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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctacttaacacatggtttatctaaccacctgtcttcgtggaatatgaatgcctgttcatctggccttgctgttctcagaaattagtatgccttgttacagGATCGCCTAAAGAAGCTTAAATCAGAGCATGGGAAGGTTCAGCTTGGAAACATAACTGTGGATATG

Basic information

species Zea mays
transcript GRMZM2G064023_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064023_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 3
ctacttaacacat-ggttta-tctaaccacctgtcttcgtggaatatgaatgcctgtt---catctggccttgctgttctcagaaattagtatgccttgttacagGATCGCCTAAAGAAGCTTAAATCAGAGCATGGGAAGGTTCAGCTTGGAAACATAACTGTGGATATG
     || | ||   ||| | | | |||     |||   |   |  ||| | |||||     ||| ||             |   | |         || ||||||||||| ||||||| ||||||||||| ||||||||||| |||||||||||||||||||| ||||||
-----tagctcaccagttcacttttacctaaactctatatatgagctgatttcctgtcaaagatcaggatagaaaagcacaactcactttaccattctggtacagGATCGCTTAAAGAAACTTAAATCAGAACATGGGAAGGTCCAGCTTGGAAACATAACTGTTGATATG
















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|149090362|gb|EE179668.2|EE179668
EST:     GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAGCAG                         GATCGCCTAAAGAAGCTTAAATCAGAGCATGGGAAGGTTCAGCTTGGAAAC
genomic: GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAGCAGgtttgctact ... cttgttacagGATCGCCTAAAGAAGCTTAAATCAGAGCATGGGAAGGTTCAGCTTGGAAAC
EST: gi|149082725|gb|EE171943.2|EE171943
EST:     GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAGCAG                         GATCGCCTAAAGAAGCTTAAATCAGAGCATGGGAAGGTTCAGCTTGGAAAC
genomic: GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAGCAGgtttgctact ... cttgttacagGATCGCCTAAAGAAGCTTAAATCAGAGCATGGGAAGGTTCAGCTTGGAAAC
EST: gi|149077813|gb|EE166538.2|EE166538
EST:     GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAGCAG                         GACCGCCTAAAGAAGCTTAAATCAGAGCATGGGAAGGTTCAGCTTGGAAAC
genomic: GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAGCAGgtttgctact ... cttgttacagGATCGCCTAAAGAAGCTTAAATCAGAGCATGGGAAGGTTCAGCTTGGAAAC
EST: gi|8103179|gb|AW927835.1|AW927835
EST:     GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAGCAG                         GATCGCCTAAAGAAGCTTAAATCAGAGCATGGGAAGGTTCAGCTTGGAAAC
genomic: GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAGCAGgtttgctact ... cttgttacagGATCGCCTAAAGAAGCTTAAATCAGAGCATGGGAAGGTTCAGCTTGGAAAC
EST: gi|213174510|gb|FM184748.1|FM184748
EST:     GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAGCAG                         GATCGCCTAAAGAAGCTTAAATCAGAGCATGGGAAGGTTCAGCTTGGAAAC
genomic: GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAGCAGgtttgctact ... cttgttacagGATCGCCTAAAGAAGCTTAAATCAGAGCATGGGAAGGTTCAGCTTGGAAAC
EST: gi|211399063|gb|FL099822.1|FL099822
EST:     GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAGCAG                         GATCGCCTAAAGAAGCTTAAATCAGAGCATGGGAAGGTTCAGCTTGGAAAC
genomic: GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAGCAGgtttgctact ... cttgttacagGATCGCCTAAAGAAGCTTAAATCAGAGCATGGGAAGGTTCAGCTTGGAAAC
EST: gi|71450120|gb|DR831170.1|DR831170
EST:     GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAGCAG                         GATCGCCTAAAGAAGCTTAAATCAGAGCATGGGAAGGTTCAGCTTGGAAAC
genomic: GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAGCAGgtttgctact ... cttgttacagGATCGCCTAAAGAAGCTTAAATCAGAGCATGGGAAGGTTCAGCTTGGAAAC
EST: gi|76287895|gb|DV027463.1|DV027463
EST:     GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAGCAG                         GATCGCCTAAAGAAGCTTAAATCAGAGCATGGGAAGGTTCAGCTTGGAAAC
genomic: GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAGCAGgtttgctact ... cttgttacagGATCGCCTAAAGAAGCTTAAATCAGAGCATGGGAAGGTTCAGCTTGGAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatgcctgttcatctggccttgctgttctcagaaattagtatgccttgttacagGATCGCCTAAAGAAGCTTAAATCAGAGCATGGGAAGGTTCAGCTTGGAAACATAACTGTGGATATG
                                            ccttgtt  CT-rich tract
                                 aaattagtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctacttaacacatggtttatctaaccacctgtcttcgtggaatatgaatgcctgttcatctggccttgctgttctcagaaattagtatgccttgttacagGATCGCCTAAAGAAGCTTAAATCAGAGCATGGGAAGGTTCAGCTTGGAAACATAACTGTGGATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT