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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatcaggttctaaatagacttagagatcaacatgaaacgtggaatcactcatctagtgatattatcctaaatttgtcagctgttatgtagaatggcttggagctcctagctaaaaccaatatatataaaaaaactaatcttttcttatacctgtagTTCATCCTCATCGTGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGCGCCGCCATTCAG

Basic information

species Zea mays
transcript GRMZM2G005859_T02
intron # 3
splice site 3'
intron type U2

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|50335119|gb|CO530245.1|CO530245
EST:     TGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAG                         TTCATCCTCATCGTGGCTGCT
genomic: TGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAGgtacatcagg ... atacctgtagTTCATCCTCATCGTGGCTGCT
EST: gi|12971486|gb|BG267506.1|BG267506
EST:     TGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAG                         TTCATCCTCATCGTGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGC
genomic: TGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAGgtacatcagg ... atacctgtagTTCATCCTCATCGTGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGC
EST: gi|9028720|gb|BE238760.1|BE238760
EST:     TGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAG                         TTCATCCTCATCGTGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGC
genomic: TGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAGgtacatcagg ... atacctgtagTTCATCCTCATCGTGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGC
EST: gi|211010141|gb|FL113888.1|FL113888
EST:     TGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAG                         TTCATCCTCATCGTGGCTGCTAGCTCAATTGGGCGAGGAGCTGTTCTACCG
genomic: TGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAGgtacatcagg ... atacctgtagTTCATCCTCATCGTGGCTGCTAGCTCAATTGG-CGAGGAGCTGTTCTACCG
EST: gi|71445181|gb|DR826231.1|DR826231
EST:     TGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAG                         TTCATCCTCATCGTGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGC
genomic: TGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAGgtacatcagg ... atacctgtagTTCATCCTCATCGTGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGC
EST: gi|9953868|gb|BE640451.1|BE640451
EST:     TGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAG                         TTCATCCTCATCGTGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGC
genomic: TGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAGgtacatcagg ... atacctgtagTTCATCCTCATCGTGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGC
EST: gi|5525259|gb|AI861098.1|AI861098
EST:     TGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAG                         TTCATCCTCATCGTGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGC
genomic: TGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAGgtacatcagg ... atacctgtagTTCATCCTCATCGTGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGC
EST: gi|78109220|gb|DV527636.1|DV527636
EST:     TGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAG                         TTCATCCTCATCGTGGCTGCTAGCTCAATTGGC
genomic: TGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAGgtacatcagg ... atacctgtagTTCATCCTCATCGTGGCTGCTAGCTCAATTGGC
EST: gi|78022617|gb|DV491004.1|DV491004
EST:     TGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAG                         TTCATCCTCATCGTGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGC
genomic: TGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAGgtacatcagg ... atacctgtagTTCATCCTCATCGTGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGC
EST: gi|9028504|gb|BE238499.1|BE238499
EST:     TGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAG                         TTCATCCTCATCGTGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGC
genomic: TGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAGgtacatcagg ... atacctgtagTTCATCCTCATCGTGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGC
EST: gi|211423764|gb|FL057577.1|FL057577
EST:     TGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAG                         TTCATCCTCATCGTGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGC
genomic: TGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAGgtacatcagg ... atacctgtagTTCATCCTCATCGTGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGC
EST: gi|76290855|gb|DV030423.1|DV030423
EST:     TGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAG                         TTCATCCTCATCGTGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGC
genomic: TGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAGgtacatcagg ... atacctgtagTTCATCCTCATCGTGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGC
EST: gi|78091085|gb|DV519459.1|DV519459
EST:     TGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAG                         TTCATCCTCATCGTGGCTGCTAGCTNCA-TTGGCGAGGAGCTGTTCTACCG
genomic: TGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAGgtacatcagg ... atacctgtagTTCATCCTCATCGTGGCTGCTAGCT-CAATTGGCGAGGAGCTGTTCTACCG
EST: gi|148964395|gb|EC905771.2|EC905771
EST:     TGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAG                         TTCATCCTCATCGTGGCTG
genomic: TGGAGGATGAGGAGCTTCGCAGCTTCTTCTGTGGCATGTCACCATGGCAGgtacatcagg ... atacctgtagTTCATCCTCATCGTGGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctcctagctaaaaccaatatatataaaaaaactaatcttttcttatacctgtagTTCATCCTCATCGTGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGCGCCGCCATTCAG
                              aactaat  putative branch site (score: 2)
                                    tcttttcttatacct  CT-rich tract
         taaaaccaatatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatcaggttctaaatagacttagagatcaacatgaaacgtggaatcactcatctagtgatattatcctaaatttgtcagctgttatgtagaatggcttggagctcctagctaaaaccaatatatataaaaaaactaatcttttcttatacctgtagTTCATCCTCATCGTGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGCGCCGCCATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT