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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcggttactagagttacaacaaaacccttttttaatggattctttgattagttcagcattcactctggccttttgccccttgataactggtgaaagagaagatattggacagtaaatattagtttttctattcttttgttgaattgatagtattgtaattaacattttatatacttttcagGAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGAC

Basic information

species Zea mays
transcript GRMZM2G118316_T01
intron # 16
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|148947432|gb|EC892855.2|EC892855
EST:     GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG                         GAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
genomic: GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAGgtcggttact ... tacttttcagGAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
EST: gi|149101261|gb|EE187373.2|EE187373
EST:     GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG                         GAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
genomic: GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAGgtcggttact ... tacttttcagGAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
EST: gi|60397506|gb|DN230322.1|DN230322
EST:     GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG                         GAATAAAAGCAAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
genomic: GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAGgtcggttact ... tacttttcagGAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
EST: gi|93017255|gb|EB642775.1|EB642775
EST:     GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG                         GAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
genomic: GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAGgtcggttact ... tacttttcagGAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
EST: gi|71757144|gb|DR955081.1|DR955081
EST:     GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG                         GAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
genomic: GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAGgtcggttact ... tacttttcagGAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
EST: gi|211267316|gb|FL091730.1|FL091730
EST:     GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG                         GAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
genomic: GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAGgtcggttact ... tacttttcagGAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
EST: gi|76922540|gb|DV169051.1|DV169051
EST:     GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG                         GAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
genomic: GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAGgtcggttact ... tacttttcagGAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
EST: gi|7135181|gb|AW497971.1|AW497971
EST:     CCGGGGCAAAG                         GAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
genomic: CCGGGGCAAAGgtcggttact ... tacttttcagGAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
EST: gi|17929416|gb|BM266376.1|BM266376
EST:     GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG                         GAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
genomic: GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAGgtcggttact ... tacttttcagGAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
EST: gi|86469547|gb|DY235917.1|DY235917
EST:     GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG                         GAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
genomic: GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAGgtcggttact ... tacttttcagGAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
EST: gi|60398827|gb|DN231643.1|DN231643
EST:     GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG                         GAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
genomic: GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAGgtcggttact ... tacttttcagGAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
EST: gi|211267317|gb|FL091731.1|FL091731
EST:     GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG                         GAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
genomic: GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAGgtcggttact ... tacttttcagGAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
EST: gi|71769071|gb|DR967008.1|DR967008
EST:     GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG                         GAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
genomic: GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAGgtcggttact ... tacttttcagGAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
EST: gi|71427930|gb|DR808980.1|DR808980
EST:     GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG                         GAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
genomic: GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAGgtcggttact ... tacttttcagGAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
EST: gi|211435107|gb|FL442358.1|FL442358
EST:     GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG                         GAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
genomic: GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAGgtcggttact ... tacttttcagGAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
EST: gi|6022509|gb|AW067542.1|AW067542
EST:     GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTGGTCCTCCGGGGCAAAG                         GAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
genomic: GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAGgtcggttact ... tacttttcagGAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
EST: gi|37397730|gb|CF636173.1|CF636173
EST:     GTTCGTCAAGGTACCCAGCCTGGAGAGAAGGTGGTCCTACGGGGCAAAG                         GAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
genomic: GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAGgtcggttact ... tacttttcagGAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
EST: gi|67040336|gb|CO466591.1|CO466591
EST:     GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTGGTCCTCCGGGGCAAAG                         GAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
genomic: GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAGgtcggttact ... tacttttcagGAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
EST: gi|40337178|gb|CK371248.1|CK371248
EST:     GTTCGTCAAGGTACCCAGCCTGGAGAGAAGGTGGTCCTACGGGGCAAAG                         GAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA
genomic: GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAGgtcggttact ... tacttttcagGAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCA

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), 47 (downstream exon)
Score: 201

GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAGgtcggttact ... tacttttcagGAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 188

GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAGgtcggttact ... tacttttcagGAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 225

GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAGgtcggttact ... tacttttcagGAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGAC


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 150

GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAGgtcggttact ... tacttttcagGAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctattcttttgttgaattgatagtattgtaattaacattttatatacttttcagGAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGAC
                              aattaac  putative branch site (score: 150)
                                             tacttttc  putative PPT
               aattgatagtattgta  TA-rich tract