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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_T01
intron # 11
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|29947291|gb|CB816579.1|CB816579
EST:     CAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCT                         TTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACT
genomic: CAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCTgtaaggcccc ... gattcttcagTTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACT
EST: gi|76292959|gb|DV032527.1|DV032527
EST:     ACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCT                         TTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACT
genomic: ACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCTgtaaggcccc ... gattcttcagTTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACT
EST: gi|31355062|gb|CD439419.1|CD439419
EST:     ACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCT                         TTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACT
genomic: ACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCTgtaaggcccc ... gattcttcagTTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACT
EST: gi|38229772|gb|CF920085.1|CF920085
EST:     ACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCT                         TTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACT
genomic: ACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCTgtaaggcccc ... gattcttcagTTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACT
EST: gi|78024451|gb|DV492838.1|DV492838
EST:     ACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCT                         TTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACT
genomic: ACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCTgtaaggcccc ... gattcttcagTTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACT
EST: gi|71322556|gb|DR797955.1|DR797955
EST:     ACCTCGTTAGCAGGTTTCTACAATACTCACCAAAGCTACGGTGCACTGCT                         TTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACT
genomic: ACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCTgtaaggcccc ... gattcttcagTTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACT
EST: gi|71312506|gb|DR792786.1|DR792786
EST:     ACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCT                         TTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACT
genomic: ACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCTgtaaggcccc ... gattcttcagTTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACT
EST: gi|32834795|gb|CD974473.1|CD974473
EST:     ACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCT                         TTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACT
genomic: ACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCTgtaaggcccc ... gattcttcagTTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACT
EST: gi|6021801|gb|AW066729.1|AW066729
EST:     CCAAATCTACGGTGCACTGCT                         TTGGAGGCCTGTATGCACCCTTTTTTCGATGAGCTGAGAGACCCAAACACT
genomic: CCAAATCTACGGTGCACTGCTgtaaggcccc ... gattcttcagTTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACT
EST: gi|32928721|gb|CF033533.1|CF033533
EST:     ACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCT                         TTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACT
genomic: ACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCTgtaaggcccc ... gattcttcagTTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACT
EST: gi|76292960|gb|DV032528.1|DV032528
EST:     ACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCT                         TTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACT
genomic: ACCTTGTTAGCAGGTTTCTACAATACTCACCAAATCTACGGTGCACTGCTgtaaggcccc ... gattcttcagTTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgggatgattccttgtgcaattttgttcttctaactaaggagtgattcttcagTTGGAGGCCTGTATGCACCCTTTCTTCGATGAGCTGAGAGACCCAAACACTCGTCTACCCAATGGTCGGCCTCTGCCGCCTCTCTTCAACTTCAGATCTC
                              ttctaac  putative branch site (score: 1)
                                               ttcttc  putative PPT
                    aattttgtt  TA-rich tract