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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggccccatgcgcttttacgttcttgccactatctatctgggatgattccttgtgcaattttgttcttctaactaaggagtgattcttcagTTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACTCGTCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTC

Basic information

species Zea mays
transcript GRMZM2G138676_T05
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138676_T05 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 11
gtaaggccccatgcgctttta--cgttct--tgccactatctatctgggatgattccttgtgcaattttgttct--tctaac-taaggagtgattcttcagTTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACTCGTCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTC
|||||||| |||| | ||||    ||| |  || |   | |   |||   || |    |||   ||||   |||  |||||| ||   | | ||||| ||| |||| ||||| |||||||||||||| |||||| ||||||| ||||||||||||||||| ||||| || ||||| || |||||||||||||||||| | |
gtaaggccacatgagattttggttgttatgatggcctgagcagcctgatgtggtatactgttagatttctctctcatctaacctatttaattattctccagATGGAAGCCTGCATGCACCCTTTCTTTGATGAGTTGAGAGATCCAAACACTCGTCTACCTAATGGGCGTCCTCTTCCTCCTCTCTTCAACTTCAGAACAC

upper sequence: GRMZM2G138676_T05 (Zea mays), 3'ss of exon 10
lower sequence: AT1G57870.1 (Arabidopsis thaliana), 3'ss of exon 12
-----------gtaaggccccatgcgcttt--tacgt-tcttgccactatctatctgggatgattccttgtgcaattttgttc-ttctaactaagga--gtgattcttcagT---TGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACTCGTCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTC
            ||      |     ||||  ||| | |  | |  | || | | |     |||         ||  |    | || ||| || |     ||||| |    |   |||| || ||||| ||||||||||| |||||||| |||||||||||  ||||||| || || || ||||| || || || || ||||| || | | | |
gtaaattattcatagcttttctctgactttgttacatattctacttccatattttttttgggatcagcatcagaagctaacccattataagtatgtcttatgattttctgatagGTGGAAGCTTGTATCCACCCTTTCTTTGATGAGCTAAGAGACCCAAATGCTCGTCTGCCAAACGGCCGGCCACTTCCTCCGCTATTCAATTTTAAACCAC

upper sequence: GRMZM2G138676_T05 (Zea mays), 3'ss of exon 10
lower sequence: AT1G09840.2 (Arabidopsis thaliana), 3'ss of exon 12
gtaaggccccatgcgcttttacgttcttgccactatctatctgggatgattccttgtgcaattttgttcttctaactaaggagtgattcttcagTTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACTCGTCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTC
|||||       |  |  || | | | |   |  |||||  ||   | | | | |    ||   | ||||            ||| |  |  ||||||| || ||||| || || || || |||||||| || ||||||||||||||||| |||||||| || || || || || || |||||||| | | | |
gtaagttaattcgttccgttccctccatattagcatctaa-tgatctaaattcattaaaaacactcttct-----------ggtgttattgtagTTGGAAGCTTGTATCCATCCGTTATTTGATGAGCTAAGGGACCCAAACACTCGTCTTCCCAATGGCCGACCACTTCCTCCACTTTTCAACTTTAAACCGC

upper sequence: GRMZM2G138676_T05 (Zea mays), 3'ss of exon 10
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 10
gtaaggccccatgcgcttttacg---ttcttgccacta-tctatctggg-----atgattccttgtgcaattttgttcttctaactaaggagtgattcttcagTTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACTCGTCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTC
|||||     || |  ||||| |   | |||  ||| | | |  ||| |      ||||    ||   ||   ||       |  |    | ||||  | |||||||| || || || ||||||||||| |||||| |||| ||||| | ||||||||| || ||||| || ||||| || || ||||| || |||| | |||
gtaag-tttaatacttttttaagcattccttctcacaaatttgcctgagtggaggtgatctaatggtaaagcatgaatgatcatttctctattgatattgcagTTGGAAGCTTGCATCCACCCTTTCTTTGATGAGTTGAGGGACCCTAGCACTCGTCTTCCTAATGGCCGTCCTCTTCCTCCCCTCTTTAATTTCAAACCTC

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|38229772|gb|CF920085.1|CF920085
EST:     ACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCT                         TTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACT
genomic: ACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCTgtaaggcccc ... gattcttcagTTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACT




















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), 48 (downstream exon)
Score: 99

GTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCTgtaaggcccc ... gattcttcagTTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACTCGTCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTC


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 67

GTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCTgtaaggcccc ... gattcttcagTTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACTCGTCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 124

GTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCTgtaaggcccc ... gattcttcagTTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACTCGTCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 82

GTTTTTCAAAGAAGGCTTCCACCTGAAGCAGTGGACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCTgtaaggcccc ... gattcttcagTTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACTCGTCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgggatgattccttgtgcaattttgttcttctaactaaggagtgattcttcagTTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACTCGTCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTC
                              ttctaac  putative branch site (score: 82)
                                               ttcttc  putative PPT
                    aattttgtt  TA-rich tract