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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcttgctccccctcttgtttgctctcctccgctacctacttgttttggattgtaacattcacttctcttttcagGGTGCCAAGGCACTTTCGAACATGCTGAAAAAGAATAAATCAATACGTATTCTACAGTTCAGCAATAATGCAATTGAATACAGT

Basic information

species Zea mays
transcript GRMZM2G110289_T01
intron # 5
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|18384842|gb|BM418041.1|BM418041
EST:     ATGTGGGTATCCAGAAACTCCTCCTGAACAGTATCAATATTGGGGACGAG                         GGTGCCAAGGCACTTTCGAACATGCTGAAAAAGAATAACTCAATACGTATT
genomic: ATGTGGGTATCCAGAAACTCCTCCTGAACAGTATCAATATTGGGGACGAGgtgcttgctc ... ctcttttcagGGTGCCAAGGCACTTTCGAACATGCTGAAAAAGAATAAATCAATACGTATT
EST: gi|18384843|gb|BM418042.1|BM418042
EST:     AGTATCAATATTGGGGACGAG                         GGTGCCAAGGCACTTTCGAACATGCTGAAAAAGAATAACTCAATACGTATT
genomic: AGTATCAATATTGGGGACGAGgtgcttgctc ... ctcttttcagGGTGCCAAGGCACTTTCGAACATGCTGAAAAAGAATAAATCAATACGTATT
EST: gi|18384685|gb|BM417884.1|BM417884
EST:     ATGTGGGTATCCAGAAACTCCTCCTGAACAGTATCAATATTGGGGACGAG                         GGTGCCAAGGCACTTTCGAACATGCTGAAAAAGAATAACTCAATACGTATT
genomic: ATGTGGGTATCCAGAAACTCCTCCTGAACAGTATCAATATTGGGGACGAGgtgcttgctc ... ctcttttcagGGTGCCAAGGCACTTTCGAACATGCTGAAAAAGAATAAATCAATACGTATT
EST: gi|18384684|gb|BM417883.1|BM417883
EST:     ATGTGGGTATCCAGAAACTCCTCCTGAACAGTATCAATATTGGGGACGAG                         GGTGCCAAGGCACTTTCGAACATGCTGAAAAAGAATAACTCAATACGTATT
genomic: ATGTGGGTATCCAGAAACTCCTCCTGAACAGTATCAATATTGGGGACGAGgtgcttgctc ... ctcttttcagGGTGCCAAGGCACTTTCGAACATGCTGAAAAAGAATAAATCAATACGTATT
EST: gi|18384683|gb|BM417882.1|BM417882
EST:     ATGTGGGTATCCAGAAACTCCTCCTGANCAGTATCAATATTGGGGACGAG                         GGTGCCAAGGCACTTTCGAACATGCTGAAAAAGAATAACTCAATACGTATT
genomic: ATGTGGGTATCCAGAAACTCCTCCTGAACAGTATCAATATTGGGGACGAGgtgcttgctc ... ctcttttcagGGTGCCAAGGCACTTTCGAACATGCTGAAAAAGAATAAATCAATACGTATT

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: 99

TGTCTTTCAGATATATTGGTTGAAAATGTGGGTATCCAGAAACTCCTCCTGAACAGTATCAATATTGGGGACGAGgtgcttgctc ... ctcttttcagGGTGCCAAGGCACTTTCGAACATGCTGAAAAAGAATAAATCAATACGTATTCTACAGTTCAGCAATAATGCAATTGAATACAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 144

TGTCTTTCAGATATATTGGTTGAAAATGTGGGTATCCAGAAACTCCTCCTGAACAGTATCAATATTGGGGACGAGgtgcttgctc ... ctcttttcagGGTGCCAAGGCACTTTCGAACATGCTGAAAAAGAATAAATCAATACGTATTCTACAGTTCAGCAATAATGCAATTGAATACAGT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 88

TGTCTTTCAGATATATTGGTTGAAAATGTGGGTATCCAGAAACTCCTCCTGAACAGTATCAATATTGGGGACGAGgtgcttgctc ... ctcttttcagGGTGCCAAGGCACTTTCGAACATGCTGAAAAAGAATAAATCAATACGTATTCTACAGTTCAGCAATAATGCAATTGAATACAGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 130

TGTCTTTCAGATATATTGGTTGAAAATGTGGGTATCCAGAAACTCCTCCTGAACAGTATCAATATTGGGGACGAGgtgcttgctc ... ctcttttcagGGTGCCAAGGCACTTTCGAACATGCTGAAAAAGAATAAATCAATACGTATTCTACAGTTCAGCAATAATGCAATTGAATACAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctctcctccgctacctacttgttttggattgtaacattcacttctcttttcagGGTGCCAAGGCACTTTCGAACATGCTGAAAAAGAATAAATCAATACGTATTCTACAGTTCAGCAATAATGCAATTGAATACAGT
                              ttgtaac  putative branch site (score: 130)
                                    cattcacttctctttt  CT-rich tract
                    ttgtttt  TA-rich tract