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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGAGCAGGGCGCTGACGGAATGGAAGGTTCGGCGTCGAAAACTGATAGGAGCGTTCACGAGGCAGTTGGCGTCGATGGCACGTACCTCACCGAGACACGgtaatgtcttgcttacttgcgtcacgaattacggaattaggttaggggatatacactgaaataccaacgtgattgctggaacttgcaacagaggattagt...

Basic information

species Zea mays
transcript GRMZM2G156158_T02
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|50333799|gb|CO528925.1|CO528925
EST:     AGCGTTCACGAGGCAGTTGGCGTCGATGGCACGTACCTCACCGAGACACG                         GTTTGATCAATGTGCCATTTCTCCACTGTCACTGAAAGCCATCAAAGATGC
genomic: AGCGTTCACGAGGCAGTTGGCGTCGATGGCACGTACCTCACCGAGACACGgtaatgtctt ... catgtcacagGTTTGATCAATGTGCCATTTCTCCACTGTCACTGAAAGCCATCAAAGATGC
EST: gi|149109358|gb|EE190158.2|EE190158
EST:     AGCGTTCACGAGGCAGTTGGCGTCGATGGCACGTACCTCACCGAGACACG                         GTTTGATCAATGTGCCATTTCTCCACTGTCACTGAAAGCCATCAAAGATGC
genomic: AGCGTTCACGAGGCAGTTGGCGTCGATGGCACGTACCTCACCGAGACACGgtaatgtctt ... catgtcacagGTTTGATCAATGTGCCATTTCTCCACTGTCACTGAAAGCCATCAAAGATGC
EST: gi|211328602|gb|FK972853.1|FK972853
EST:     AGCGTTCACGAGGCAGTTGGCGTCGATGGCACGTACCTCACCGAGACACG                         GTTTGATCAATGTGCCCATTTCTCCACTATCACTGAAAGCCATCAAAGATG
genomic: AGCGTTCACGAGGCAGTTGGCGTCGATGGCACGTACCTCACCGAGACACGgtaatgtctt ... catgtcacagGTTTGATCAATGTGCC-ATTTCTCCACTGTCACTGAAAGCCATCAAAGATG
EST: gi|76289610|gb|DV029178.1|DV029178
EST:     AGCGTTCACGAGGCAGTTGGCGTCGATGGCACGTACCTCACCGAGACACG                         GTTTGATCAATGTGCCATTTCTCCACTGTCACTGAAAGCCATCAAAGATGC
genomic: AGCGTTCACGAGGCAGTTGGCGTCGATGGCACGTACCTCACCGAGACACGgtaatgtctt ... catgtcacagGTTTGATCAATGTGCCATTTCTCCACTGTCACTGAAAGCCATCAAAGATGC
EST: gi|211328611|gb|FK972862.1|FK972862
EST:     AGCGTTCACGAGGCAGTTGGCGTCGATGGCACGTACCTCACCGAGACACG                         GTTTGATCAATGTGCCATTTCTCCACTGTCACTGAAAGCCATCAAAGATGC
genomic: AGCGTTCACGAGGCAGTTGGCGTCGATGGCACGTACCTCACCGAGACACGgtaatgtctt ... catgtcacagGTTTGATCAATGTGCCATTTCTCCACTGTCACTGAAAGCCATCAAAGATGC
EST: gi|211330760|gb|FK972863.1|FK972863
EST:     AGCGTTCACGAGGCAGTTGGCGTCGATGGCACGTACCTCACCGAGACACG                         GTTTGATCAATGTGCCATTTCTCCACTGTCACTGAAAGCCATCAAAGATGC
genomic: AGCGTTCACGAGGCAGTTGGCGTCGATGGCACGTACCTCACCGAGACACGgtaatgtctt ... catgtcacagGTTTGATCAATGTGCCATTTCTCCACTGTCACTGAAAGCCATCAAAGATGC
EST: gi|149103306|gb|EE288682.2|EE288682
EST:     AGCGTTCACGAGGCAGTTGGCGTCGATGGCACGTACCTCACCGAGACACG                         GTTTGATCAATGTGCCATTTCTCCACTGTCACTGAAAGCCATCAAAGATGC
genomic: AGCGTTCACGAGGCAGTTGGCGTCGATGGCACGTACCTCACCGAGACACGgtaatgtctt ... catgtcacagGTTTGATCAATGTGCCATTTCTCCACTGTCACTGAAAGCCATCAAAGATGC
EST: gi|211328605|gb|FK972856.1|FK972856
EST:     AGCGTTCACGAGGCAGTTGGCGTCGATGGCACGTACCTCACCGAGACACG                         GTTTGATCAATGTGCCATTTCTCCACTGTCACTGAAAGCCATCAAAGATGC
genomic: AGCGTTCACGAGGCAGTTGGCGTCGATGGCACGTACCTCACCGAGACACGgtaatgtctt ... catgtcacagGTTTGATCAATGTGCCATTTCTCCACTGTCACTGAAAGCCATCAAAGATGC

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: 47 (upstream exon), 44 (downstream exon)
Score: 108

TTGAGCAGGGCGCTGACGGAATGGAAGGTTCGGCGTCGAAAACTGATAGGAGCGTTCACGAGGCAGTTGGCGTCGATGGCACGTACCTCACCGAGACACGgtaatgtctt ... catgtcacagGTTTGATCAATGTGCCATTTCTCCACTGTCACTGAAAGCCATCAAAGATGCTGGATATGAGAGGATGACTCGGGTGCAGGAGGCTACTCTGCCAATAATT


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 70

TTGAGCAGGGCGCTGACGGAATGGAAGGTTCGGCGTCGAAAACTGATAGGAGCGTTCACGAGGCAGTTGGCGTCGATGGCACGTACCTCACCGAGACACGgtaatgtctt ... catgtcacagGTTTGATCAATGTGCCATTTCTCCACTGTCACTGAAAGCCATCAAAGATGCTGGATATGAGAGGATGACTCGGGTGCAGGAGGCTACTCTGCCAATAATT


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 81

TTGAGCAGGGCGCTGACGGAATGGAAGGTTCGGCGTCGAAAACTGATAGGAGCGTTCACGAGGCAGTTGGCGTCGATGGCACGTACCTCACCGAGACACGgtaatgtctt ... catgtcacagGTTTGATCAATGTGCCATTTCTCCACTGTCACTGAAAGCCATCAAAGATGCTGGATATGAGAGGATGACTCGGGTGCAGGAGGCTACTCTGCCAATAATT


Block sizes: 46 (upstream exon), 44 (downstream exon)
Score: 58

TTGAGCAGGGCGCTGACGGAATGGAAGGTTCGGCGTCGAAAACTGATAGGAGCGTTCACGAGGCAGTTGGCGTCGATGGCACGTACCTCACCGAGACACGgtaatgtctt ... catgtcacagGTTTGATCAATGTGCCATTTCTCCACTGTCACTGAAAGCCATCAAAGATGCTGGATATGAGAGGATGACTCGGGTGCAGGAGGCTACTCTGCCAATAATT