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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAATTAAGTTTCTTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTATGGCAGTGAAACTgtaagttctcctttgtcacttaagtagccttagtacttactttccagtgctttgtaatggttgtttattcaaatcttgcag

Basic information

species Zea mays
transcript GRMZM2G156800_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G156800_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g55560.2 (Oryza sativa), 5'ss of exon 4
GAAATTAAGTTTCTTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTATGGCAGTGAAACTgtaagttctcctttgtc--acttaagtagccttagtacttactttccagtgctttgtaatggttgtttattcaaatcttgcag
||||| || |||||||||||||| ||||||||||| || ||||||||||| |||||||||  ||||||||||| | || |  | | | ||    |||     || ||   | ||  |   |||| |  | |    | |  ||||||
GAAATAAAATTTCTTAGTCAATTCAAGCATGAAAACATAGTGCAGTACTACGGCAGTGAATATgtaagttctcatgtgccaaattgaggtgatattatgcgctagttattaatgtatc-caatgatcatctgg--atactttgcag

upper sequence: GRMZM2G156800_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv18s0001g11240.t01 (Vitis vinifera), 5'ss of exon 3
GAAATTAAGTTTCTTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTATGGCAGTGAAACTgtaagttctcctttgtcacttaagtagccttagtacttactttccagtgctttgtaatggttgtttattcaaatcttgcag--
||||||||  ||||   ||| || ||||||  ||||||||||||||||||||||||||||| ||||| |  |   |||   | ||     |  || |  | |  ||  | |  ||    ||  ||    |      |  |||    
GAAATTAAAGTTCTCCATCATTTAAAGCATCCAAATATTGTGCAGTACTATGGCAGTGAAATTgtaaatatttgcttggtccctattagtctgtaatggtcaaatttgacttattaaagatctttcacaaactggtttatgcgcag
















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|87156020|gb|DY400809.1|DY400809
EST:     TTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTATGGCAGTGAAACT                         ATCGAAGATAGATTCTACATATACCTGGAGTATGTTCATCCTGGTTCAATC
genomic: TTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTATGGCAGTGAAACTgtaagttctc ... aatcttgcagATCGAAGATAGATTCTACATATACCTGGAGTATGTTCATCCTGGTTCAATC
EST: gi|22542085|gb|BU092523.1|BU092523
EST:     TTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTATGGCAGTGAAACT                         ATCGAAGATAGATTCTACATATACCTGGAGTATGTTCATCCTGGTTCAATC
genomic: TTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTATGGCAGTGAAACTgtaagttctc ... aatcttgcagATCGAAGATAGATTCTACATATACCTGGAGTATGTTCATCCTGGTTCAATC
EST: gi|22473422|gb|BU037902.1|BU037902
EST:     TTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTATGGCAGTGAAACT                         ATCGAAGATAGATTCTACATATACCTGGAGTATGTTCATCCTGGTTCAATC
genomic: TTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTATGGCAGTGAAACTgtaagttctc ... aatcttgcagATCGAAGATAGATTCTACATATACCTGGAGTATGTTCATCCTGGTTCAATC
EST: gi|50338068|gb|CO533194.1|CO533194
EST:     TTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTATGGCAGTGAAACT                         ATCGAAGATAGATTCTACATATACCTGGAGTATGTTCATCCTGGTTCAATC
genomic: TTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTATGGCAGTGAAACTgtaagttctc ... aatcttgcagATCGAAGATAGATTCTACATATACCTGGAGTATGTTCATCCTGGTTCAATC
EST: gi|87157200|gb|DY401989.1|DY401989
EST:     TTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTATGGCAGTGAAACT                         ATCGAAGATAGATTCTACATATACCTGGAGTATGTTCATCCTGGTTCAATC
genomic: TTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTATGGCAGTGAAACTgtaagttctc ... aatcttgcagATCGAAGATAGATTCTACATATACCTGGAGTATGTTCATCCTGGTTCAATC
EST: gi|26558715|gb|CA830950.1|CA830950
EST:     TTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTATGGCAGTGAAACT                         ATCGAAGATAGATTCTACATATACCTGGAGTATGTTCATCCTGGTTCAATC
genomic: TTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTATGGCAGTGAAACTgtaagttctc ... aatcttgcagATCGAAGATAGATTCTACATATACCTGGAGTATGTTCATCCTGGTTCAATC
EST: gi|6031429|gb|AW076331.1|AW076331
EST:     TTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTATGGCAGTGAAACT                         ATCGAAGATAGATTCTACATATACCTGGAGTATGTTCATCCTGGTTCAATC
genomic: TTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTATGGCAGTGAAACTgtaagttctc ... aatcttgcagATCGAAGATAGATTCTACATATACCTGGAGTATGTTCATCCTGGTTCAATC

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), 49 (downstream exon)
Score: 115

GAAATTAAGTTTCTTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTATGGCAGTGAAACTgtaagttctc ... aatcttgcagATCGAAGATAGATTCTACATATACCTGGAGTATGTTCATCCTGGTTCAATCCATAAGTATGTTCATCAACACTGTGGATCGCTGACAGAAGCAGTCATCC


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 119

GAAATTAAGTTTCTTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTATGGCAGTGAAACTgtaagttctc ... aatcttgcagATCGAAGATAGATTCTACATATACCTGGAGTATGTTCATCCTGGTTCAATCCATAAGTATGTTCATCAACACTGTGGATCGCTGACAGAAGCAGTCATCC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 159

GAAATTAAGTTTCTTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTATGGCAGTGAAACTgtaagttctc ... aatcttgcagATCGAAGATAGATTCTACATATACCTGGAGTATGTTCATCCTGGTTCAATCCATAAGTATGTTCATCAACACTGTGGATCGCTGACAGAAGCAGTCATCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 99

GAAATTAAGTTTCTTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTATGGCAGTGAAACTgtaagttctc ... aatcttgcagATCGAAGATAGATTCTACATATACCTGGAGTATGTTCATCCTGGTTCAATCCATAAGTATGTTCATCAACACTGTGGATCGCTGACAGAAGCAGTCATCC