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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacggaacaaaatgacaattctactcttcatccttttctcttttatgtaccattctgtacttatcttaatttcctggcaccatgaagattcttttaccaagtttattagataattaaacctgcatgttggtttaactctatgattctttgttcagGTCTATGTAATTGGTGGAGATGGTACTCAAAGGGGTGCTGGAGTGATTTTCGAA

Basic information

species Zea mays
transcript GRMZM2G443985_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g05860.1 (Oryza sativa), 3'ss of exon 6
gtaaacggaacaaaatgacaattctactcttcatccttttctcttttatgtaccattctgtacttatcttaatttcctggcaccatgaagattcttttaccaagtttattagataattaaacctgcatgttggtt-taactctatgattctttgttcagGTCTATGTAATTGGTGGAGATGGTACTCAAAGGGGTGCTGGAGTGATTTTCGAA
               | |      |      |||  | ||   ||| |   ||  || | |   |     ||||| | |  |  |||||||||||| |||| |  | |    | |  | |   |    |||||||  || | | ||   | |||| ||||| |||||||||||||| |||||||||||||||||||| ||||||||||| |||
--------------gtaaaggaaatggatgccattttattacttttcagacactgttttatgaat----caatttacagatagtatgaagattcttctacctaactga---aacatcttacattcagcgttggttacaagtttgtg---cattgtccagGTTTATGTAATTGGTGGTGATGGTACTCAAAGGGGTGCAGGAGTGATTTTTGAA
















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|211132978|gb|FL170883.1|FL170883
EST:     ATGACACCGTGAAGATAGTTGACAGCATCCAAGATCGTGACATAAATCAG                         GTCTATGTAATTGGTGGAGATGGTACTCAAAGGGGTGCTGGAGTGATATTC
genomic: ATGACACCGTGAAGATAGTTGACAGCATCCAAGATCGTGACATAAATCAGgtaaacggaa ... ctttgttcagGTCTATGTAATTGGTGGAGATGGTACTCAAAGGGGTGCTGGAGTGATTTTC
EST: gi|148972520|gb|EE023481.2|EE023481
EST:     ATGACACCGTGAAGATAGTTGACAGCATCCAAGATCGTGACATAAATCAG                         GTCTATGTAATTGGTGGAGATGGTACTCAAAGGGGTGCTGGAGTGATTTTT
genomic: ATGACACCGTGAAGATAGTTGACAGCATCCAAGATCGTGACATAAATCAGgtaaacggaa ... ctttgttcagGTCTATGTAATTGGTGGAGATGGTACTCAAAGGGGTGCTGGAGTGATTTT-
EST: gi|13557855|gb|BG549211.1|BG549211
EST:     ATGACACCGTGAAGATAGTTGACAGCATCCAAGATCGTGACATAAATCAG                         GTCTATGTAATTGGTGGAGATGGTACTCAAAGGGGTGCTGGAGTGATTTTC
genomic: ATGACACCGTGAAGATAGTTGACAGCATCCAAGATCGTGACATAAATCAGgtaaacggaa ... ctttgttcagGTCTATGTAATTGGTGGAGATGGTACTCAAAGGGGTGCTGGAGTGATTTTC
EST: gi|76921243|gb|DV168509.1|DV168509
EST:     ATGACACCGTGAAGATAGTTGACAGCATCCAAGATCGTGACATAAATCAG                         GTCTATGTAATTGGTGGAGATGGTACTCAAAGGGGTGCTGGAGTGATTTTC
genomic: ATGACACCGTGAAGATAGTTGACAGCATCCAAGATCGTGACATAAATCAGgtaaacggaa ... ctttgttcagGTCTATGTAATTGGTGGAGATGGTACTCAAAGGGGTGCTGGAGTGATTTTC
EST: gi|211132969|gb|FL170874.1|FL170874
EST:     ATGACACCGTGAAGATAGTTGACAGCATCCAAGATCGTGACATAAATCAG                         GTCTATGTAATTGGTGGAGATGGTACTCAAAGGGGTGCTGGAGTGATATTC
genomic: ATGACACCGTGAAGATAGTTGACAGCATCCAAGATCGTGACATAAATCAGgtaaacggaa ... ctttgttcagGTCTATGTAATTGGTGGAGATGGTACTCAAAGGGGTGCTGGAGTGATTTTC

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: 187

TGACATTCACAAAAGGGGTGGAACTATTCTTGGATCATCTCGAGGAGGTCATGACACCGTGAAGATAGTTGACAGCATCCAAGATCGTGACATAAATCAGgtaaacggaa ... ctttgttcagGTCTATGTAATTGGTGGAGATGGTACTCAAAGGGGTGCTGGAGTGATTTTCGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 225

TGACATTCACAAAAGGGGTGGAACTATTCTTGGATCATCTCGAGGAGGTCATGACACCGTGAAGATAGTTGACAGCATCCAAGATCGTGACATAAATCAGgtaaacggaa ... ctttgttcagGTCTATGTAATTGGTGGAGATGGTACTCAAAGGGGTGCTGGAGTGATTTTCGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 277

TGACATTCACAAAAGGGGTGGAACTATTCTTGGATCATCTCGAGGAGGTCATGACACCGTGAAGATAGTTGACAGCATCCAAGATCGTGACATAAATCAGgtaaacggaa ... ctttgttcagGTCTATGTAATTGGTGGAGATGGTACTCAAAGGGGTGCTGGAGTGATTTTCGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 278

TGACATTCACAAAAGGGGTGGAACTATTCTTGGATCATCTCGAGGAGGTCATGACACCGTGAAGATAGTTGACAGCATCCAAGATCGTGACATAAATCAGgtaaacggaa ... ctttgttcagGTCTATGTAATTGGTGGAGATGGTACTCAAAGGGGTGCTGGAGTGATTTTCGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttattagataattaaacctgcatgttggtttaactctatgattctttgttcagGTCTATGTAATTGGTGGAGATGGTACTCAAAGGGGTGCTGGAGTGATTTTCGAA
                             gtttaac  putative branch site (score: 278)
                                           ttctttgttc  putative PPT
     ttagataattaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacggaacaaaatgacaattctactcttcatccttttctcttttatgtaccattctgtacttatcttaatttcctggcaccatgaagattcttttaccaagtttattagataattaaacctgcatgttggtttaactctatgattctttgttcagGTCTATGTAATTGGTGGAGATGGTACTCAAAGGGGTGCTGGAGTGATTTTCGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA