACG
genomic: CCTCTGGACCGTCGGCTTCGACGATTCGAACAGCACAATCTCCAGGAAAGgtcagtagct ... actcatgcagCATCGGAGTCATGGCACCAGTATGCTCAGGGTGGTTTTGGAATCATGCACG

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: 39 (upstream exon), 40 (downstream exon)
Score: 4

GTGCAGCGGAAGCTGGAGTTCGCGGCGAGGTCTCAGTTGCTCGGCTACTTCCTCTGGACCGTCGGCTTCGACGATTCGAACAGCACAATCTCCAGGAAAGgtcagtagct ... actcatgcagCATCGGAGTCATGGCACCAGTATGCTCAGGGTGGTTTTGGAATCATGCACGCAGGAGGTTCAAACCAATACGTTGCATTTAACTCGTCTTCAGTATCACT


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

GTGCAGCGGAAGCTGGAGTTCGCGGCGAGGTCTCAGTTGCTCGGCTACTTCCTCTGGACCGTCGGCTTCGACGATTCGAACAGCACAATCTCCAGGAAAGgtcagtagct ... actcatgcagCATCGGAGTCATGGCACCAGTATGCTCAGGGTGGTTTTGGAATCATGCACGCAGGAGGTTCAAACCAATACGTTGCATTTAACTCGTCTTCAGTATCACT


Block sizes: 47 (upstream exon), 42 (downstream exon)
Score: 11

GTGCAGCGGAAGCTGGAGTTCGCGGCGAGGTCTCAGTTGCTCGGCTACTTCCTCTGGACCGTCGGCTTCGACGATTCGAACAGCACAATCTCCAGGAAAGgtcagtagct ... actcatgcagCATCGGAGTCATGGCACCAGTATGCTCAGGGTGGTTTTGGAATCATGCACGCAGGAGGTTCAAACCAATACGTTGCATTTAACTCGTCTTCAGTATCACT


Block sizes: 40 (upstream exon), 26 (downstream exon)
Score: 6

GTGCAGCGGAAGCTGGAGTTCGCGGCGAGGTCTCAGTTGCTCGGCTACTTCCTCTGGACCGTCGGCTTCGACGATTCGAACAGCACAATCTCCAGGAAAGgtcagtagct ... actcatgcagCATCGGAGTCATGGCACCAGTATGCTCAGGGTGGTTTTGGAATCATGCACGCAGGAGGTTCAAACCAATACGTTGCATTTAACTCGTCTTCAGTATCACT