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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATGTGGTCTCCAAAGTCTGCATCTTCCTGCAAGAGAACAACAGACCTTTCAATGTCCTCATCTCTGAATCTGGCAAGAGAATTTTCCTTCTACCACAGgtattcccatgcgacctcagttgtgtataagctctgaaacaaatgttcacaacacgtccttcagtaatgtgttgatgtttatctccaccaaaatcgattggccag

Basic information

species Zea mays
transcript GRMZM2G359397_T03
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G359397_T03 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g67520.2 (Oryza sativa), 5'ss of exon 4
AGATGTGGTCTCCAAAGTCTGCATCTTCCTGCAAGAGAACAACAGACCTTTCAATGTCCTCATCTCTGAATCTGGCAAGAGAATTTTCCTTCTACCACAGgtattcccatgcgacctcagttgtgtataagctctgaaacaaatgttcacaacacgtccttcagtaatgt--gttgatg-----tttatctccaccaaaatcgattggccag
 ||||| || || ||||||||||||||| |||||||||| || | ||||||||||| ||||||||||||||||||||||||| | ||||| |||||||||||| | || |   ||     |||   ||||  |||||||  ||| ||||||     |    |||||      | | |       ||| |||||  |  | ||||| |  |||
CGATGTTGTTTCAAAAGTCTGCATCTTCTTGCAAGAGAATAATAAACCTTTCAATGCCCTCATCTCTGAATCTGGCAAGAGAGTGTTCCTGCTACCACAGgtactaccctagaacacttattgc--ataacttctgaaaataat-ttcacactctatatcacagtagcaatggataacaaacattttgtctccgtctgattcgatcgatcag
















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|60336718|gb|DN203691.1|DN203691
EST:     TCAATGTCCTCATCTCTGAATCTGGCAAGAGAATTTTCCTTCTACCACAG                         TGCTATGCGGAGAAGCAGCTCCTCGGAAAGGCGAGCCAAGAGTTCCTGGAC
genomic: TCAATGTCCTCATCTCTGAATCTGGCAAGAGAATTTTCCTTCTACCACAGgtattcccat ... gattggccagTGCTATGCGGAGAAGCAGCTCCTCGGAAAGGCGAGCCAAGAGTTCCTGGAC
EST: gi|211436233|gb|FL480979.1|FL480979
EST:     TCAATGTCCTCATCTCTGAATCTGGCAAGAGAATTTTCCTTCTACCACAG                         TGCTATGCGGAGAAGCAGCTTCTCGGAAAGGCGAGCCAAGAGTTCCTCGAC
genomic: TCAATGTCCTCATCTCTGAATCTGGCAAGAGAATTTTCCTTCTACCACAGgtattcccat ... gattggccagTGCTATGCGGAGAAGCAGCTCCTCGGAAAGGCGAGCCAAGAGTTCCTGGAC
EST: gi|94472555|gb|EB701513.1|EB701513
EST:     TCAATGTCCTCATCTCTGAATCTGGCAAGAGAATTTTCCTTCTACCACAG                         TGCTATGCGGAGAAGCAGCTCCTCGGAAAGGCGAGCCAAGAGTTCCTGGAC
genomic: TCAATGTCCTCATCTCTGAATCTGGCAAGAGAATTTTCCTTCTACCACAGgtattcccat ... gattggccagTGCTATGCGGAGAAGCAGCTCCTCGGAAAGGCGAGCCAAGAGTTCCTGGAC
EST: gi|31364173|gb|CD448528.1|CD448528
EST:     TCAATGTCCTCATCTCTGAATCTGGCAAGAGAATTTTCCTTCTACCACAG                         TGCTATGCGGAGAAGCAGCTCCTCGGAAAGGCGAGCCAAGAGTTCCTCGAC
genomic: TCAATGTCCTCATCTCTGAATCTGGCAAGAGAATTTTCCTTCTACCACAGgtattcccat ... gattggccagTGCTATGCGGAGAAGCAGCTCCTCGGAAAGGCGAGCCAAGAGTTCCTGGAC
EST: gi|67017472|gb|CO446221.1|CO446221
EST:     TCAATGTCCTCATCTCTGAATCTGGCAAGAGAATTTTCCTTCTACCACAG                         TGCTATGCGGAGAAGCAGCTCCTCGGAAAGGCGAGCCAAGAGTTCCTCGAC
genomic: TCAATGTCCTCATCTCTGAATCTGGCAAGAGAATTTTCCTTCTACCACAGgtattcccat ... gattggccagTGCTATGCGGAGAAGCAGCTCCTCGGAAAGGCGAGCCAAGAGTTCCTGGAC
EST: gi|24768733|gb|CA403862.1|CA403862
EST:     TCAATGTCCTCATCTCTGAATCTGGCAAGAGAATTTTCCTTCTACCACAG                         TGCTATGCGGAGAAGCAGCTCCTCGGAAAGGCGAGCCAAGAGTTCCTCGAC
genomic: TCAATGTCCTCATCTCTGAATCTGGCAAGAGAATTTTCCTTCTACCACAGgtattcccat ... gattggccagTGCTATGCGGAGAAGCAGCTCCTCGGAAAGGCGAGCCAAGAGTTCCTGGAC
EST: gi|78119880|gb|DV538264.1|DV538264
EST:     TCAATGTCCTCATCTCTGAATCTGGCAAGAGAATTTTCCTTCTACCACAG                         TGCTATGCGGAGAAGCAGCTCCTCGGAAAGGCGAGCCAAGAGTTCCTGGAC
genomic: TCAATGTCCTCATCTCTGAATCTGGCAAGAGAATTTTCCTTCTACCACAGgtattcccat ... gattggccagTGCTATGCGGAGAAGCAGCTCCTCGGAAAGGCGAGCCAAGAGTTCCTGGAC
EST: gi|76282139|gb|DV021707.1|DV021707
EST:     TCAATGTCCTCATTTCTGAATCTGGCAAGAGAATTTTCCTTCTCCCCCAG                         TGCTATGCGGAGAAGCAGCTCCTCGGAAAGGCGAGCCAAGAGTTCCTGGAC
genomic: TCAATGTCCTCATCTCTGAATCTGGCAAGAGAATTTTCCTTCTACCACAGgtattcccat ... gattggccagTGCTATGCGGAGAAGCAGCTCCTCGGAAAGGCGAGCCAAGAGTTCCTGGAC
EST: gi|211001655|gb|FL448344.1|FL448344
EST:     TCAATGTCCTCATCTCTGAATCTGGCAAGAGAATTTTCCTTCTACCACAG                         TGCTATGCGGAGAAGCAGCTCCTCGGAAAGGCGAGCCAAGAGTTCCTCGAC
genomic: TCAATGTCCTCATCTCTGAATCTGGCAAGAGAATTTTCCTTCTACCACAGgtattcccat ... gattggccagTGCTATGCGGAGAAGCAGCTCCTCGGAAAGGCGAGCCAAGAGTTCCTGGAC
EST: gi|32866924|gb|CF006606.1|CF006606
EST:     GGCAAGAGAATTTTCCTTCTACCACAG                         TGCTATGCGGAGAAGCAGCTTCTCGGAAAGGCGAGCCAAGAGTTCCTCGAC
genomic: GGCAAGAGAATTTTCCTTCTACCACAGgtattcccat ... gattggccagTGCTATGCGGAGAAGCAGCTCCTCGGAAAGGCGAGCCAAGAGTTCCTGGAC

