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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagttattattattaccatgatgtacatcagtagtattacaggtcatctgatacctctgcgatgatgtaactggtcactgttttgatctattgttgtcagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGCAATGCAGCTGAACATGCAAGCGCAATAATGTTTG

Basic information

species Zea mays
transcript GRMZM2G143356_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143356_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os04g55940.1 (Oryza sativa), 3'ss of exon 7
tagttattattattaccatgatgtacatcagtagtattacaggtcatctga-tacctctgcgatgatgta--actggtcactgttttgatctat------tgttgtcagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGCAATGCAGCTGAACATGCAAGCGCAATAATGTTTG
          | |  ||||| | |||||   | || |||||||||| |||| |||||||||   | | ||  | || |||||| |||| ||| |      || | |||||| |||||||||||| |||||||||| |||||||||||||||||||||||||||||||||||||| || || ||||||||||| || |||||||||||||
---------ctctggccatgttatacattgtttgtcttacaggtcacctgagtacctctgcatgggtatactattgatcactgctttgctctttgctatttgctatcagGGGGCATCTGATTCACTGAACCTACCCGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGAAACGCTGCTGAACATGCTAGTGCAATAATGTTTG

upper sequence: GRMZM2G143356_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA15G00380.2 (Glycine max), 3'ss of exon 6
-----------------------------------tagttattattatt-----accatgatgtacatcagtagtattacaggtc--atctgatacctctgcg--atgatgtaactggtcactgttttgatctattgttgtc----agGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGCAATGCAGCTGAACATGCAAGCGCAATAATGTTTG
                                   || ||  |||||||     || |     |  |  | |  ||||   | ||   ||    | | |||||  || |  | | |  |     | |||   |  || | ||    ||||||||||||| ||||||||  |  | |||||||||||   ||| || |||||||| ||||| |||||||| || |||||||| || || || |||||||
gtatagctatatcattttcagaatttcttgatcattaatttctattattgtacaactaaagcttctaatattcctattcttgttcttgtccataaacactgcgtcataagttcattcatagacatattgtgtttctggtctcttgcagGGAGCATCTGAGTCATTGAATATGTCAGTGGCTTTTATTTCTGTCATCTTGCTTCCAATTGTAGGCAATGCTGCAGAACATGCCAGTGCTATCATGTTTG

upper sequence: GRMZM2G143356_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA13G44960.1 (Glycine max), 3'ss of exon 6
tagttattattattaccatgatgtacatcagtagtattacaggtcatctgatacctctgcg--atgatgtaactggtcactgttttgatct--attgttgtcagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGCAATGCAGCTGAACATGCAAGCGCAATAATGTTTG
   | || |  | |         |||||    | |||| |   | |||    |  |||||   || |  | | |  |     || || |     |   |  |||||||||||||| ||||||||  |  | |||||||||||   ||| || |||||||| ||||| |||||||| || |||||||| || || || |||||||
---tcatcaaaactctgtattcatacattcacaatattccta-ttatccataaattctgcatcataagttcattcattgacattgtgtttctggtctcttgcagGGAGCATCTGAGTCATTGAATATGTCAGTGGCTTTTATTTCTGTCATCTTGCTTCCAATTGTAGGCAATGCTGCAGAACATGCCAGTGCTATCATGTTTG

upper sequence: GRMZM2G143356_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv09s0018g01840.t01 (Vitis vinifera), 3'ss of exon 7
tagttattattattaccat-gatgtacatcagtagtattacaggtcatctgatacct--ctgcgatgatgtaactggtcactgttttgatctattgttgtcagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGCAATGCAGCTGAACATGCAAGCGCAATAATGTTTG
   |||||||  || || |  |  |  ||   | ||  |  ||||     |     |   || ||  |  | ||   ||| | ||||  |   || || ||||||||||||||| ||||| ||| | || ||||||||||| ||||| ||| ||||||| ||||| || ||||| ||||| ||||| || ||||| |||||||
--tttattatgctttccttcaacattaatttat-gttctggaggtagaaaggctattggttgtgaacagttgacaaatcaatttttttctggtttcttttcagGGAGCATCTGAGTCATTAAACATGCCAGTGGCTTTTATTAGTGTCATTCTGCTTCCAATTGTAGGAAATGCTGCTGAGCATGCCAGTGCAATTATGTTTG

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|211145245|gb|FL448473.1|FL448473
EST:     TAACATTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAG                         GGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG
genomic: TAACATTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAGgtattcttct ... ttgttgtcagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG
EST: gi|148952029|gb|EC897815.2|EC897815
EST:     TAACATTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAG                         GGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG
genomic: TAACATTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAGgtattcttct ... ttgttgtcagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG
EST: gi|211410157|gb|FL246131.1|FL246131
EST:     TAACATTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAG                         GGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG
genomic: TAACATTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAGgtattcttct ... ttgttgtcagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG
EST: gi|12968375|gb|BG265321.1|BG265321
EST:     TAACATTCTGGGTGTCTTTTCTTTCTGAGTACCTAG-TAACGCCATTGAG                         GGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG
genomic: TAACATTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAGgtattcttct ... ttgttgtcagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG
EST: gi|91870161|gb|EB400733.1|EB400733
EST:     TAACATTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAG                         GGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG
genomic: TAACATTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAGgtattcttct ... ttgttgtcagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG
EST: gi|110949660|gb|EE169817.1|EE169817
EST:     TAACATTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAG                         GGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG
genomic: TAACATTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAGgtattcttct ... ttgttgtcagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG
EST: gi|148951917|gb|EC897693.2|EC897693
EST:     TAACATTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAG                         GGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG
genomic: TAACATTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAGgtattcttct ... ttgttgtcagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG

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: 169

TGAAGAAGCTGAGATTGGCATGTGGGAGGCAGTAACATGGCTTGCGGTGTTAACATTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAGgtattcttct ... ttgttgtcagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGCAATGCAGCTGAACATGCAAGCGCAATAATGTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 270

TGAAGAAGCTGAGATTGGCATGTGGGAGGCAGTAACATGGCTTGCGGTGTTAACATTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAGgtattcttct ... ttgttgtcagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGCAATGCAGCTGAACATGCAAGCGCAATAATGTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 327

TGAAGAAGCTGAGATTGGCATGTGGGAGGCAGTAACATGGCTTGCGGTGTTAACATTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAGgtattcttct ... ttgttgtcagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGCAATGCAGCTGAACATGCAAGCGCAATAATGTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 386

TGAAGAAGCTGAGATTGGCATGTGGGAGGCAGTAACATGGCTTGCGGTGTTAACATTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAGgtattcttct ... ttgttgtcagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGCAATGCAGCTGAACATGCAAGCGCAATAATGTTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctgatacctctgcgatgatgtaactggtcactgttttgatctattgttgtcagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGCAATGCAGCTGAACATGCAAGCGCAATAATGTTTG
                                   ttttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagttattattattaccatgatgtacatcagtagtattacaggtcatctgatacctctgcgatgatgtaactggtcactgttttgatctattgttgtcagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGCAATGCAGCTGAACATGCAAGCGCAATAATGTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - tgatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttttg