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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agactagtcctcggatgaacaaccctgtttcgttggtttttctttttgcttagtttattgtgccattgaccttttttatgcgctattattatgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT

Basic information

species Zea mays
transcript GRMZM2G139462_T06
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139462_T06 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g73450.1 (Oryza sativa), 3'ss of exon 5
------agactagtcctcggatgaacaaccctg----tttcgttggtttttctttttgcttagtttattgtgccattgaccttttttatgcgctattattatgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT-----------------------------------------------------------
        ||| ||| |   || |  |   ||        | |   | | || ||||| ||| |  ||  | | || | | ||||||     || | ||| ||    ||||||||||||||||||| || || |||||||||||||| |||                                                           
gagtttgaacttgtctttctataatgatttctcaaataaacatcattgtctcattttgtttattccatcttacaat-ggcttttttt-----ctttcattttg----cagTCAATGCAGAGGTAGTACTTAAGGCAACAAATGTTGACGGTGTGTACGACGCAGACCCCAAGCGTAACCCAAATGCCCGCCTTCTTGAGGCTGTGAGCTA

upper sequence: GRMZM2G139462_T06 (Zea mays), 3'ss of exon 5
lower sequence: AT3G18680.1 (Arabidopsis thaliana), 3'ss of exon 5
agactagtcctcggatgaacaaccctgtttcgtt--ggtttttctttttgcttagtttattgtgccattgaccttttttatgcgctattattatgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT-----------------------------------------------------------
               | || |      || ||||   |||||      || ||| ||       | |   |     |||  ||  |        |    |||| |||||||| |||||||||||||||||||||||||||||                                                            
----------gtaagtaaagaggtggtttccgtttaagttttctccaatgatta-ttcgcaacactaaaaaaaaacttttcgcatt--------ggacacagTTAATGCAGAAGTAGTGCTGAAAGCAACAAATGTTGATGGCGTGTTCGACGATGATCCTAAAAGAAACCCAAACGCTCGTCTGCTTGACTCACTAACTTA

upper sequence: GRMZM2G139462_T06 (Zea mays), 3'ss of exon 5
lower sequence: Vv04s0044g00890.t01 (Vitis vinifera), 3'ss of exon 6
agactagtcctcggatgaacaaccctgtttcgttg--gtttttctttttgcttagtttattgtgccattgaccttttttatgcgctattattatgtgagc-agTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT-----------------------------------------------------------
    |  | | |  ||     |   | | | |     ||  ||| |  ||   | |||  |  |   |||     |  |||  ||  |||||   ||| | ||| ||||||||||| ||||||||||| ||||||||||||||                                                            
--tttttttcccaaattttacattttatctggcaaaagtaattcatcatgtggaatttgcta-gttgttgtgaactgatattggcatttatttgttgatctagTTAATGCAGAGGTTGTGCTGAAAGCTACAAATGTTGATGGGGTTTTCGATGATGACCCCAGGCGTAACCCAAATGCTCGTCTCCTTGATTCTCTTACTTA

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|74244525|gb|DT652439.1|DT652439
EST:     AACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCCGT-GTGCCGAAA                         TCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
genomic: AACCCATTCTTCACGACTGATACAGCTGCTGCTCTCC-GTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
EST: gi|16377611|gb|BI992021.1|BI992021
EST:     GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
EST: gi|78076648|gb|DV505082.1|DV505082
EST:     AACCCATTCCTCACGACTGATACAGCTGCTGCTCTCCCGTTGTGC-GAAA                         TCAATGCAGAGGTAGTGCTGAAAGCAAC
genomic: AACCCATTCTTCACGACTGATACAGCTGCTGCTCTCC-GTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAAC
EST: gi|76286637|gb|DV026205.1|DV026205
EST:     GACCCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGC
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGC
EST: gi|86468320|gb|DY234690.1|DY234690
EST:     GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
EST: gi|211532297|gb|FL466472.1|FL466472
EST:     GAMCCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
EST: gi|76285329|gb|DV024897.1|DV024897
EST:     GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
EST: gi|60343359|gb|DN210332.1|DN210332
EST:     GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
EST: gi|91878695|gb|EB408652.1|EB408652
EST:     GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
EST: gi|50335608|gb|CO530734.1|CO530734
EST:     GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTG
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTG
EST: gi|74235298|gb|DT643212.1|DT643212
EST:     GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
EST: gi|71758718|gb|DR956655.1|DR956655
EST:     GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
EST: gi|13126431|gb|BG317001.1|BG317001
EST:     GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
EST: gi|78076647|gb|DV505081.1|DV505081
EST:     GAACCCATTCTTCACGACTGATACAGCTGCTGCTTTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
EST: gi|86466838|gb|DY233208.1|DY233208
EST:     GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
EST: gi|211243939|gb|FL442196.1|FL442196
EST:     GAMCCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
EST: gi|211175203|gb|FL094960.1|FL094960
EST:     GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTGAAAGCAACAAATAGTTGATGGT
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAAT-GTTGATGGT
EST: gi|91056257|gb|EB166675.1|EB166675
EST:     GA-CCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGGTGGGCCAAAA                         TCAATGCAAAGGAAGTGCTGAAA
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAA
EST: gi|50335607|gb|CO530733.1|CO530733
EST:     GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
EST: gi|78106045|gb|DV524463.1|DV524463
EST:     GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
EST: gi|78119796|gb|DV538180.1|DV538180
EST:     GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGGTGAAAGCAACAAATGTTGATGGT
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
EST: gi|78119797|gb|DV538181.1|DV538181
EST:     GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
EST: gi|78106046|gb|DV524464.1|DV524464
EST:     GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
EST: gi|148960320|gb|EE153576.2|EE153576
EST:     GTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTGAAAGCAACAAAT-TTGATGGGT
genomic: GTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGAT-GGT
EST: gi|74235299|gb|DT643213.1|DT643213
EST:     GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTGATAGCAACAAATGTTGATGGT
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
EST: gi|76013764|gb|DT940934.1|DT940934
EST:     ATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
genomic: ATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
EST: gi|6918328|gb|AW399858.1|AW399858
EST:     GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
EST: gi|71437591|gb|DR818641.1|DR818641
EST:     GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
EST: gi|60395240|gb|DN228109.1|DN228109
EST:     GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
EST: gi|71766564|gb|DR964501.1|DR964501
EST:     GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
EST: gi|76285330|gb|DV024898.1|DV024898
EST:     GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTGAAAGC
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGC
EST: gi|211173534|gb|FL094954.1|FL094954
EST:     GA-CCCAATCNTCACGACTGATACAGCTGCTGCTCTTCGGTGTGCCGAA-                         TCCATGCAAAG-TAGTGCTGAA
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAA
EST: gi|50326141|gb|CO521267.1|CO521267
EST:     GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
EST: gi|71433983|gb|DR815033.1|DR815033
EST:     GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTGAAAGCAACAAAT
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAAT
EST: gi|76291661|gb|DV031229.1|DV031229
EST:     GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAA                         TCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
genomic: GAACCCATTCTTCACGACTGATACAGCTGCTGCTCTCCGTTGTGCCGAAAgtgagtccat ... atgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcttagtttattgtgccattgaccttttttatgcgctattattatgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT
                  cattgac  putative branch site (score: 3)
                                      tattattatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agactagtcctcggatgaacaaccctgtttcgttggtttttctttttgcttagtttattgtgccattgaccttttttatgcgctattattatgtgagcagTCAATGCAGAGGTAGTGCTGAAAGCAACAAATGTTGATGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - -aacaacc
- - - - - - - - - - - - ctgtttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgccatt