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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcggggacaaggctacatctttttctgaaacttggtgtcatgtgcgagcacaaggtcaataatgtagattaggagccaattctgtaggtattgttttatctaagattgtactgtgtgattcatttgcagGTGCGTCCACAAACAATAGGTCAAGCTAGCAGAATCGGCGGTGTGAGCCCAGCAGACATGACAGTTCTCCTCATTTGGATGGAGAGCAACCGACGCATGG

Basic information

species Zea mays
transcript GRMZM2G481548_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G481548_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os01g72980.2 (Oryza sativa), 3'ss of exon 12
gtaagttcggggacaaggctacatctttttctgaaacttggtgtcatgtgcgagc-acaaggtcaataatgtagattaggagccaattctgtaggtattgttttatctaagattgtactgtgtgattcatttgcagGTGCGTCCACAAACAATAGGTCAAGCTAGCAGAATCGGCGGTGTGAGCCCAGCAGACATGACAGTTCTCCTCATTTGGATGGAGAGCAACCGACGCATGG
                           |   | |   |  ||   |  | | |||  | || |    | |  | |     | | |||| | |    |  ||   ||  ||  || || | |||| |   |||  ||||  | |||||||||||||| || ||||||||||| ||||| ||||||||||| || ||||| ||||| ||||||||||||||||||||||| |||||||
---------------------------tcattcatgatctgtaagaaattcaagctgctagatttgcatttaatac----aactaattttttt--caccgtgcaatgcaat-ttatattatgtggtatgttt--agGTAAGGCCACAAACAATAGGCCAGGCTAGCAGAATTGGCGGGGTGAGCCCAGCTGATATGACTGTTCTTCTCATTTGGATGGAGAGCAACCGTCGCATGG
















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|76017300|gb|DT944470.1|DT944470
EST:     ACCACTCAATGACAAATCTATCACTTGAAGCTCGTGAGAAACTTTCCAAG                         GTGCGTCCACAAACAATAGGTCAAGCTAGCAGAATCGGCGGTGTGAGCCCA
genomic: ACCACTCAATGACAAATCTATCACTTGAAGCTCGTGAGAAACTTTCCAAGgtaagttcgg ... tcatttgcagGTGCGTCCACAAACAATAGGTCAAGCTAGCAGAATCGGCGGTGTGAGCCCA
EST: gi|83279108|gb|DV943116.1|DV943116
EST:     ACCACTCAATGACAAATCTATCACTTGAAGCTCGTGAGAAACTTTCCAAG                         GTGCGTCCACAAACAATAGGTCAAGCTAGCAGAATCGGCGGTGTGAGCCCA
genomic: ACCACTCAATGACAAATCTATCACTTGAAGCTCGTGAGAAACTTTCCAAGgtaagttcgg ... tcatttgcagGTGCGTCCACAAACAATAGGTCAAGCTAGCAGAATCGGCGGTGTGAGCCCA
EST: gi|32864358|gb|CF004040.1|CF004040
EST:     ACCACTCAATGACAAATCTATCACTTGAAGCTCGTGAGAAACTTTCCAAG                         GTGCGTCCACAAACAATAGGTCAAGCTAGCAGAATCGGCGGTGTGAGCCCA
genomic: ACCACTCAATGACAAATCTATCACTTGAAGCTCGTGAGAAACTTTCCAAGgtaagttcgg ... tcatttgcagGTGCGTCCACAAACAATAGGTCAAGCTAGCAGAATCGGCGGTGTGAGCCCA
EST: gi|4621669|gb|AI612502.1|AI612502
EST:     ACCACTCAATGACAAATCTATCACTTGAAGCTCGTGAGAAACTTTCCAAG                         GTGCGTCCACAAACAATAGGTCAAGCTAGCAGA
genomic: ACCACTCAATGACAAATCTATCACTTGAAGCTCGTGAGAAACTTTCCAAGgtaagttcgg ... tcatttgcagGTGCGTCCACAAACAATAGGTCAAGCTAGCAGA
EST: gi|71329102|gb|DR801260.1|DR801260
EST:     ACCACTCAATGACAAATTTATCACTTGAAGCTCGTGAGAAACTTTCCAAG                         GTGCGTCCACAAACAATAGGTCAAGCTAGCAGAATCGGCGGTGTGAGCCCA
genomic: ACCACTCAATGACAAATCTATCACTTGAAGCTCGTGAGAAACTTTCCAAGgtaagttcgg ... tcatttgcagGTGCGTCCACAAACAATAGGTCAAGCTAGCAGAATCGGCGGTGTGAGCCCA
EST: gi|16919165|gb|BM074067.1|BM074067
EST:     ACCACTCAATGACAAATCTATCACTTGAAGGTCGTGAGAAACTTTCCAAG                         GTGCGT-CATCAAACAATAGGTCAAGCTAGCAGAATCGGCGGTGTGAGCCC
genomic: ACCACTCAATGACAAATCTATCACTTGAAGCTCGTGAGAAACTTTCCAAGgtaagttcgg ... tcatttgcagGTGCGTCCA-CAAACAATAGGTCAAGCTAGCAGAATCGGCGGTGTGAGCCC
EST: gi|149088053|gb|EE287257.2|EE287257
EST:     ACCACTCAATGACAAATCTATCACTTGAAGCTCGTGAGAAACTTTCCAAG                         GTGCGTCCACAAACAATAGGTCAAGCTAGCAGAATCGGCGGTGTGAGCCCA
genomic: ACCACTCAATGACAAATCTATCACTTGAAGCTCGTGAGAAACTTTCCAAGgtaagttcgg ... tcatttgcagGTGCGTCCACAAACAATAGGTCAAGCTAGCAGAATCGGCGGTGTGAGCCCA
EST: gi|16925054|gb|BM078122.1|BM078122
EST:     ACCACTCAATGACAAATCTATCACTTGAAGCTCGTGAGAAACTTTCCAAG                         GTGCGTCCACAAACAATAGGTCAAGCTAGCAGAATCGGCGGTGTGAGCCCA
genomic: ACCACTCAATGACAAATCTATCACTTGAAGCTCGTGAGAAACTTTCCAAGgtaagttcgg ... tcatttgcagGTGCGTCCACAAACAATAGGTCAAGCTAGCAGAATCGGCGGTGTGAGCCCA

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: 31

ATCGTAAACCAAGAACACAGGAAACTTCCTGAAGATTTGGATTACCACTCAATGACAAATCTATCACTTGAAGCTCGTGAGAAACTTTCCAAGgtaagttcgg ... tcatttgcagGTGCGTCCACAAACAATAGGTCAAGCTAGCAGAATCGGCGGTGTGAGCCCAGCAGACATGACAGTTCTCCTCATTTGGATGGAGAGCAACCGACGCATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 59

ATCGTAAACCAAGAACACAGGAAACTTCCTGAAGATTTGGATTACCACTCAATGACAAATCTATCACTTGAAGCTCGTGAGAAACTTTCCAAGgtaagttcgg ... tcatttgcagGTGCGTCCACAAACAATAGGTCAAGCTAGCAGAATCGGCGGTGTGAGCCCAGCAGACATGACAGTTCTCCTCATTTGGATGGAGAGCAACCGACGCATGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 46

ATCGTAAACCAAGAACACAGGAAACTTCCTGAAGATTTGGATTACCACTCAATGACAAATCTATCACTTGAAGCTCGTGAGAAACTTTCCAAGgtaagttcgg ... tcatttgcagGTGCGTCCACAAACAATAGGTCAAGCTAGCAGAATCGGCGGTGTGAGCCCAGCAGACATGACAGTTCTCCTCATTTGGATGGAGAGCAACCGACGCATGG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 50

ATCGTAAACCAAGAACACAGGAAACTTCCTGAAGATTTGGATTACCACTCAATGACAAATCTATCACTTGAAGCTCGTGAGAAACTTTCCAAGgtaagttcgg ... tcatttgcagGTGCGTCCACAAACAATAGGTCAAGCTAGCAGAATCGGCGGTGTGAGCCCAGCAGACATGACAGTTCTCCTCATTTGGATGGAGAGCAACCGACGCATGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccaattctgtaggtattgttttatctaagattgtactgtgtgattcatttgcagGTGCGTCCACAAACAATAGGTCAAGCTAGCAGAATCGGCGGTGTGAGCCCAGCAGACATGACAGTTCTCCTCATTTGGATGGAGAGCAACCGACGCATGG
                                            ttcattt  CT-rich tract
              tattgttttatctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcggggacaaggctacatctttttctgaaacttggtgtcatgtgcgagcacaaggtcaataatgtagattaggagccaattctgtaggtattgttttatctaagattgtactgtgtgattcatttgcagGTGCGTCCACAAACAATAGGTCAAGCTAGCAGAATCGGCGGTGTGAGCCCAGCAGACATGACAGTTCTCCTCATTTGGATGGAGAGCAACCGACGCATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA