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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctggtaagacgaacactaccataattaagtaattaaccttggctttacttacatataccattgagtccttcacctggttcctggttttctttttcttcagGTATCCAACTTTTTTATTGGCCTGTACTTCTTGAGTGTTGTCAACAAGTTTGGGATCAGCAATGTATATTTGGGATTTGCATCAGTGTGCGTCCTTGCAG

Basic information

species Zea mays
transcript GRMZM2G098011_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098011_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os01g04190.1 (Oryza sativa), 3'ss of exon 13
-ctgg-taagacgaacactaccataattaagtaattaaccttggctttacttacatataccattgagtccttcacctggttcctggttttctttttcttcagGTATCCAACTTTTTTATTGGCCTGTACTTCTTGAGTGTTGTCAACAAGTTTGGGATCAGCAATGTATATTTGGGATTTGCATCAGTGTGCGTCCTTGCAG
 || | |||| ||| ||      ||    |  | |  |   | | |||| |  | ||     |     |  | |        ||| |||| |||||   ||||| || ||||| ||||||||||| ||||||||||| || |||||||| || || ||||||| ||| ||||||||||||||||| || ||||  ||||| |
tctagctaaggcgatcatcgttgtag--gataagtgcagtgttgttttattgccttacctactgtcaccagtgaatcatcgtctgcttttttttttgggcagGTTTCGAACTTCTTTATTGGCCTCTACTTCTTGAGCGTCGTCAACAAATTCGGAATCAGCACTGTGTATTTGGGATTTGCATCTGTTTGCGCTCTTGCTG

upper sequence: GRMZM2G098011_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA13G07780.2 (Glycine max), 3'ss of exon 13
------ctggtaagacgaacact-accataattaagtaattaaccttggctttacttacatataccattgagtccttcacctggttcctggttttctttttcttcagGTATCCAACTTTTTTATTGGCCTGTACTTCTTGAGTGTTGTCAACAAGTTTGGGATCAGCAATGTATATTTGGGATTTGCATCAGTGTGCGTCCTTGCAG
       || ||     | |  | |    |||  | |  || |  ||||  || | || ||||    ||||    |  | ||| ||  |  ||||   | |  |||| | ||||||||  | || ||||| ||||||||||||||||| ||||||||||| ||||||   || || ||||||||  |  | || || || ||||| |
tgatttatgctacattaagcttttattgcaat--actggtttatattgg--ttgcctaaatatgatgttga-caatgaaactgattatt--tttttggtgttatcagATCTCCAACTTCGTCATCGGCCTCTACTTCTTGAGTGTTGTAAACAAGTTTGGTATCAGCTCCGTGTACTTGGGATTCTCGGCTGTCTGTGTTCTTGCTG

upper sequence: GRMZM2G098011_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 13
----ctggtaagacgaacactaccataattaagtaattaaccttggctttacttacatataccattgagtccttcacctggttcctggttttctttttct-tcagGTATCCAACTTTTTTATTGGCCTGTACTTCTTGAGTGTTGTCAACAAGTTTGGGATCAGCAATGTATATTTGGGATTTGCATCAGTGTGCGTCCTTGCAG
        |   |  ||||||  || |   ||||  ||   | |||   || |    || ||  |    |  |  | ||   || || |||||   || | |||| | || |||||| | ||||| || ||||||||||| ||||| |||||||| ||||||||||  || || ||||||||| || | || ||  | ||||| |
gaagtactttctaaaaacactgtcaaatggaagt--ttcttcatggtgctaatgcagtagactttcatctaatggaact---tcatgattttcccattgtatcagATCTCAAACTTTGTGATTGGGCTTTACTTCTTGAGCGTTGTAAACAAGTTCGGGATCAGCACAGTTTACTTGGGATTTTCAGCCGTCTGTCTTCTTGCTG

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|211274460|gb|FL458547.1|FL458547
EST:     CCTCCAGAATAAGGGCCAAGGCTGTTGCATTATCTCTAGGCATGCACTGG                         GTATCCAACTTTTTTATTGGCCTGTACTTCTTGAGTGTCGTCAACAAGTTC
genomic: CCTCCAGAATAAGGGCCAAGGCTGTTGCATTATCTCTAGGCATGCACTGGgtgagtcaca ... ttttcttcagGTATCCAACTTTTTTATTGGCCTGTACTTCTTGAGTGTTGTCAACAAGTTT
EST: gi|32907066|gb|CF011879.1|CF011879
EST:     CCTCCAGAATAAGGGCCAAGGCTGTTGCATTATCTCTAGGCATGCACTGG                         GTATCCAACTTTTTTATTGGCCTGTACTTCTTGAGTGTCGTCAACAAGTTC
genomic: CCTCCAGAATAAGGGCCAAGGCTGTTGCATTATCTCTAGGCATGCACTGGgtgagtcaca ... ttttcttcagGTATCCAACTTTTTTATTGGCCTGTACTTCTTGAGTGTTGTCAACAAGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacttacatataccattgagtccttcacctggttcctggttttctttttcttcagGTATCCAACTTTTTTATTGGCCTGTACTTCTTGAGTGTTGTCAACAAGTTTGGGATCAGCAATGTATATTTGGGATTTGCATCAGTGTGCGTCCTTGCAG
 tacttac  putative branch site (score: 1)
                                ttcctggttttctttt  putative PPT
                                       ttttcttttt  TA-rich tract