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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctaaagagtcagttgctgttgttaggctggcgtgtatctaattgaatttcctgtaatgatatatcattgctagactgattgctataaccaatcctgcagAAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG

Basic information

species Zea mays
transcript GRMZM2G113742_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113742_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g25799.1 (Oryza sativa), 3'ss of exon 1
gctaaagagtcagttgctgttgttag-gctggcgtgtatctaattgaatttcctgtaatgatatat--------cattgctagactgattgctataaccaatcctgcagAAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG
        |    || ||||| | |    ||  |  |      ||||  ||    |||||| || |        |||||||| |||||||   |||   || ||||||||||||||||| ||| ||||||||||||||||||| |||||||| |||||||||||||||||||||||||| ||||||
--------gatgcttactgttataaatagtgtagccttgtagcttgacatttggctaatgacatgttacttactcattgctatactgattataata-ttaaccctgcagAAGCAACACCCAAAACTATCATGAGGACAATGGGTGTGAAGGGTCTCACCCTTTTTCACTTGAAAAGCCACCTTCAG
















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|211108291|gb|FL269574.1|FL269574
EST:     CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATA                         AAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
genomic: CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATAgtaagcattt ... aatcctgcagAAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
EST: gi|211108289|gb|FL269572.1|FL269572
EST:     CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATA                         AAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
genomic: CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATAgtaagcattt ... aatcctgcagAAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
EST: gi|24773354|gb|CA408608.1|CA408608
EST:     CCTCCACGACCGTTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATA                         AAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
genomic: CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATAgtaagcattt ... aatcctgcagAAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
EST: gi|24961617|gb|CA483617.1|CA483617
EST:     CCTCCACGACCGTTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATA                         AAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
genomic: CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATAgtaagcattt ... aatcctgcagAAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
EST: gi|101389911|gb|EB816886.1|EB816886
EST:     CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATA                         AAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
genomic: CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATAgtaagcattt ... aatcctgcagAAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
EST: gi|76909193|gb|DV163265.1|DV163265
EST:     CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATA                         AAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
genomic: CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATAgtaagcattt ... aatcctgcagAAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
EST: gi|88757895|gb|DY542036.1|DY542036
EST:     CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATA                         AAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
genomic: CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATAgtaagcattt ... aatcctgcagAAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
EST: gi|78073924|gb|DV502358.1|DV502358
EST:     CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATA                         AAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
genomic: CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATAgtaagcattt ... aatcctgcagAAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
EST: gi|71309882|gb|DR791225.1|DR791225
EST:     CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATA                         AAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
genomic: CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATAgtaagcattt ... aatcctgcagAAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
EST: gi|71426738|gb|DR807788.1|DR807788
EST:     CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATA                         AAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
genomic: CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATAgtaagcattt ... aatcctgcagAAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
EST: gi|211108290|gb|FL269573.1|FL269573
EST:     CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATA                         AAGCAACACCGAAAGCTATCATGAGGACAATGGGGAGTGAAGGGCCTCACC
genomic: CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATAgtaagcattt ... aatcctgcagAAGCAACACCGAAAGCTATCATGAGGACAATGGG-AGTGAAGGGCCTCACC
EST: gi|211108297|gb|FL269580.1|FL269580
EST:     CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATA                         AAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
genomic: CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATAgtaagcattt ... aatcctgcagAAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
EST: gi|74235191|gb|DT643105.1|DT643105
EST:     CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATA                         AAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
genomic: CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATAgtaagcattt ... aatcctgcagAAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
EST: gi|211109197|gb|FL269582.1|FL269582
EST:     CCTCCACGACCGTTTCGTCGATGCCGTCGCCCAGCTCGGC-GGCCTGATA                         AAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
genomic: CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATAgtaagcattt ... aatcctgcagAAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
EST: gi|149007848|gb|EE040277.2|EE040277
EST:     CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATA                         AAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
genomic: CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATAgtaagcattt ... aatcctgcagAAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
EST: gi|211108293|gb|FL269576.1|FL269576
EST:     CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATA                         AAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
genomic: CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATAgtaagcattt ... aatcctgcagAAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
EST: gi|211108288|gb|FL269571.1|FL269571
EST:     CTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGANCA                         AAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACC
genomic: CTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGAT-Agtaagcattt ... aatcctgcagAAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACC
EST: gi|76932640|gb|DV173098.1|DV173098
EST:     CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATA                         AAGCAACACCGAAAACTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
genomic: CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATAgtaagcattt ... aatcctgcagAAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
EST: gi|74240765|gb|DT648679.1|DT648679
EST:     CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATA                         AAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
genomic: CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATAgtaagcattt ... aatcctgcagAAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
EST: gi|101386138|gb|EB815112.1|EB815112
EST:     CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATA                         AAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
genomic: CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATAgtaagcattt ... aatcctgcagAAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
EST: gi|71318298|gb|DR795913.1|DR795913
EST:     CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATA                         AAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
genomic: CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATAgtaagcattt ... aatcctgcagAAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
EST: gi|30087488|gb|CB885694.1|CB885694
EST:     CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATA                         AAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
genomic: CCTCCACGACCGCTTCGTCGATGCCGTCGCCCAGCTCGGCGGGCCTGATAgtaagcattt ... aatcctgcagAAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
EST: gi|76916798|gb|DV166558.1|DV166558
EST:     GCCCAGCTCGGCGGGCCTGATA                         AAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC
genomic: GCCCAGCTCGGCGGGCCTGATAgtaagcattt ... aatcctgcagAAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttcctgtaatgatatatcattgctagactgattgctataaccaatcctgcagAAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG
                                     ctataac  putative branch site (score: 3)
         taatgatatatcatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctaaagagtcagttgctgttgttaggctggcgtgtatctaattgaatttcctgtaatgatatatcattgctagactgattgctataaccaatcctgcagAAGCAACACCGAAAGCTATCATGAGGACAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG

- - - - - - gttgctg
- - - - - - - - - - - - - gctggcg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgattgc