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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaattgtccgttatttttttgtcactttgagggcctccatgtgttgctctttatcttattgcaaaatactcgtatctgactccacttttgttgatgcagTATCATTCGTGATATCATTCAGAACCACTTGTTGCAG

Basic information

species Zea mays
transcript GRMZM2G031107_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031107_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g38840.1 (Oryza sativa), 3'ss of exon 8
--gcaattgtccgttatttttttgtcactttgagggcctcc-atgtgttgctctttatcttattgcaaaatactcgtatctgactccacttttgttgatgcagTATCATTCGTGATATCATTCAGAACCACTTGTTGCAG
| ||| | |||| | |||| ||||| || | | | || |||| || | | ||| |||| | ||||||||| ||||| |||||||||||||||||||||||||| |||||||||
gtgtttatgttatgagacaaataatcacctagaggacctcccgtgcatcgttattcgtctt--cgctga-tgtaaatatttgacctcgcttttgttgctgcagCATCATTCGTGATATCATTCAGAACCATTTGTTGCAG
















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|111146774|gb|EE258268.1|EE258268
EST:     AAGGAAGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGG                         TATCATTCGTGATATCATTCAAAACCACTTGTTGCAG
genomic: AAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGGgtacgttgga ... gttgatgcagTATCATTCGTGATATCATTCAGAACCACTTGTTGCAG
EST: gi|60672339|gb|DN475101.1|DN475101
EST:     AAGGAAGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGG                         TATCATTCGTGATATCATTCAAAACCACTTGTTGCAG
genomic: AAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGGgtacgttgga ... gttgatgcagTATCATTCGTGATATCATTCAGAACCACTTGTTGCAG
EST: gi|18661166|gb|BM501251.1|BM501251
EST:     NAGGNGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGG                         TATCATTCGTGATATCATTCAGAACCACTTGTTGCAG
genomic: AAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGGgtacgttgga ... gttgatgcagTATCATTCGTGATATCATTCAGAACCACTTGTTGCAG
EST: gi|76281884|gb|DV021452.1|DV021452
EST:     AAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGG                         TATCATTCGTGATATCATTCAGAACCACTTGTTGCAG
genomic: AAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGGgtacgttgga ... gttgatgcagTATCATTCGTGATATCATTCAGAACCACTTGTTGCAG
EST: gi|78109019|gb|DV527436.1|DV527436
EST:     AAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGG                         TATCATTCGTGATATCATTCAGAACCACTTGTTGCAG
genomic: AAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGGgtacgttgga ... gttgatgcagTATCATTCGTGATATCATTCAGAACCACTTGTTGCAG

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), 37 (downstream exon)
Score: 100

ATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGGgtacgttgga ... gttgatgcagTATCATTCGTGATATCATTCAGAACCACTTGTTGCAG


Block sizes: 49 (upstream exon), 37 (downstream exon)
Score: 443

ATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGGgtacgttgga ... gttgatgcagTATCATTCGTGATATCATTCAGAACCACTTGTTGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 455

ATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGGgtacgttgga ... gttgatgcagTATCATTCGTGATATCATTCAGAACCACTTGTTGCAG


Block sizes: 48 (upstream exon), 37 (downstream exon)
Score: 236

ATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGGgtacgttgga ... gttgatgcagTATCATTCGTGATATCATTCAGAACCACTTGTTGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctctttatcttattgcaaaatactcgtatctgactccacttttgttgatgcagTATCATTCGTGATATCATTCAGAACCACTTGTTGCAG
                                        cttttgtt  CT-rich tract
 tttatcttatt  TA-rich tract