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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatcttctgattcctcttttatgtttgtaattttgtccctgctaatgacttgcactattaaatgcactttggctgggttttcagttgtgatagataaatttgttgtagGTATCGAATCACAGAGGGTGTAAACCTTCCATTCCGTGTTCTGCCGACAATCAAGGAATTGGGCCGAACACGCATGGAGATCAACGTGAAA

Basic information

species Zea mays
transcript GRMZM2G331032_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 8
gtaaatcttctgattcctcttttatgtttgtaatt-ttgtccctgctaatgacttgcactattaaatgcactttggctgggttttcagttgtgatagataaatttgttgtagGTATCGAATCACAGAGGGTGTAAACCTTCCATTCCGTGTTCTGCCGACAATCAAGGAATTGGGCCGAACACGCATGGAGATCAACGTGAAA
|||| | || |||| |||| || ||| ||||| |  || ||||   || |||| |    ||||       ||||   ||| |||| |        | | || | |||||||| ||||||||||| ||||||||||| || |||||||| ||||| || || || ||||||||||||||||||||||||||||| || || |||
gtaa-tattatgatccctcctt-atgcttgtattagttttcccctgtagtgacattt-ttatt-------ctttacttggcttttgacc------acaaaattctgttgtagATATCGAATCACTGAGGGTGTAAATCTCCCATTCCGGGTTCTACCAACGATTAAGGAATTGGGCCGAACACGCATGGAGATAAATGTTAAA

upper sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT5G46630.2 (Arabidopsis thaliana), 3'ss of exon 8
gtaaatcttctgattcctcttttatgtttgtaattttgtccctgctaatgacttgcactattaaatgcactttggctgggttttcagt-tgtgatagataaatt-tgttgtagGTATCGAATCACAGAGGGTGTAAACCTTCCATTCCGTGTTCTGCCGACAATCAAGGAATTGGGCCGAACACGCATGGAGATCAACGTGAAA
                                    |     | | ||||   | |||| ||    |||  |||    |||    | | |||  ||  |  ||  |||   ||||||||||| |||||||||||||| || || ||||||||  | || |||||||| ||| | || || ||||| |||||  | || || || 
-----------------------------------gtaagttttcgaatg---tccactgtt----gcaaattgttctggtaccaaatgtgtattaactttatgatgtctcagGTATCGAATAACAGAGGGTGTAAATCTGCCTTTCCGTGTATTACCAACAATCAAAGAACTTGGTCGTACACGTATGGAAGTAAATGTCAAG

upper sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv02s0012g00910.t01 (Vitis vinifera), 3'ss of exon 8
gtaaatcttctgattcctcttttatgtttgtaattttgtccctgctaatgacttgcactattaaatgcactttggctgggttttcagttgtgatagataaatttgttgtagGTATCGAATCACAGAGGGTGTAAACCTTCCATTCCGTGTTCTGCCGACAATCAAGGAATTGGGCCGAACACGCATGGAGATCAACGTGAAA
  | |  | |    |    | || |  |||     | || || |  |||||    |  | || |||    |||  ||     || |        |  || ||||    ||||||||| ||||| ||||||||||| ||||||||||| ||  |||| ||||| |||||| |||| || |||||||||||  | || || || 
-aagagataccagatggggtgttgtagttggttaatggttccag--aatgaagatccttgtttaattt-ttttacctccaccttta-------caattatattttccatagGTATCGTATCACTGAGGGTGTAAATCTTCCATTCCGAGTATTGCCAACAATTAAGGAACTGGGTCGGACACGCATGGAAGTGAATGTCAAG

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|18660565|gb|BM500930.1|BM500930
EST:     GAAAAGACAGTCAGTTTCGTGCCACCTGACGGTGAATTTGAGTTGATGAA                         GTATCGAATCACAGAGGGTGTAAACCTTCCATTCCGTGTTCTGCCGACAAT
genomic: GAAAAGACAGTCAGTTTCGTGCCACCTGACGGTGAATTTGAGTTGATGAAgtaaatcttc ... tttgttgtagGTATCGAATCACAGAGGGTGTAAACCTTCCATTCCGTGTTCTGCCGACAAT
EST: gi|6101968|gb|AW126438.1|AW126438
EST:     GAGTTGATGAA                         GTATCGAATCACAGAGGGTGTAAACCTTCCATTCCGTGTTCTGCCGACAAT
genomic: GAGTTGATGAAgtaaatcttc ... tttgttgtagGTATCGAATCACAGAGGGTGTAAACCTTCCATTCCGTGTTCTGCCGACAAT
EST: gi|91054998|gb|EB165416.1|EB165416
EST:     TTAACAAGATTTAACTCAGAAAAGACAGTCAGTTTCGTGCCACCTGACGGTGAATTTGAGTTGATGAA        
genomic: GAAAAGACAGTCAGTTTCGTGCCACCTGACGGTGAATTTGAGTTGATGAAgtaaatcttc ... tttgttgtagG
EST: gi|32935086|gb|CF039898.1|CF039898
EST:     GAAAAGACAGTCAGTTTCGTGCCACCTGACGGTGAATTTGAGTTGATGAA                         GTATCGAATCACAGAGGGTGTAAACCTTCCATTCCGTGTTCTGCCGACAAT
genomic: GAAAAGACAGTCAGTTTCGTGCCACCTGACGGTGAATTTGAGTTGATGAAgtaaatcttc ... tttgttgtagGTATCGAATCACAGAGGGTGTAAACCTTCCATTCCGTGTTCTGCCGACAAT
EST: gi|31354959|gb|CD439316.1|CD439316
EST:     TTAACAAGATTTAACTCAGAAAAGACAGTCAGTTTCGTGCCACCTGACGGTGAATTTGAGTTGATGAA        
genomic: GAAAAGACAGTCAGTTTCGTGCCACCTGACGGTGAATTTGAGTTGATGAAgtaaatcttc ... tttgttgtagG
EST: gi|6021406|gb|AW066334.1|AW066334
EST:     AAAAAGACAGTCAGTTTCGTGCCACCTGACGGTGAATTTGAGTTGATGAA                         GTATCGAATCACAGAGGGTGTAAACCTTCCATTCCGTGTTCTGCCGACAAT
genomic: GAAAAGACAGTCAGTTTCGTGCCACCTGACGGTGAATTTGAGTTGATGAAgtaaatcttc ... tttgttgtagGTATCGAATCACAGAGGGTGTAAACCTTCCATTCCGTGTTCTGCCGACAAT

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), 48 (downstream exon)
Score: 178

TTGATGATGTCACATTCCACCAGTGTGTCAACTTAACAAGATTTAACTCAGAAAAGACAGTCAGTTTCGTGCCACCTGACGGTGAATTTGAGTTGATGAAgtaaatcttc ... tttgttgtagGTATCGAATCACAGAGGGTGTAAACCTTCCATTCCGTGTTCTGCCGACAATCAAGGAATTGGGCCGAACACGCATGGAGATCAACGTGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 231

TTGATGATGTCACATTCCACCAGTGTGTCAACTTAACAAGATTTAACTCAGAAAAGACAGTCAGTTTCGTGCCACCTGACGGTGAATTTGAGTTGATGAAgtaaatcttc ... tttgttgtagGTATCGAATCACAGAGGGTGTAAACCTTCCATTCCGTGTTCTGCCGACAATCAAGGAATTGGGCCGAACACGCATGGAGATCAACGTGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 319

TTGATGATGTCACATTCCACCAGTGTGTCAACTTAACAAGATTTAACTCAGAAAAGACAGTCAGTTTCGTGCCACCTGACGGTGAATTTGAGTTGATGAAgtaaatcttc ... tttgttgtagGTATCGAATCACAGAGGGTGTAAACCTTCCATTCCGTGTTCTGCCGACAATCAAGGAATTGGGCCGAACACGCATGGAGATCAACGTGAAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 181

TTGATGATGTCACATTCCACCAGTGTGTCAACTTAACAAGATTTAACTCAGAAAAGACAGTCAGTTTCGTGCCACCTGACGGTGAATTTGAGTTGATGAAgtaaatcttc ... tttgttgtagGTATCGAATCACAGAGGGTGTAAACCTTCCATTCCGTGTTCTGCCGACAATCAAGGAATTGGGCCGAACACGCATGGAGATCAACGTGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actattaaatgcactttggctgggttttcagttgtgatagataaatttgttgtagGTATCGAATCACAGAGGGTGTAAACCTTCCATTCCGTGTTCTGCCGACAATCAAGGAATTGGGCCGAACACGCATGGAGATCAACGTGAAA
                                    atagataaatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatcttctgattcctcttttatgtttgtaattttgtccctgctaatgacttgcactattaaatgcactttggctgggttttcagttgtgatagataaatttgttgtagGTATCGAATCACAGAGGGTGTAAACCTTCCATTCCGTGTTCTGCCGACAATCAAGGAATTGGGCCGAACACGCATGGAGATCAACGTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA