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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctattttctcaacatttggtcagttagcttacaattgggcatttcagggttcgtataacttgcattactcgatcttttttggtctatggtattaattatctattggtcttttatcagGATCCGTACATATTATGTTGGGATATTCGCAATACTGTGGACATTGTTTACAA

Basic information

species Zea mays
transcript GRMZM2G133749_T02
intron # 8
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|71758651|gb|DR956588.1|DR956588
EST:     GTGCTTTTTTCGAAAGATGGGAACTATCTGTATACTGGAGGGCGCAAG                         GATCCGTACATATTATGTTGGGATATTCGCAATACTGTGGACATTGTTTAC
genomic: GTGCTTTTTTCGAAAGATGGGAACTATCTGTATACTGGAGGGCGCAAGgtacctattt ... cttttatcagGATCCGTACATATTATGTTGGGATATTCGCAATACTGTGGACATTGTTTAC
EST: gi|60349571|gb|DN216544.1|DN216544
EST:     GTGCTTTTTTCGAAAGATGGGAACTATCTGTATACTGGAGGGCGCAAG                         GATCCGTACATATTATGTTGGGATATTCGCAATACTGTGGACATTGTTTAC
genomic: GTGCTTTTTTCGAAAGATGGGAACTATCTGTATACTGGAGGGCGCAAGgtacctattt ... cttttatcagGATCCGTACATATTATGTTGGGATATTCGCAATACTGTGGACATTGTTTAC
EST: gi|78110506|gb|DV528916.1|DV528916
EST:     GTGCTTTTTTCGAAAGATGGGAACTATCTGTATACTGGAGGGCGCAAG                         GATCCGTACATATTATGTTGGGATATTCGCAATACTGTGGACATTGTTTAC
genomic: GTGCTTTTTTCGAAAGATGGGAACTATCTGTATACTGGAGGGCGCAAGgtacctattt ... cttttatcagGATCCGTACATATTATGTTGGGATATTCGCAATACTGTGGACATTGTTTAC
EST: gi|78110507|gb|DV528917.1|DV528917
EST:     GTGCTTTTTTCGAAAGATGGGAACTATCTGTATACTGGAGGGCGCAAG                         GATCCGTACATATTATGTTGGGATATTCGCAATACTGTGGACATTGTTTAC
genomic: GTGCTTTTTTCGAAAGATGGGAACTATCTGTATACTGGAGGGCGCAAGgtacctattt ... cttttatcagGATCCGTACATATTATGTTGGGATATTCGCAATACTGTGGACATTGTTTAC
EST: gi|78120249|gb|DV538633.1|DV538633
EST:     GTGCTTTTTTCGAAAGATGGGAACTATCTGTATACTGGAGGGCGCAAG                         GATCCGTACATATTATGTTGGGATATTCGCAATACTGTGGACATTGTTTAC
genomic: GTGCTTTTTTCGAAAGATGGGAACTATCTGTATACTGGAGGGCGCAAGgtacctattt ... cttttatcagGATCCGTACATATTATGTTGGGATATTCGCAATACTGTGGACATTGTTTAC
EST: gi|60355334|gb|DN222307.1|DN222307
EST:     GTGCTTTTTTCGAAAGATGGGAACTATCTGTATACTGGAGGGCGCAAG                         GATCCGTACATATTATGTTGGGATATTCGCAATACTGTGGACATTGTTTAC
genomic: GTGCTTTTTTCGAAAGATGGGAACTATCTGTATACTGGAGGGCGCAAGgtacctattt ... cttttatcagGATCCGTACATATTATGTTGGGATATTCGCAATACTGTGGACATTGTTTAC
EST: gi|76287081|gb|DV026649.1|DV026649
EST:     GTGCTTTTTTCGAAAGATGGGAACTATCTGTATACTGGAGGGCGCAAG                         GATCCGTACATATTATGTTGGGATATTCGCAATACTGTGGACATTGTTTAC
genomic: GTGCTTTTTTCGAAAGATGGGAACTATCTGTATACTGGAGGGCGCAAGgtacctattt ... cttttatcagGATCCGTACATATTATGTTGGGATATTCGCAATACTGTGGACATTGTTTAC
EST: gi|5932732|gb|AW057093.1|AW057093
EST:     CTTTTTTCGAAAGATGGGAACTATCTGTATACTGGAGGGCGCAAG                         GATCCGTACATATTATGTTGGGATATTCGCAATACTGTGGACATTGTTTAC
genomic: CTTTTTTCGAAAGATGGGAACTATCTGTATACTGGAGGGCGCAAGgtacctattt ... cttttatcagGATCCGTACATATTATGTTGGGATATTCGCAATACTGTGGACATTGTTTAC
EST: gi|31664125|gb|CD573305.1|CD573305
EST:     GTGCTTTTTTCGAAAGATGGGAACTATCTGTATACTGGAGGGCGCAAG                         GATCCGTACATATTATGTTGGGATATTCGCAATACTGTGGACATTGTTTAC
genomic: GTGCTTTTTTCGAAAGATGGGAACTATCTGTATACTGGAGGGCGCAAGgtacctattt ... cttttatcagGATCCGTACATATTATGTTGGGATATTCGCAATACTGTGGACATTGTTTAC
EST: gi|213186763|gb|FM190552.1|FM190552
EST:     GTGCTTTTTTCGAAAGATGGGAACTATCTGTATACTGGAGGGCGCAAG                         GATCCGTACATATTATGTTGGGATATTCGCAATACTGTGGACATTGTTTAC
genomic: GTGCTTTTTTCGAAAGATGGGAACTATCTGTATACTGGAGGGCGCAAGgtacctattt ... cttttatcagGATCCGTACATATTATGTTGGGATATTCGCAATACTGTGGACATTGTTTAC

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: 48 (upstream exon), 49 (downstream exon)
Score: 103

GTGCTTTTTTCGAAAGATGGGAACTATCTGTATACTGGAGGGCGCAAGgtacctattt ... cttttatcagGATCCGTACATATTATGTTGGGATATTCGCAATACTGTGGACATTGTTTACAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 69

GTGCTTTTTTCGAAAGATGGGAACTATCTGTATACTGGAGGGCGCAAGgtacctattt ... cttttatcagGATCCGTACATATTATGTTGGGATATTCGCAATACTGTGGACATTGTTTACAA


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 105

GTGCTTTTTTCGAAAGATGGGAACTATCTGTATACTGGAGGGCGCAAGgtacctattt ... cttttatcagGATCCGTACATATTATGTTGGGATATTCGCAATACTGTGGACATTGTTTACAA


Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 32

GTGCTTTTTTCGAAAGATGGGAACTATCTGTATACTGGAGGGCGCAAGgtacctattt ... cttttatcagGATCCGTACATATTATGTTGGGATATTCGCAATACTGTGGACATTGTTTACAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattactcgatcttttttggtctatggtattaattatctattggtcttttatcagGATCCGTACATATTATGTTGGGATATTCGCAATACTGTGGACATTGTTTACAA
                           tattaat  putative branch site (score: 32)
                                            tcttttatc  putative PPT
                           tattaattatctatt  TA-rich tract