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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgactattgtttcagtattgaaattatgtctgatccaatgctgaaatatctggtcggtactcaaaatgttgatgggcttatgctgtaataagtagaaaagcaatcgtgcactttgtattggataatgtttagatatacggtaatcttgatatcctcttgcagTGCGCTGAGGGACCGACGCTTTCCCCCAATACAATCAAAGGAACTCCCAACCTTGGAGTGCACGGTATCTATACTCACTGATTATGAAATTGCAGAGGAC

Basic information

species Zea mays
transcript GRMZM2G131667_T01
intron # 2
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|37381281|gb|CF627515.1|CF627515
EST:     CTGGAGTCCCGTCAGATTGTCAGCGGCTTTAGGGACTACGCCCTAACTAG                         TGCGCTGAGGGACCGACGCTTTCCCCCAATACAATCAAAGGAACTCCCAAC
genomic: CTGGAGTCCCGTCAGATTGTCAGCGGCTTTAGGGACTACGCCCTAACTAGgtgactattg ... cctcttgcagTGCGCTGAGGGACCGACGCTTTCCCCCAATACAATCAAAGGAACTCCCAAC
EST: gi|211302255|gb|FL001844.1|FL001844
EST:     CTGGAGTCCCGTCAGATTGTCAGCGGCTTTAGGGACTACGCCCTAACTAG                         TGCGCTGAGGGACCGACGCTTTCCCCCAATACAATCAAAGGAACTCCCAAC
genomic: CTGGAGTCCCGTCAGATTGTCAGCGGCTTTAGGGACTACGCCCTAACTAGgtgactattg ... cctcttgcagTGCGCTGAGGGACCGACGCTTTCCCCCAATACAATCAAAGGAACTCCCAAC
EST: gi|21987668|gb|BQ779196.1|BQ779196
EST:     GTCAGCGGCTTTAGGGACTACGCCCTAACTAG                         -GCGCTGAGGGACCGACGCTTTCCCCCAATACAATCAAAGGAACTCCCAAC
genomic: GTCAGCGGCTTTAGGGACTACGCCCTAACTAGgtgactattg ... cctcttgcagTGCGCTGAGGGACCGACGCTTTCCCCCAATACAATCAAAGGAACTCCCAAC
EST: gi|30160506|gb|CB924235.1|CB924235
EST:     CTGGAGTCCCGTCAGATTGTCAGCGGCTTTAGGGACTACGCCCTAACTAG                         TGCGCTGAGGGACCGACGCTTTCCCCCAATACAATCAAAGGAACTCCCAAC
genomic: CTGGAGTCCCGTCAGATTGTCAGCGGCTTTAGGGACTACGCCCTAACTAGgtgactattg ... cctcttgcagTGCGCTGAGGGACCGACGCTTTCCCCCAATACAATCAAAGGAACTCCCAAC
EST: gi|44900457|gb|CK827002.1|CK827002
EST:     CTACGCCCTAACTAG                         TGCGCTGAGGGACCGACGCTTTCCCCCAATACAATCAAAGGAACTCCCAAC
genomic: CTACGCCCTAACTAGgtgactattg ... cctcttgcagTGCGCTGAGGGACCGACGCTTTCCCCCAATACAATCAAAGGAACTCCCAAC
EST: gi|60343398|gb|DN210371.1|DN210371
EST:     CTGGAGTCCCGTCAGATTGTCAGCGGCTTTAGGGACTACGCCCTAACTAG                         TGCGCTGAGGGACCGACGCTTTCCCCCAATACAATCAAAGGAACTCCCAAC
genomic: CTGGAGTCCCGTCAGATTGTCAGCGGCTTTAGGGACTACGCCCTAACTAGgtgactattg ... cctcttgcagTGCGCTGAGGGACCGACGCTTTCCCCCAATACAATCAAAGGAACTCCCAAC
EST: gi|9731124|gb|BE509876.1|BE509876
EST:     CCGTCAGATTGTCAGCGGCTTTAGGGACTACGCCCTAACTAG                         TGCGCTGAGGGACCGACGCTTTCCCCCAATACAATCAAAGGAACTCCCAAC
genomic: CCGTCAGATTGTCAGCGGCTTTAGGGACTACGCCCTAACTAGgtgactattg ... cctcttgcagTGCGCTGAGGGACCGACGCTTTCCCCCAATACAATCAAAGGAACTCCCAAC
EST: gi|60351758|gb|DN218731.1|DN218731
EST:     CTGGAGTCCCGTCAGATTGTCAGCGGCTTTAGGGACTACGCCCTAACTAG                         TGCGCTGAGGGACCGACGCTTTCCCCCAATACAATCAAAGGAACTCCCAAC
genomic: CTGGAGTCCCGTCAGATTGTCAGCGGCTTTAGGGACTACGCCCTAACTAGgtgactattg ... cctcttgcagTGCGCTGAGGGACCGACGCTTTCCCCCAATACAATCAAAGGAACTCCCAAC
EST: gi|5895985|gb|AW037231.1|AW037231
EST:     CTGGAGTCCCGTCAGATTGTCAGCGGCTTTAGGGACTACGCCCTAACTAG                         TGCGCTGAGGGACCGACGCTTTCCCCCAATACAATCAAAGGAACTCCCAAC
genomic: CTGGAGTCCCGTCAGATTGTCAGCGGCTTTAGGGACTACGCCCTAACTAGgtgactattg ... cctcttgcagTGCGCTGAGGGACCGACGCTTTCCCCCAATACAATCAAAGGAACTCCCAAC
EST: gi|38229665|gb|CF919978.1|CF919978
EST:     CTGGAGTCCCGTCAGATTGTCAGCGGCTTTAGGGACTACGCCCTAACTAG                         TGCGCTGAGGGACCGACGCTTTCCCCCAATACAATCAAAGGAACTCCCAAC
genomic: CTGGAGTCCCGTCAGATTGTCAGCGGCTTTAGGGACTACGCCCTAACTAGgtgactattg ... cctcttgcagTGCGCTGAGGGACCGACGCTTTCCCCCAATACAATCAAAGGAACTCCCAAC

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: 120

AGAAGGCTGCCAATGGTTCAGAACCACGCCTCCGGGGATGCATAGGAACTCTGGAGTCCCGTCAGATTGTCAGCGGCTTTAGGGACTACGCCCTAACTAGgtgactattg ... cctcttgcagTGCGCTGAGGGACCGACGCTTTCCCCCAATACAATCAAAGGAACTCCCAACCTTGGAGTGCACGGTATCTATACTCACTGATTATGAAATTGCAGAGGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 207

AGAAGGCTGCCAATGGTTCAGAACCACGCCTCCGGGGATGCATAGGAACTCTGGAGTCCCGTCAGATTGTCAGCGGCTTTAGGGACTACGCCCTAACTAGgtgactattg ... cctcttgcagTGCGCTGAGGGACCGACGCTTTCCCCCAATACAATCAAAGGAACTCCCAACCTTGGAGTGCACGGTATCTATACTCACTGATTATGAAATTGCAGAGGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 191

AGAAGGCTGCCAATGGTTCAGAACCACGCCTCCGGGGATGCATAGGAACTCTGGAGTCCCGTCAGATTGTCAGCGGCTTTAGGGACTACGCCCTAACTAGgtgactattg ... cctcttgcagTGCGCTGAGGGACCGACGCTTTCCCCCAATACAATCAAAGGAACTCCCAACCTTGGAGTGCACGGTATCTATACTCACTGATTATGAAATTGCAGAGGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 289

AGAAGGCTGCCAATGGTTCAGAACCACGCCTCCGGGGATGCATAGGAACTCTGGAGTCCCGTCAGATTGTCAGCGGCTTTAGGGACTACGCCCTAACTAGgtgactattg ... cctcttgcagTGCGCTGAGGGACCGACGCTTTCCCCCAATACAATCAAAGGAACTCCCAACCTTGGAGTGCACGGTATCTATACTCACTGATTATGAAATTGCAGAGGAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcactttgtattggataatgtttagatatacggtaatcttgatatcctcttgcagTGCGCTGAGGGACCGACGCTTTCCCCCAATACAATCAAAGGAACTCCCAACCTTGGAGTGCACGGTATCTATACTCACTGATTATGAAATTGCAGAGGAC
                                    tcttgat  putative branch site (score: 289)
                                          tatcctctt  CT-rich tract
              ataatgtttagatata  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgactattgtttcagtattgaaattatgtctgatccaatgctgaaatatctggtcggtactcaaaatgttgatgggcttatgctgtaataagtagaaaagcaatcgtgcactttgtattggataatgtttagatatacggtaatcttgatatcctcttgcagTGCGCTGAGGGACCGACGCTTTCCCCCAATACAATCAAAGGAACTCCCAACCTTGGAGTGCACGGTATCTATACTCACTGATTATGAAATTGCAGAGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA