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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACTCTAGTTGGCTCTCTTGAAATGCCAAAGGCTGATGTATGGGTTGTAATAGCAATCTTGTCTGGTGTGATTGGATACTGTGCTAAGATATACTTCACgtaagtgcttaattgacagatcttttccttcttaccttgagcctcattcggttgttagtgctctgtaacaaatttaatgttagtgctatgtaataaattt...

Basic information

species Zea mays
transcript GRMZM2G011136_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011136_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os12g29550.1 (Oryza sativa), 5'ss of exon 11
TCACTCTAGTTGGCTCTCTTGAAATGCCAAAGGCTGATGTATGGGTTGTAATAGCAATCTTGTCTGGTGTGATTGGATACTGTGCTAAGATATACTTCACgtaagtgcttaattgacagatcttttccttcttaccttgagcctcattcg--gttgttagtgctctgtaacaaatttaatgttagtgctatgtaataaattt----------------
||||| || |||| || ||||||||||||||||||||| |||||||||| |||||||||||||| |||||||||||||| ||||||||||| |||||||||||||||||||  |     || || |  | | |    | |   || |||    | || |  |     |  | |    ||   |||||| |||| ||| ||||                
TCACTTTATTTGGTTCCCTTGAAATGCCAAAGGCTGATATATGGGTTGTCATAGCAATCTTGTCGGGTGTGATTGGATATTGTGCTAAGATCTACTTCACgtaagtgcttaggttttgtatattattatccatttgatcaatgtcgttctacatggtgaaggaagatttcctagggcaaatgtagtgcaatgtgatagatttatcttttgtgatacag
















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|78023012|gb|DV491399.1|DV491399
EST:     AAGATATACTTCAC                         ATTTCAACAAAATATGACAATGTATCAGAATTTGATTACAAAATCAATGTA
genomic: AAGATATACTTCACgtaagtgctt ... ttatatacagATTTCAACAAAATATGACAATGTATCAGAATTTGATTACAAAATCAATGTA
EST: gi|6227171|gb|AW155700.1|AW155700
EST:     ATAGCAATCTTGTCTGGTGTGATTGGATACTGTGCTAAGATATACTTCAC                         ATTTCAACAAAATATGACAATGTATCAGAATTTGATTACAAAATCAATGTA
genomic: ATAGCAATCTTGTCTGGTGTGATTGGATACTGTGCTAAGATATACTTCACgtaagtgctt ... ttatatacagATTTCAACAAAATATGACAATGTATCAGAATTTGATTACAAAATCAATGTA
EST: gi|71767790|gb|DR965727.1|DR965727
EST:     ATAGCAATCTTGTCTGGTGTGATTGGATACTGTGCTAAGATATACTTCAC                         ATTTCAACAAAATATGACAATGTATCAGAATTTGATTACAAAATCAATGTA
genomic: ATAGCAATCTTGTCTGGTGTGATTGGATACTGTGCTAAGATATACTTCACgtaagtgctt ... ttatatacagATTTCAACAAAATATGACAATGTATCAGAATTTGATTACAAAATCAATGTA
EST: gi|32850036|gb|CD989717.1|CD989717
EST:     ATAGCAATCTTGTCTGGTGTGATTGGATACTGTGCTAAGATATACTTCAC                         ATTTCAACAAAATATGACAATGTATCAGAATTTGATTACAAAATCAATGTA
genomic: ATAGCAATCTTGTCTGGTGTGATTGGATACTGTGCTAAGATATACTTCACgtaagtgctt ... ttatatacagATTTCAACAAAATATGACAATGTATCAGAATTTGATTACAAAATCAATGTA
EST: gi|40303291|gb|CK347678.1|CK347678
EST:     ATAGCAATCTTGTCTGGTGTGATTGGATACTGTGCTAAGATATACTTCAC                         ATTTCAACAAAATATGACAATGTATCAGAATTTGATTACAAAATCAATGTA
genomic: ATAGCAATCTTGTCTGGTGTGATTGGATACTGTGCTAAGATATACTTCACgtaagtgctt ... ttatatacagATTTCAACAAAATATGACAATGTATCAGAATTTGATTACAAAATCAATGTA
EST: gi|6031446|gb|AW076348.1|AW076348
EST:     ATAGCAATCTTGTCTGGTGTGATTGGATACTGTGCTAAGATATACTTCAC                         ATTTCAACAAAATATGACAATGTATCAGAATTTGATTACAAAATCAATATA
genomic: ATAGCAATCTTGTCTGGTGTGATTGGATACTGTGCTAAGATATACTTCACgtaagtgctt ... ttatatacagATTTCAACAAAATATGACAATGTATCAGAATTTGATTACAAAATCAATGTA
EST: gi|32839351|gb|CD979032.1|CD979032
EST:     ATAGCAATCTTGTCTGGTGTGATTGGATACTGTGCTAAGATATACTTCAC                         ATTTCAACAAAATATGACAATGTATCAGAATTTGATTACAAAATCAATGTA
genomic: ATAGCAATCTTGTCTGGTGTGATTGGATACTGTGCTAAGATATACTTCACgtaagtgctt ... ttatatacagATTTCAACAAAATATGACAATGTATCAGAATTTGATTACAAAATCAATGTA

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: 117

TCACTCTAGTTGGCTCTCTTGAAATGCCAAAGGCTGATGTATGGGTTGTAATAGCAATCTTGTCTGGTGTGATTGGATACTGTGCTAAGATATACTTCACgtaagtgctt ... ttatatacagATTTCAACAAAATATGACAATGTATCAGAATTTGATTACAAAATCAATGTATGACAAACAGCTTGATAGTGGGAAAGGAACTCTTCTTCACTTATGCGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 215

TCACTCTAGTTGGCTCTCTTGAAATGCCAAAGGCTGATGTATGGGTTGTAATAGCAATCTTGTCTGGTGTGATTGGATACTGTGCTAAGATATACTTCACgtaagtgctt ... ttatatacagATTTCAACAAAATATGACAATGTATCAGAATTTGATTACAAAATCAATGTATGACAAACAGCTTGATAGTGGGAAAGGAACTCTTCTTCACTTATGCGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 247

TCACTCTAGTTGGCTCTCTTGAAATGCCAAAGGCTGATGTATGGGTTGTAATAGCAATCTTGTCTGGTGTGATTGGATACTGTGCTAAGATATACTTCACgtaagtgctt ... ttatatacagATTTCAACAAAATATGACAATGTATCAGAATTTGATTACAAAATCAATGTATGACAAACAGCTTGATAGTGGGAAAGGAACTCTTCTTCACTTATGCGAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 154

TCACTCTAGTTGGCTCTCTTGAAATGCCAAAGGCTGATGTATGGGTTGTAATAGCAATCTTGTCTGGTGTGATTGGATACTGTGCTAAGATATACTTCACgtaagtgctt ... ttatatacagATTTCAACAAAATATGACAATGTATCAGAATTTGATTACAAAATCAATGTATGACAAACAGCTTGATAGTGGGAAAGGAACTCTTCTTCACTTATGCGAT