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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttatctctttggcctagcattttacatcaaattgctcctctacattcttagcagctcctatttgctgacttactttcttattgttttcctttgtcacagACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTCTTTGTCTGCATCCCCCCTGCAATTATT

Basic information

species Zea mays
transcript GRMZM2G083344_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083344_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os05g15160.1 (Oryza sativa), 3'ss of exon 7
gtttatctctttggcctagcattttacatcaaattgctcctctacattcttagcagctcctatttgctgacttactttcttattgttttcctttgtcacagACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTCTTTGTCTGCATCCCCCCTGCAATTATT
||||   | ||    |||    | | |||  |  | | |   | |  | ||   |   ||  ||   |   ||||||| ||  ||||   |||| |||||||||||||||||||| |||||| ||||||| ||||| ||||||||||||||| ||||||||||||| ||||||||||||
gtttgcttgttacctctaatgatctgcatgcatattcactcttcc--ttttgatactcccgtttcatttttttactttgttgctgtt---ctttatcacagACTGACATGGATAGCACCAACCTGTATGCGTACATCTCAATAATTGCTCTCCTTGTCTGCATCCCTCCTGCAATTATT
















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|78087779|gb|DV516172.1|DV516172
EST:     TCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATG                         ACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTC
genomic: TCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATGgtttatctct ... tttgtcacagACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTC
EST: gi|148961156|gb|EE011865.2|EE011865
EST:     TCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATG                         ACTGACATGGATAGTACCCACTTGTATGCATACATAT
genomic: TCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATGgtttatctct ... tttgtcacagACTGACATGGATAGTACCAACTTGTATGCATACATAT
EST: gi|9028706|gb|BE238746.1|BE238746
EST:     TCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATG                         ACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTC
genomic: TCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATGgtttatctct ... tttgtcacagACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTC
EST: gi|71328475|gb|DR800887.1|DR800887
EST:     GCATCTATTCTAAGAAGGCTATG                         ACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTC
genomic: GCATCTATTCTAAGAAGGCTATGgtttatctct ... tttgtcacagACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTC
EST: gi|76930049|gb|DV172255.1|DV172255
EST:     TCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATG                         ACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTC
genomic: TCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATGgtttatctct ... tttgtcacagACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTC
EST: gi|71768355|gb|DR966292.1|DR966292
EST:     TCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATG                         ACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTC
genomic: TCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATGgtttatctct ... tttgtcacagACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTC
EST: gi|32862760|gb|CF002442.1|CF002442
EST:     TCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATG                         ACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTC
genomic: TCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATGgtttatctct ... tttgtcacagACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTC
EST: gi|149095075|gb|EE180680.2|EE180680
EST:     TCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATG                         ACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCT
genomic: TCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATGgtttatctct ... tttgtcacagACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCT

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), 49 (downstream exon)
Score: 100

ATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCATTAATGCCATGATCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATGgtttatctct ... tttgtcacagACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTCTTTGTCTGCATCCCCCCTGCAATTATT


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 24

ATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCATTAATGCCATGATCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATGgtttatctct ... tttgtcacagACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTCTTTGTCTGCATCCCCCCTGCAATTATT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 37

ATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCATTAATGCCATGATCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATGgtttatctct ... tttgtcacagACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTCTTTGTCTGCATCCCCCCTGCAATTATT


Block sizes: 47 (upstream exon), 42 (downstream exon)
Score: 12

ATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCATTAATGCCATGATCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATGgtttatctct ... tttgtcacagACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTCTTTGTCTGCATCCCCCCTGCAATTATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttagcagctcctatttgctgacttactttcttattgttttcctttgtcacagACTGACATGGATAGTACCAACTTGTATGCATACATATCAATAATTGCTCTCTTTGTCTGCATCCCCCCTGCAATTATT
                      gacttac  putative branch site (score: 12)
                        cttactttcttattgt  CT-rich tract
                             tttcttattgtttt  TA-rich tract