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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgatatcttcatctgacaaactttgttactgtgttctctctgtccctagcttatatcctacaatcacataagattgcagtactctgatgcttttttggcattcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTATGGCGGTACTTGTCCATCTGACCAAGTCACTATTTCATGTTTCAGTCCA

Basic information

species Zea mays
transcript GRMZM2G140689_T01
intron # 7
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|19769624|gb|BQ034345.1|BQ034345
EST:     AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG                         CACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA
genomic: AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA
EST: gi|89252677|gb|DY624463.1|DY624463
EST:     AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGGGGAG                         CACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA
genomic: AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA
EST: gi|19770099|gb|BQ034820.1|BQ034820
EST:     AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG                         CACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA
genomic: AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA
EST: gi|211091999|gb|FL476412.1|FL476412
EST:     AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG                         CACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA
genomic: AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA
EST: gi|19436894|gb|BM953304.1|BM953304
EST:     AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG                         CACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA
genomic: AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA
EST: gi|37383195|gb|CF628588.1|CF628588
EST:     AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG                         CACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA
genomic: AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA
EST: gi|19057702|gb|BM736369.1|BM736369
EST:     AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG                         CACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA
genomic: AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA
EST: gi|78083854|gb|DV512247.1|DV512247
EST:     AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG                         CACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA
genomic: AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA
EST: gi|19436893|gb|BM953303.1|BM953303
EST:     AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG                         CACCAAGAATCTGATCGGTGCAGACATGAG
genomic: AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAG
EST: gi|50330326|gb|CO525452.1|CO525452
EST:     AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG                         CACCAAGAATCTGATCGGTGCAGACATGAGATGTTTTGGGATGTAATACTA
genomic: AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA
EST: gi|5649962|gb|AI920322.1|AI920322
EST:     AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG                         CACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACT
genomic: AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACT
EST: gi|19057549|gb|BM736231.1|BM736231
EST:     AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG                         CACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA
genomic: AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA

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: 46 (upstream exon), 49 (downstream exon)
Score: 176

GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTATGGCGGTACTTGTCCATCTGACCAAGTCACTATTTCATGTTTCAGTCCA


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

GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTATGGCGGTACTTGTCCATCTGACCAAGTCACTATTTCATGTTTCAGTCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 156

GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTATGGCGGTACTTGTCCATCTGACCAAGTCACTATTTCATGTTTCAGTCCA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 103

GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTATGGCGGTACTTGTCCATCTGACCAAGTCACTATTTCATGTTTCAGTCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcctacaatcacataagattgcagtactctgatgcttttttggcattcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTATGGCGGTACTTGTCCATCTGACCAAGTCACTATTTCATGTTTCAGTCCA
                           ctctgat  putative branch site (score: 103)
                                            cattctt  putative PPT
             ataagatt  TA-rich tract