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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtgctaccattttttgcctggacagaagctcttgcgttttctggtgctttatttctgcccaccaggtcttcatctcagttttgtcctctatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGATGATGGGACTGAATGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGC

Basic information

species Zea mays
transcript GRMZM2G000393_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000393_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os06g08005.1 (Oryza sativa), 3'ss of exon 10
------atgtgctaccattttttgcctggacagaagctcttgcgttttctggtgctttatttctgcccaccaggtcttcatctcagttttgtcctctatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGATGATGGGACTGAATGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGC
      |   |  |||| ||  |  ||  |   ||  | | |   | | ||  |    | ||      |||     || | |    | ||   ||     |  |||||| || || ||||| ||||| || ||||| |||||||||||||||||||||||||| |||||| | ||||| || ||||| ||||| ||||||||| ||
taatacaacagtaaccaattgatatctctagtcaa--tataggagtatatgcagtcaaaatttg----accgaaatttgagcaatttgtttctcttcgatatgcagTGCATCGCTACAGAGCTATGCCCATGATGACATATCAGTAGGTTCATGGATGATGGGGCTGAATACTACTTATGTTGATGACGACCGTTTGTGCTGCGGC
















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|32928477|gb|CF033289.1|CF033289
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|71435122|gb|DR816172.1|DR816172
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|60338589|gb|DN205562.1|DN205562
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|71436236|gb|DR817286.1|DR817286
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCCCCCGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|50323552|gb|CO518678.1|CO518678
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|4775973|gb|AI664976.1|AI664976
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|78021331|gb|DV489718.1|DV489718
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|32846895|gb|CD986576.1|CD986576
EST:     TTTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|33091019|gb|CF051013.1|CF051013
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|60346760|gb|DN213733.1|DN213733
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|71426993|gb|DR808043.1|DR808043
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|32929367|gb|CF034179.1|CF034179
EST:     TCTTTGGTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|211130918|gb|FL136656.1|FL136656
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|4621425|gb|AI612258.1|AI612258
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|61119808|gb|DN560769.1|DN560769
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|60344825|gb|DN211798.1|DN211798
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|149005473|gb|EE040028.2|EE040028
EST:     TTTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCCCCCGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|71772159|gb|DR970096.1|DR970096
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCGGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|149096404|gb|EE182138.2|EE182138
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|110200892|gb|EC882789.1|EC882789
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|24765385|gb|CA400544.1|CA400544
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|45847888|gb|CN071831.1|CN071831
EST:     AAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: AAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|26557287|gb|CA829522.1|CA829522
EST:     CTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCCCCCGATGATATATCAGTAGGTTCATGGAT
genomic: CTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|21828587|gb|BQ703271.1|BQ703271
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCCCCCGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|78093004|gb|DV521378.1|DV521378
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|211130920|gb|FL136658.1|FL136658
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|60346466|gb|DN213439.1|DN213439
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|148940752|gb|EC885572.2|EC885572
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|15082759|gb|BI389443.1|BI389443
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|113703856|gb|EE681360.1|EE681360
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|5124017|gb|AI745858.1|AI745858
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgctttatttctgcccaccaggtcttcatctcagttttgtcctctatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGATGATGGGACTGAATGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGC
                                   ttttgtcctctatc  CT-rich tract
     ttatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtgctaccattttttgcctggacagaagctcttgcgttttctggtgctttatttctgcccaccaggtcttcatctcagttttgtcctctatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGATGATGGGACTGAATGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG