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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_T02
intron # 9
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|32846895|gb|CD986576.1|CD986576
EST:     TTTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|211130920|gb|FL136658.1|FL136658
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|33091019|gb|CF051013.1|CF051013
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|74246238|gb|DT654152.1|DT654152
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|149005473|gb|EE040028.2|EE040028
EST:     TTTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCCCCCGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|24765385|gb|CA400544.1|CA400544
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|50323552|gb|CO518678.1|CO518678
EST:     TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG                         TGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
genomic: TCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGAT
EST: gi|5124017|gb|AI745858.1|AI745858
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|110200892|gb|EC882789.1|EC882789
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

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGATGATGGGACTGAATGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGC


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 192

GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGATGATGGGACTGAATGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168

GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGATGATGGGACTGAATGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 136

GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAGgtaagtgaca ... tatcacacagTGCGTCACTGCAGAGTTATGCACACGATGATATATCAGTAGGTTCATGGATGATGGGACTGAATGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGC




 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
- -tgctacc
- - - - - - - - -gcctgga
- - - - - - - - - - - - cagaagc
- - - - - - - - - - - - - - - - - - - - -tctggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttcatc