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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagctcacatatgcttcgcttaaaatatcatcttcgtttagactactgatcgggtctcatcttttatcagcttcttaccacgacactgtttcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAATGTCGGTTGGGGAGACTGCATCATCAGGTTGTATGAGACGCAATGCAAA

Basic information

species Zea mays
transcript GRMZM2G048277_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G048277_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g24540.1 (Oryza sativa), 3'ss of exon 3
aagctcacatatgcttcgcttaaaatatcatcttcgtttagactactgatcgg--gtctcatcttttatcagcttcttaccacgacactgtttcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAATGTC-GGTTGGGGAGACTGCATCATCAGGTTGTATGAGACGCA-ATGCAAA
| || | | || || | | | | ||| | |||||| || | |||| | |||||| || | ||| | | | || | |||||| ||||| ||||| |||||||| |||||||||||||||||||| | || |||||| ||| | |||| | || ||| ||| ||||
-acttctaaattatttagcctgcactgttatcacc-tttagattattaatcgcctgcctcatcattaaccagttaacatgatcattgtttgtttacattcagGCATGGGTACCACTTCATCCTCTGTGAAGGAAGGAAGAACTGATCAGTCTGCTTCAGGTTGGAACAGAAGCACC-TCAGTCTATACAAGATGCAGATGCCT-
















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|32828122|gb|CD967800.1|CD967800
EST:     GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCAC                         GCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
genomic: GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
EST: gi|33096518|gb|CF056512.1|CF056512
EST:     GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCAC                         GCACGGGCATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
genomic: GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
EST: gi|18177877|gb|BM379087.1|BM379087
EST:     GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCAC                         GCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
genomic: GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
EST: gi|211061968|gb|FL461781.1|FL461781
EST:     GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCAC                         GCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
genomic: GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
EST: gi|51592806|gb|CV071952.1|CV071952
EST:     GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCAC                         GCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
genomic: GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
EST: gi|60337887|gb|DN204860.1|DN204860
EST:     GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCAC                         GCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
genomic: GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
EST: gi|32827994|gb|CD967672.1|CD967672
EST:     GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCAC                         GCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
genomic: GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
EST: gi|32823460|gb|CD963182.1|CD963182
EST:     GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCAC                         GCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
genomic: GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
EST: gi|76283286|gb|DV022854.1|DV022854
EST:     GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCAC                         GCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
genomic: GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
EST: gi|211106101|gb|FL459223.1|FL459223
EST:     GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCMCCATTCAAGTCCAC                         GCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
genomic: GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
EST: gi|110524567|gb|EE028751.1|EE028751
EST:     GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCAC                         GCACGGGTATCACTTTATCCTTTGCGAAGGAAGGAAGAACTGATCTGGAAA
genomic: GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
EST: gi|67017951|gb|CO446700.1|CO446700
EST:     GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCAC                         GCACGGGTATCACTTTATCCTCTGCGAAAGAAGGA-GAACTGATCTGGAAA
genomic: GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
EST: gi|166410049|gb|EG271119.1|EG271119
EST:     GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCAC                         GCACGGGTATCACTTTATC
genomic: GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATC

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: 379

GAGATCTTGGTTGGTTCCCGCGTGGCAAGATGGCTGGTCCTTTCCAGGAGGTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAATGTCGGTTGGGGAGACTGCATCATCAGGTTGTATGAGACGCAATGCAAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 425

GAGATCTTGGTTGGTTCCCGCGTGGCAAGATGGCTGGTCCTTTCCAGGAGGTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAATGTCGGTTGGGGAGACTGCATCATCAGGTTGTATGAGACGCAATGCAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 437

GAGATCTTGGTTGGTTCCCGCGTGGCAAGATGGCTGGTCCTTTCCAGGAGGTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAATGTCGGTTGGGGAGACTGCATCATCAGGTTGTATGAGACGCAATGCAAA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 229

GAGATCTTGGTTGGTTCCCGCGTGGCAAGATGGCTGGTCCTTTCCAGGAGGTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAATGTCGGTTGGGGAGACTGCATCATCAGGTTGTATGAGACGCAATGCAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgatcgggtctcatcttttatcagcttcttaccacgacactgtttcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAATGTCGGTTGGGGAGACTGCATCATCAGGTTGTATGAGACGCAATGCAAA
                          ttcttac  putative branch site (score: 229)
 ctgtttcct  putative PPT
 atcttttat  TA-rich tract