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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcacagattcttatcaagcctctgatatgtgttcagtaaaaaatgctattccatttgccctaatcgtgtcccccatgctgttgttcaaactattcttactgcagAGGCTACCTGATGGTGTACGTTTAAGAGGGGACATTCATGTCTTGCTTCTCGGTGATCCCTCCACAGCAAAATCACAG

Basic information

species Zea mays
transcript GRMZM2G075978_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g55410.1 (Oryza sativa), 3'ss of exon 8
gcacagatt----cttatcaagcctctgatatgtgttcagtaaaaaatgctattccatttgccctaatcgtgtcccccatgctgttgttcaaactattcttactgcagAGGCTACCTGATGGTGTACGTTTAAGAGGGGACATTCATGTCTTGCTTCTCGGTGATCCCTCCACAGCAAAATCACAG
| | |  ||    ||||||| |   || |||||||   | || ||| |  | ||  ||      |       |       |||||   | ||  |  |  ||  |||||||||||| |||||||| ||||| ||||||||||||||||||||||| || |||||||| || |||||||||||||||
gtatatttttgatcttatca-gtggctaatatgtgaa-aatacaaagttgtgttggatccag--tggctagttggaatgagctgtaactaaactttcttctatggcagAGGCTACCGGATGGTGTCCGTTTGAGAGGGGACATTCATGTCTTGCTGCTGGGTGATCCATCAACAGCAAAATCACAG
















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|87153503|gb|DY398292.1|DY398292
EST:     CTGATGTCAAGAAAGCTATTGCATGCTTGTTATTTGGGGGATCTAAGAAG                         AGGCTACCTGATGGTGTACGTTTAAGAGGGG
genomic: CTGATGTCAAGAAAGCTATTGCATGCTTGTTATTTGGGGGATCTAAGAAGgcacagattc ... cttactgcagAGGCTACCTGATGGTGTACGTTTAAGAGGGG
EST: gi|211329963|gb|FL157736.1|FL157736
EST:     CTGATGTCAAGAAAGCTATTGCATGCTTGTTATTTGGGGGATCTAAGAAG                         AGGCTACCTGATGGTGTACGTTTAAGAGGGGACATTCATGTCTTGCTTCTC
genomic: CTGATGTCAAGAAAGCTATTGCATGCTTGTTATTTGGGGGATCTAAGAAGgcacagattc ... cttactgcagAGGCTACCTGATGGTGTACGTTTAAGAGGGGACATTCATGTCTTGCTTCTC
EST: gi|211329958|gb|FL157731.1|FL157731
EST:     CTGATGTCAAGAAAGCTATTGCATGCTTGTTATTTGGGGGATCTAAGAAG                         AGGCTACCTGATGGTGTACGTTTAAGAGGGGACATTCATGTCTTGCTTCTC
genomic: CTGATGTCAAGAAAGCTATTGCATGCTTGTTATTTGGGGGATCTAAGAAGgcacagattc ... cttactgcagAGGCTACCTGATGGTGTACGTTTAAGAGGGGACATTCATGTCTTGCTTCTC
EST: gi|32945450|gb|CF050269.1|CF050269
EST:     CTGATGTCAAGAAAGCTATTGCATGCTTGTTATTTGGGGGATCTAAGAAG                         AGGCTACCTGATGGTGT
genomic: CTGATGTCAAGAAAGCTATTGCATGCTTGTTATTTGGGGGATCTAAGAAGgcacagattc ... cttactgcagAGGCTACCTGATGGTGT
EST: gi|211542713|gb|FK958380.1|FK958380
EST:     CTGATGTCAAGAAAGCTATTGCATGCTTGTTATTTGGGGGATCTAAGAAG                         AGGCTACCTGATGGTGTACGTTTAAGAGGGGACATTCATGTCTTGCTTCTC
genomic: CTGATGTCAAGAAAGCTATTGCATGCTTGTTATTTGGGGGATCTAAGAAGgcacagattc ... cttactgcagAGGCTACCTGATGGTGTACGTTTAAGAGGGGACATTCATGTCTTGCTTCTC
EST: gi|211329962|gb|FL157735.1|FL157735
EST:     CTGATGTCAAGAAAGCTATTGCATGCTTGTTATTTGGGGGATCTAAGAAG                         AGGCTACCTGATGGTGTACGTTTAAGAGGGGACATTCATGTCTTGCTTCTC
genomic: CTGATGTCAAGAAAGCTATTGCATGCTTGTTATTTGGGGGATCTAAGAAGgcacagattc ... cttactgcagAGGCTACCTGATGGTGTACGTTTAAGAGGGGACATTCATGTCTTGCTTCTC
EST: gi|211329960|gb|FL157733.1|FL157733
EST:     CTGATGTCAAGAAAGCTATTGCATGCTTGTTATTTGGGGGATCTAAGAAG                         AGGCTACCTGATGGTGTACGTTTAAGAGGGGACATTCATGTCTTGCTTCTC
genomic: CTGATGTCAAGAAAGCTATTGCATGCTTGTTATTTGGGGGATCTAAGAAGgcacagattc ... cttactgcagAGGCTACCTGATGGTGTACGTTTAAGAGGGGACATTCATGTCTTGCTTCTC
EST: gi|211329965|gb|FL157738.1|FL157738
EST:     CTGATGTCAAGAAAGCTATTGCATGCTTGNTATTTGGGGGATCTAAGAAG                         AGGCTACCTGATGGNGTACGTTTAAGAGGGGACATTCATGTCTTGCTTCTC
genomic: CTGATGTCAAGAAAGCTATTGCATGCTTGTTATTTGGGGGATCTAAGAAGgcacagattc ... cttactgcagAGGCTACCTGATGGTGTACGTTTAAGAGGGGACATTCATGTCTTGCTTCTC

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: 182

TGCATATGCCAAGCTATGCTCAATGATTGGTCCTTCAATTTATGGTCATTCTGATGTCAAGAAAGCTATTGCATGCTTGTTATTTGGGGGATCTAAGAAGgcacagattc ... cttactgcagAGGCTACCTGATGGTGTACGTTTAAGAGGGGACATTCATGTCTTGCTTCTCGGTGATCCCTCCACAGCAAAATCACAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 46

TGCATATGCCAAGCTATGCTCAATGATTGGTCCTTCAATTTATGGTCATTCTGATGTCAAGAAAGCTATTGCATGCTTGTTATTTGGGGGATCTAAGAAGgcacagattc ... cttactgcagAGGCTACCTGATGGTGTACGTTTAAGAGGGGACATTCATGTCTTGCTTCTCGGTGATCCCTCCACAGCAAAATCACAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 25

TGCATATGCCAAGCTATGCTCAATGATTGGTCCTTCAATTTATGGTCATTCTGATGTCAAGAAAGCTATTGCATGCTTGTTATTTGGGGGATCTAAGAAGgcacagattc ... cttactgcagAGGCTACCTGATGGTGTACGTTTAAGAGGGGACATTCATGTCTTGCTTCTCGGTGATCCCTCCACAGCAAAATCACAG


Block sizes: 21 (upstream exon), 41 (downstream exon)
Score: 4

TGCATATGCCAAGCTATGCTCAATGATTGGTCCTTCAATTTATGGTCATTCTGATGTCAAGAAAGCTATTGCATGCTTGTTATTTGGGGGATCTAAGAAGgcacagattc ... cttactgcagAGGCTACCTGATGGTGTACGTTTAAGAGGGGACATTCATGTCTTGCTTCTCGGTGATCCCTCCACAGCAAAATCACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccatttgccctaatcgtgtcccccatgctgttgttcaaactattcttactgcagAGGCTACCTGATGGTGTACGTTTAAGAGGGGACATTCATGTCTTGCTTCTCGGTGATCCCTCCACAGCAAAATCACAG
                                           ttcttac  putative branch site (score: 4)
                                        ctattctt  CT-rich tract
                                     aaactatt  TA-rich tract