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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttaacagactagtattctgctttgtacctaattcatttaggatattgttgttttacatgtgcttggttcatttgttttagTTGGATCAAAAGGAAATTCAGAGAACAGTGTGGCTAGAAGATTCTCAACTGGAACTCTATCTACAATGAAATCTCATAGCAATGCATCCGCAAAATTAAA

Basic information

species Zea mays
transcript GRMZM2G108829_T01
intron # 15
splice site 3'
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|60349468|gb|DN216441.1|DN216441
EST:     ACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCTAGAACACCTCCATGTG                         TTGGATCAAAAGGAAATTCAGAGAACAGTGTGGCTAGAAGATTCTCAACTG
genomic: ACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCTAGAACACCTCCATGTGgttagttaac ... tttgttttagTTGGATCAAAAGGAAATTCAGAGAACAGTGTGGCTAGAAGATTCTCAACTG
EST: gi|78022750|gb|DV491137.1|DV491137
EST:     CCAAAAGCTTCATCACTTCCTAGAACACCTCCATGTG                         TTGGATCAAAAGGAAATTCAGAGAACAGTGTGGCTAGAAGATTCTCAACTG
genomic: CCAAAAGCTTCATCACTTCCTAGAACACCTCCATGTGgttagttaac ... tttgttttagTTGGATCAAAAGGAAATTCAGAGAACAGTGTGGCTAGAAGATTCTCAACTG
EST: gi|211496287|gb|FL041699.1|FL041699
EST:     ACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCTAGAACACCTCCATGTG                         TTGGATCAAAAGGAAATTCAGAGAACAGTGTGGCTAGAAGATTCTCAACTG
genomic: ACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCTAGAACACCTCCATGTGgttagttaac ... tttgttttagTTGGATCAAAAGGAAATTCAGAGAACAGTGTGGCTAGAAGATTCTCAACTG
EST: gi|32870331|gb|CF010013.1|CF010013
EST:     ACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCTAGAACACCTCCATGTG                         TTGGATCAAAAGGAAATTCAGAGAACAGTGTGGCTAGAAGATTCTCAACTG
genomic: ACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCTAGAACACCTCCATGTGgttagttaac ... tttgttttagTTGGATCAAAAGGAAATTCAGAGAACAGTGTGGCTAGAAGATTCTCAACTG
EST: gi|32788458|gb|CD940694.1|CD940694
EST:     ACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCTAGAACACCTCCATGTG                         TTGGATCAAAAGGAAATTCAGAGAACAGTGTGGCTAGAAGATTCTCAACTG
genomic: ACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCTAGAACACCTCCATGTGgttagttaac ... tttgttttagTTGGATCAAAAGGAAATTCAGAGAACAGTGTGGCTAGAAGATTCTCAACTG
EST: gi|67011156|gb|CO439905.1|CO439905
EST:     ACTTNCTGTCCGTCCAAAAGCTTCATCACTTNCTAGAACAC-TNCATGTG                         NTGGNATCAAAAGGAAATNCAGAGAACAGTGTGGCTAGAAGATTCTCAACT
genomic: ACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCTAGAACACCTCCATGTGgttagttaac ... tttgttttagTTGG-ATCAAAAGGAAATTCAGAGAACAGTGTGGCTAGAAGATTCTCAACT
EST: gi|5325074|gb|AI783265.1|AI783265
EST:     ACTTCCTGTCCGTCCAAAAGCTTCATCACTTCCTAGAACACCTCCATGTG                         TTGGATCAAAAGGAAATTCAGAGAACAGTGTGGCTAGAAGATTCTCAACTG
genomic: ACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCTAGAACACCTCCATGTGgttagttaac ... tttgttttagTTGGATCAAAAGGAAATTCAGAGAACAGTGTGGCTAGAAGATTCTCAACTG
EST: gi|5846886|gb|AI999969.1|AI999969
EST:     ACTTCCTGTCCGTCCAAAAGCTTCATCACTTCCTAGAACACCTCCATGTG                         TTGGATCAAAAGGAAATTCAGAGAACAGTGTGGCTAGAAGATTCTCAACTG
genomic: ACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCTAGAACACCTCCATGTGgttagttaac ... tttgttttagTTGGATCAAAAGGAAATTCAGAGAACAGTGTGGCTAGAAGATTCTCAACTG

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: 335

GGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCTAGAACACCTCCATGTGgttagttaac ... tttgttttagTTGGATCAAAAGGAAATTCAGAGAACAGTGTGGCTAGAAGATTCTCAACTGGAACTCTATCTACAATGAAATCTCATAGCAATGCATCCGCAAAATTAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 248

GGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCTAGAACACCTCCATGTGgttagttaac ... tttgttttagTTGGATCAAAAGGAAATTCAGAGAACAGTGTGGCTAGAAGATTCTCAACTGGAACTCTATCTACAATGAAATCTCATAGCAATGCATCCGCAAAATTAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 258

GGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCTAGAACACCTCCATGTGgttagttaac ... tttgttttagTTGGATCAAAAGGAAATTCAGAGAACAGTGTGGCTAGAAGATTCTCAACTGGAACTCTATCTACAATGAAATCTCATAGCAATGCATCCGCAAAATTAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 339

GGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCTAGAACACCTCCATGTGgttagttaac ... tttgttttagTTGGATCAAAAGGAAATTCAGAGAACAGTGTGGCTAGAAGATTCTCAACTGGAACTCTATCTACAATGAAATCTCATAGCAATGCATCCGCAAAATTAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctaattcatttaggatattgttgttttacatgtgcttggttcatttgttttagTTGGATCAAAAGGAAATTCAGAGAACAGTGTGGCTAGAAGATTCTCAACTGGAACTCTATCTACAATGAAATCTCATAGCAATGCATCCGCAAAATTAAA
 acctaat  putative branch site (score: 339)
                                             tttgtttt  putative PPT
                atattgttgtttta  TA-rich tract