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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactgatgtttgtaagaaccatattttgctctgctacatcctcagttttagtagcagaacattttgaagcttccatcactcttactaccttctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAGGAATGGAGTCATCGATGGGGAAGCTTTACATTCTTATCGATGAGATCTA

Basic information

species Zea mays
transcript GRMZM2G025214_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G025214_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os05g01450.1 (Oryza sativa), 3'ss of exon 3
aactgatgtttgtaagaaccatattttgctctgctacat-cctcagttttagtagcagaa-cattt-tgaagcttccatcactcttactaccttctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAGGAATGGAGTCATCGATGGGGAAGCTTTACATTCTTATCGATGAGATCTA
   |  |   |||  ||   | | | | || || |   | | |  || || || | | |  ||||| |   |  |   ||| | ||| | | || ||| |||||||| |||||||||||||| || || |||||||||||||||||||||||||||||||| || || ||||  ||||| ||  | ||||| || ||||||||
--ttatttcctgttggaggaaaactattctgtgttttttgcatttgtcttggttgtacattcatttatttcgtgttggtcattattattgcttt-tgtgacagTTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAGGAATGGAATCCTCCATGGAAAAGCTGTATGTCCTTATTGACGAGATCTA
















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|148949750|gb|EC895233.2|EC895233
EST:     AAAAGGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAA
genomic: AAAA-GGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAA
EST: gi|71433383|gb|DR814433.1|DR814433
EST:     TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|45567465|gb|CK985585.1|CK985585
EST:     TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|71768478|gb|DR966415.1|DR966415
EST:     TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAGAAGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCT
genomic: TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCT
EST: gi|93283340|gb|EB675604.1|EB675604
EST:     TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|60346906|gb|DN213879.1|DN213879
EST:     TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|94472259|gb|EB701217.1|EB701217
EST:     TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|13150046|gb|BG320368.1|BG320368
EST:     TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|71768477|gb|DR966414.1|DR966414
EST:     TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|67026697|gb|CO455446.1|CO455446
EST:     TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|78077229|gb|DV505663.1|DV505663
EST:     TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|23199556|gb|BU582121.1|BU582121
EST:     TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAA
genomic: TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAA
EST: gi|18650129|gb|BM498948.1|BM498948
EST:     CTGAAGATGATTGAGGCGGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: CTGAAGATGATTGAGGCGGAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|91879003|gb|EB408960.1|EB408960
EST:     TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGGTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGA
genomic: TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGA
EST: gi|13150112|gb|BG320434.1|BG320434
EST:     TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|89250749|gb|DY622535.1|DY622535
EST:     TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGAAGAGAAGCTCCCCCATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|78077230|gb|DV505664.1|DV505664
EST:     TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|148962408|gb|EE013259.2|EE013259
EST:     TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|87156720|gb|DY401509.1|DY401509
EST:     TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAA
genomic: TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|211117497|gb|FL139016.1|FL139016
EST:     TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|4624423|gb|AI615256.1|AI615256
EST:     AAGATGATTGAGGCGGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: AAGATGATTGAGGCGGAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|76015041|gb|DT942211.1|DT942211
EST:     TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|148949751|gb|EC895234.2|EC895234
EST:     TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|148963080|gb|EE014037.2|EE014037
EST:     TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|93283339|gb|EB675603.1|EB675603
EST:     TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|78079108|gb|DV507520.1|DV507520
EST:     TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|15057042|gb|BI361014.1|BI361014
EST:     GAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: GAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|93011766|gb|EB637286.1|EB637286
EST:     TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|74232963|gb|DT640877.1|DT640877
EST:     TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|76935848|gb|DV174490.1|DV174490
EST:     TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGANAAGGCTGGAT                         TTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG
genomic: TCAGGAAATCCCTCTGGATCTGAAGATGATTGAGGCGGAAAAGGCTGGATgtatgttacc ... tctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttagtagcagaacattttgaagcttccatcactcttactaccttctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAGGAATGGAGTCATCGATGGGGAAGCTTTACATTCTTATCGATGAGATCTA
                                 ctcttac  putative branch site (score: 3)
                                 ctcttactaccttct  CT-rich tract
            aacatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactgatgtttgtaagaaccatattttgctctgctacatcctcagttttagtagcagaacattttgaagcttccatcactcttactaccttctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAGGAATGGAGTCATCGATGGGGAAGCTTTACATTCTTATCGATGAGATCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC