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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaaaatatagattattttgatgatttatggcccgtgttaactccatgtagatctggaacgaaggtttgagttaacttgggtgtgttttttttatgccagATCTTCAATGAGTTCAATGCACGAAAACCCGAGGAAAAGAATGTCTTCAAAGGGGTCACGAAGAATCACCTGTTCATGGGAATAATCGGTATAACGACAG

Basic information

species Zea mays
transcript GRMZM2G132712_T03
intron # 31
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G132712_T01 (Zea mays), 3'ss of exon 30
lower sequence: LOC_Os08g40530.1 (Oryza sativa), 3'ss of exon 15
-tgaaaatatagattattttgatgatttatggcccgtgttaactccatgtagatct--ggaacgaaggtttgagttaacttgggt--gtgttttttttatgccagATCTTCAATGAGTTCAATGCACGAAAACCCGAGGAAAAGAATGTCTTCAAAGGGGTCACGAAGAATCACCTGTTCATGGGAATAATCGGTATAACGACAG
 |  |  | | | | | | |   | | | | | ||   |||     ||  ||   |  ||||| ||| |||   ||   |    |   | |   ||  ||||||||||||||| |||||||||||||| || |||||||| | |||||||||||||||  | ||||| || || || |||||||||||||| | |||||| || |
cttgatgt-tggctcactatatagttctgtagtcccactta----tataaagtcttgaggaacaaagttttatttttgttacacttgatatgcattgcatgccagATCTTCAACGAGTTCAATGCACGCAAGCCCGAGGAGAGGAATGTCTTCAAAGGAATAACGAAAAACCATCTCTTCATGGGAATAATTGCTATAACTACTG
















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|6020890|gb|AW065818.1|AW065818
EST:     CTGAGAAGATAACAAATACTTTCATCTTCAACACATTTGTATTTTGCCAG                         ATCTTCAATGAGTTCAATGCACGAAAACCCGAGGAAAAGAATGTCTTCAAA
genomic: CTGAGAAGATAACAAATACTTTCATCTTCAACACATTTGTATTTTGCCAGgtggagtatt ... tttatgccagATCTTCAATGAGTTCAATGCACGAAAACCCGAGGAAAAGAATGTCTTCAAA
EST: gi|60340338|gb|DN207311.1|DN207311
EST:     CTGAGAAGATAACAAATACTTTCATCTTCAACACATTTGTATTTTGCCAG                         ATCTTCAATGAGTTCAATGCACGAAAACCCGAGGAAAAGAATGTCTTCAAA
genomic: CTGAGAAGATAACAAATACTTTCATCTTCAACACATTTGTATTTTGCCAGgtggagtatt ... tttatgccagATCTTCAATGAGTTCAATGCACGAAAACCCGAGGAAAAGAATGTCTTCAAA
EST: gi|5296205|gb|AI782885.1|AI782885
EST:     CTGAGAAGATAACAAATACTTTCATCTTCAACACATTTGTATTTTGCCAG                         ATCTTCAATGAGTTCAATGCACGAAAACCCGAGGAAAAGAATGTCTTCAAA
genomic: CTGAGAAGATAACAAATACTTTCATCTTCAACACATTTGTATTTTGCCAGgtggagtatt ... tttatgccagATCTTCAATGAGTTCAATGCACGAAAACCCGAGGAAAAGAATGTCTTCAAA

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: 44 (upstream exon), 49 (downstream exon)
Score: 81

TTTTGATGGAGTAAGGATTCTGCGTCTGCAGAATGAAAGCCGATCTGATGCTGAGAAGATAACAAATACTTTCATCTTCAACACATTTGTATTTTGCCAGgtggagtatt ... tttatgccagATCTTCAATGAGTTCAATGCACGAAAACCCGAGGAAAAGAATGTCTTCAAAGGGGTCACGAAGAATCACCTGTTCATGGGAATAATCGGTATAACGACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 117

TTTTGATGGAGTAAGGATTCTGCGTCTGCAGAATGAAAGCCGATCTGATGCTGAGAAGATAACAAATACTTTCATCTTCAACACATTTGTATTTTGCCAGgtggagtatt ... tttatgccagATCTTCAATGAGTTCAATGCACGAAAACCCGAGGAAAAGAATGTCTTCAAAGGGGTCACGAAGAATCACCTGTTCATGGGAATAATCGGTATAACGACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 167

TTTTGATGGAGTAAGGATTCTGCGTCTGCAGAATGAAAGCCGATCTGATGCTGAGAAGATAACAAATACTTTCATCTTCAACACATTTGTATTTTGCCAGgtggagtatt ... tttatgccagATCTTCAATGAGTTCAATGCACGAAAACCCGAGGAAAAGAATGTCTTCAAAGGGGTCACGAAGAATCACCTGTTCATGGGAATAATCGGTATAACGACAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 91

TTTTGATGGAGTAAGGATTCTGCGTCTGCAGAATGAAAGCCGATCTGATGCTGAGAAGATAACAAATACTTTCATCTTCAACACATTTGTATTTTGCCAGgtggagtatt ... tttatgccagATCTTCAATGAGTTCAATGCACGAAAACCCGAGGAAAAGAATGTCTTCAAAGGGGTCACGAAGAATCACCTGTTCATGGGAATAATCGGTATAACGACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtagatctggaacgaaggtttgagttaacttgggtgtgttttttttatgccagATCTTCAATGAGTTCAATGCACGAAAACCCGAGGAAAAGAATGTCTTCAAAGGGGTCACGAAGAATCACCTGTTCATGGGAATAATCGGTATAACGACAG
                        agttaac  putative branch site (score: 91)
                                      tgtttttttt  putative PPT
                                    tgtgttttttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaaaatatagattattttgatgatttatggcccgtgttaactccatgtagatctggaacgaaggtttgagttaacttgggtgtgttttttttatgccagATCTTCAATGAGTTCAATGCACGAAAACCCGAGGAAAAGAATGTCTTCAAAGGGGTCACGAAGAATCACCTGTTCATGGGAATAATCGGTATAACGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA