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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgtaaatatatgaagtgccacattgcttcatatctcgctactgagataataatctttcgtgcttgttatccaaaacatgcttccattcttctttaaacctttagaactttgatgatttcatgttaatggccctgttagaactttgacttgagaagtttaactgcaaagccttttcttcaactgcagGTGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAAGAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAAT

Basic information

species Zea mays
transcript GRMZM2G080652_T01
intron # 6
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|211040785|gb|FL108285.1|FL108285
EST:     CAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAG                         GTGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAA
genomic: CAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAGgtccgtaaat ... tcaactgcagGTGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAA
EST: gi|32837961|gb|CD977639.1|CD977639
EST:     CAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAG                         GTGACATTCCACTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAA
genomic: CAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAGgtccgtaaat ... tcaactgcagGTGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAA
EST: gi|32823725|gb|CD963447.1|CD963447
EST:     CAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAG                         GTGACATTCCACTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAA
genomic: CAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAGgtccgtaaat ... tcaactgcagGTGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAA
EST: gi|32823775|gb|CD963497.1|CD963497
EST:     CAATAGCAGGGTCCGTGTTATCCATCAGTATCTCATTGCCATGCAAAAAG                         GTGACATTCCACTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAA
genomic: CAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAGgtccgtaaat ... tcaactgcagGTGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAA
EST: gi|71309452|gb|DR791013.1|DR791013
EST:     CAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAG                         GTGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAA
genomic: CAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAGgtccgtaaat ... tcaactgcagGTGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAA
EST: gi|24768059|gb|CA403191.1|CA403191
EST:     CAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAG                         GTGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAA
genomic: CAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAGgtccgtaaat ... tcaactgcagGTGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAA
EST: gi|61119643|gb|DN560604.1|DN560604
EST:     CAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAG                         GTGACATTCCACTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAA
genomic: CAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAGgtccgtaaat ... tcaactgcagGTGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAA
EST: gi|78117500|gb|DV535887.1|DV535887
EST:     CAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAG                         GTGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAA
genomic: CAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAGgtccgtaaat ... tcaactgcagGTGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAA
EST: gi|71330843|gb|DR802223.1|DR802223
EST:     CAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAG                         GTGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAA
genomic: CAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAGgtccgtaaat ... tcaactgcagGTGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAA
EST: gi|18169407|gb|BM339247.1|BM339247
EST:     GTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAG                         GTGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAA
genomic: GTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAGgtccgtaaat ... tcaactgcagGTGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAA
EST: gi|71309454|gb|DR791014.1|DR791014
EST:     CAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAG                         GTGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAA
genomic: CAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAGgtccgtaaat ... tcaactgcagGTGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAA

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: 47 (upstream exon), 46 (downstream exon)
Score: 47

TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAGgtccgtaaat ... tcaactgcagGTGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAAGAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAAT


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 39

TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAGgtccgtaaat ... tcaactgcagGTGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAAGAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAAT


Block sizes: 41 (upstream exon), 45 (downstream exon)
Score: 36

TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAGgtccgtaaat ... tcaactgcagGTGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAAGAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAAT


Block sizes: 36 (upstream exon), 48 (downstream exon)
Score: 46

TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAGgtccgtaaat ... tcaactgcagGTGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAAGAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttagaactttgacttgagaagtttaactgcaaagccttttcttcaactgcagGTGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAAGAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAAT
                       gtttaac  putative branch site (score: 46)
                                     ccttttcttcaact  putative PPT
                     aagtttaa  TA-rich tract