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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgaatgtcatgttgtacattacatgacagaaatacacatcattagccctgtgcgccagttcttgcattacccctgtcgacttcatggttttctaacatttttatgaatctttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACTCGTCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTC

Basic information

species Zea mays
transcript GRMZM5G835235_T04
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G835235_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g14860.3 (Oryza sativa), 3'ss of exon 10
gtaagtgaatgtcatgttgtacattacatgacagaaatacacatca-ttagccctgtg-cgcc-agttcttgcattacccctgtcgacttcatggttttctaacatttttatgaatctttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACTCGTCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTC
          || |   | || |||  |||   ||| |||| || | ||||   | || | |  ||||| ||   ||    ||  ||| |  |  |||  |||   |||| ||  |   |||| ||||||||| || ||||| |||||||||||||| ||||||||||| |||||| |||| ||||| |||||||||||  |||| || || ||||||||||||||||
----------gtaag--tatatatttaatggttgaagtacagataaattagtattatggcacttagttcctgagataattgtgcagacat--tcatttcataaatattttctgt-tacctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCTCGCCTTCCGAATGGCCGCTTTTTGCCTCCTCTCTTCAACTTCAAGCCTC

upper sequence: GRMZM5G835235_T02 (Zea mays), 3'ss of exon 9
lower sequence: EFJ10962 (Selaginella moellendorffii), 3'ss of exon 10
gtaagtgaatgtcatgttgtacattacatgacagaaatacacatcattagccctgtgcgccagttcttgcattacccctgtcgacttcatggttttctaacatttttatgaatctttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACTCGTCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTC
                                                          |  ||||  | |   | |   ||| ||||    |    || ||| |  |   |  |  ||    ||| | || |||||||  |||||||||||||| ||| | || |||||||| ||||| ||||||||||| ||    || ||||| || | ||| |||||||   
----------------------------------------------------------gtaagtttctcccaaatc---gtccactttgaagggccctgacactggtggtatacacttca--cagCTAGAAGCGCTTGCACACCCATTCTTTGATGAGTTGCGGGATCCTAACACTCGACTTCCAAATGGTCGTCCGCTACCACCTCTGTACAATTTCAAGCAAT

upper sequence: GRMZM5G835235_T02 (Zea mays), 3'ss of exon 9
lower sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 10
gtaagtgaatgtcatgttgtacattacatgacagaaatacacatcattagccctgtgcgccagttcttgcattacccctgtcgacttcatggttttctaacatttttatgaatctttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACTCGTCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTC
                                                          |  ||||  | |   | |   ||| ||||    |    || ||| |  |   |  |  ||    ||| | || |||||||  |||||||||||||| ||| | || |||||||| ||||| ||||||||||| ||    || ||||| || | ||| |||||||   
----------------------------------------------------------gtaagtttctcccaaatc---gtccactttgaagagcactgacactggtggtatacacttca--cagCTAGAAGCGCTTGCACACCCATTCTTTGATGAGTTGCGGGATCCTAACACTCGACTTCCAAATGGTCGTCCGCTACCACCTCTGTACAATTTCAAGCAAT

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|20337055|gb|BQ172685.1|BQ172685
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|32859083|gb|CD998764.1|CD998764
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|5740140|gb|AI947830.1|AI947830
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATTTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|33092593|gb|CF052587.1|CF052587
EST:     GTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: GTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|32865480|gb|CF005162.1|CF005162
EST:     AGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: AGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|32865498|gb|CF005180.1|CF005180
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|32928745|gb|CF033557.1|CF033557
EST:     ACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: ACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|60348494|gb|DN215467.1|DN215467
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|78544269|gb|DV621767.1|DV621767
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|22543122|gb|BU093560.1|BU093560
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|60349422|gb|DN216395.1|DN216395
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCGTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|60395660|gb|DN228530.1|DN228530
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|18172726|gb|BM348114.1|BM348114
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|32916889|gb|CF021701.1|CF021701
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|30087357|gb|CB885563.1|CB885563
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|16379449|gb|BI992951.1|BI992951
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|32865481|gb|CF005163.1|CF005163
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAG
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAG
EST: gi|32865499|gb|CF005181.1|CF005181
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGA
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGA
EST: gi|18170275|gb|BM340115.1|BM340115
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|26456580|gb|CA828163.1|CA828163
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attacccctgtcgacttcatggttttctaacatttttatgaatctttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACTCGTCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTC
                        ttctaac  putative branch site (score: 1)
                                          tctttttgtcc  putative PPT
                      ttttctaacattttta  TA-rich tract