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: 47 (upstream exon), 47 (downstream exon)
Score: 10

AGATGTGGTCTCCAAAGTCTGCATCTTCCTGCAAGAGAACAACAGACCTTTCAATGTCCTCATCTCTGAATCTGGCAAGAGAATTTTCCTTCTACCACAGgtattcccat ... gattggccagTGCTATGCGGAGAAGCAGCTCCTCGGAAAGGCGAGCCAAGAGTTCCTGGACATGAGAATCAATCCAGCAATCTGGGAGCTCAGTGGCCATCTGGTACTGA


Block sizes: 34 (upstream exon), 33 (downstream exon)
Score: 5

AGATGTGGTCTCCAAAGTCTGCATCTTCCTGCAAGAGAACAACAGACCTTTCAATGTCCTCATCTCTGAATCTGGCAAGAGAATTTTCCTTCTACCACAGgtattcccat ... gattggccagTGCTATGCGGAGAAGCAGCTCCTCGGAAAGGCGAGCCAAGAGTTCCTGGACATGAGAATCAATCCAGCAATCTGGGAGCTCAGTGGCCATCTGGTACTGA


Block sizes: 9 (upstream exon), 41 (downstream exon)
Score: 1

AGATGTGGTCTCCAAAGTCTGCATCTTCCTGCAAGAGAACAACAGACCTTTCAATGTCCTCATCTCTGAATCTGGCAAGAGAATTTTCCTTCTACCACAGgtattcccat ... gattggccagTGCTATGCGGAGAAGCAGCTCCTCGGAAAGGCGAGCCAAGAGTTCCTGGACATGAGAATCAATCCAGCAATCTGGGAGCTCAGTGGCCATCTGGTACTGA


Block sizes: 17 (upstream exon), 44 (downstream exon)
Score: 2

AGATGTGGTCTCCAAAGTCTGCATCTTCCTGCAAGAGAACAACAGACCTTTCAATGTCCTCATCTCTGAATCTGGCAAGAGAATTTTCCTTCTACCACAGgtattcccat ... gattggccagTGCTATGCGGAGAAGCAGCTCCTCGGAAAGGCGAGCCAAGAGTTCCTGGACATGAGAATCAATCCAGCAATCTGGGAGCTCAGTGGCCATCTGGTACTGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATGTGGTCTCCAAAGTCTGCATCTTCCTGCAAGAGAACAACAGACCTTTCAATGTCCTCATCTCTGAATCTGGCAAGAGAATTTTCCTTCTACCACAGgtattcccatgcgacctcagttgtgtataagctctgaaacaaatgttcacaacacgtccttcagtaatgtgttgatgtttatctccaccaaaatcgattggccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA