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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagtatgttcattcaattggcctgtattactatttttatggtattattgtatactgtatgtttgcctcatcagtaccttgttatttgtgcgcaccactcatcagGGATTTGAGGCAGCTATTGCAGCAGGGGCAAAAGAAATCGCAATATTTGCATCAGCTTCTGAAGGATTTTCCAAGTCAAACATAAACTGCACCATTAAAG

Basic information

species Zea mays
transcript GRMZM2G175071_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G175071_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g16350.1 (Oryza sativa), 3'ss of exon 4
gtgaagtatgttcattcaattggcctgtattactatttttatggtattattgtatactgtatgtttgcctcatcagtaccttgttatttgtgcgcaccactcatcagGGATTTGAGGCAGCTATTGCAGCAGGGGCAAAAGAAATCGCAATATTTGCATCAGCTTCTGAAGGATTTTCCAAGTCAAACATAAACTGCACCATTAAAG
                           ||| | |   || |    | | |||  |||  ||||| ||  |     ||  |   ||  || ||  |     | |||||||||||||||||||| |||||||||| ||||||||| | ||| ||||||| ||||||||||||| |||||||||||||||||||||||| ||||||||||
-----------------------gtaatataatttgattcagataacttttgagtac-atatgtctgtttacctcgtttcacatttattctgttcgttggtaatcagGGATTTGAGGCAGCTGTTGCAGCAGGTGCAAAAGAAGTTGCAGTATTTGCGTCAGCTTCTGAAGCATTTTCCAAGTCAAACATAAACTGTACCATTAAAG

upper sequence: GRMZM2G175071_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv06s0009g02640.t01 (Vitis vinifera), 3'ss of exon 4
gtgaagtatgttcattcaattggcctgtattactatttttatggtattattgtatactgtatgtttgcctcatcagtaccttgttatttgtgcgcaccactcatcagGGATTTGAGGCAGCTATTGCAGCAGGGGCAAAAGAAATCGCAATATTTGCATCAGCTTCTGAAGGATTTTCCAAGTCAAACATAAACTGCACCATTAAAG
||||   ||  |      |       | |  || ||   |        ||| | | ||||||||  |        | |  || | || |      || |||  | |||||||||| |||||||||||||| || || || ||| | || || ||||| |||||||||||    ||||| ||||||||||| || || |  ||| |||
gtgagtaattgtttccagaaaaaggggaaaaaccatgagttcaaagcaattctgt-ctgtatgtgag--------ggaatttctcatatca----actacttgt-agGGATTTGAAGCAGCTATTGCAGCTGGTGCTAAGGAAGTTGCCATCTTTGCTTCAGCTTCTGAGTCCTTTTCAAAGTCAAACATCAATTGTAGTATTGAAG
















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|76293872|gb|DV033440.1|DV033440
EST:     TTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCTAAACCTTAAG                         GGATTTGAAGCAGC
genomic: TTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAGgtgaagtatg ... cactcatcagGGATTTGAGGCAGC
EST: gi|211148321|gb|FL359569.1|FL359569
EST:     TTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAG                         GGATTTGAGGCAGCTATTGCAGCTGGGGCAAAAGAAATCGCAATATTTGCA
genomic: TTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAGgtgaagtatg ... cactcatcagGGATTTGAGGCAGCTATTGCAGCAGGGGCAAAAGAAATCGCAATATTTGCA
EST: gi|149111653|gb|EE190797.2|EE190797
EST:     TTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAG                         GGATTTGAGGCAGCTATTGCAGCAGGGGCAAAAGAAATCGCAATATTTGCA
genomic: TTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAGgtgaagtatg ... cactcatcagGGATTTGAGGCAGCTATTGCAGCAGGGGCAAAAGAAATCGCAATATTTGCA
EST: gi|60401129|gb|DN233936.1|DN233936
EST:     TTCGGACTATTGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAG                         GGATTTGAGGCAGCTATTGCAGCTGGGGCAAAAGAAATCGCAATATTTGCA
genomic: TTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAGgtgaagtatg ... cactcatcagGGATTTGAGGCAGCTATTGCAGCAGGGGCAAAAGAAATCGCAATATTTGCA
EST: gi|71430395|gb|DR811445.1|DR811445
EST:     TTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAG                         GGATTTGAGGCAGCTATTGCAGCAGGGGCAAAAGAAATCGCAATATTTGCA
genomic: TTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAGgtgaagtatg ... cactcatcagGGATTTGAGGCAGCTATTGCAGCAGGGGCAAAAGAAATCGCAATATTTGCA
EST: gi|74237799|gb|DT645713.1|DT645713
EST:     TTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAG                         GGATTTGAGGCAGCTATTGCAGCAGGGGCAAAAGAAATCGCAATATTTG
genomic: TTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAGgtgaagtatg ... cactcatcagGGATTTGAGGCAGCTATTGCAGCAGGGGCAAAAGAAATCGCAATATTTG
EST: gi|149010241|gb|EE042063.2|EE042063
EST:     TTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAG                         GGATTTGAGGCAGCTATTGCAGCAGGGGCAAAAGAAATCGCAATATTTGCA
genomic: TTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAGgtgaagtatg ... cactcatcagGGATTTGAGGCAGCTATTGCAGCAGGGGCAAAAGAAATCGCAATATTTGCA
EST: gi|148969536|gb|EE020363.2|EE020363
EST:     TTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAG                         GGATTTGAGGCAGCTATTGCAGCAGGGGCAAAAGAAATCGCAATATTTGCA
genomic: TTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAGgtgaagtatg ... cactcatcagGGATTTGAGGCAGCTATTGCAGCAGGGGCAAAAGAAATCGCAATATTTGCA
EST: gi|76013106|gb|DT940276.1|DT940276
EST:     TTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAG                         GGATTTGAGGCAGCTATTGCAGCANGGGCAAAAGAAATCGCAATATTTGCA
genomic: TTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAGgtgaagtatg ... cactcatcagGGATTTGAGGCAGCTATTGCAGCAGGGGCAAAAGAAATCGCAATATTTGCA
EST: gi|71772253|gb|DR970190.1|DR970190
EST:     TTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAG                         GGATTTGAGGCAGCTATTGCAGCAGGGGCAAAAGAAATCGCAATATTTGCA
genomic: TTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAGgtgaagtatg ... cactcatcagGGATTTGAGGCAGCTATTGCAGCAGGGGCAAAAGAAATCGCAATATTTGCA
EST: gi|74235239|gb|DT643153.1|DT643153
EST:     TTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAG                         GGATTTGAGGCAGCTATTGCAGCAGGGGCAAAAGAAATCGCAATATTTGCA
genomic: TTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAGgtgaagtatg ... cactcatcagGGATTTGAGGCAGCTATTGCAGCAGGGGCAAAAGAAATCGCAATATTTGCA

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: 362

TTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAGgtgaagtatg ... cactcatcagGGATTTGAGGCAGCTATTGCAGCAGGGGCAAAAGAAATCGCAATATTTGCATCAGCTTCTGAAGGATTTTCCAAGTCAAACATAAACTGCACCATTAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 368

TTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAGgtgaagtatg ... cactcatcagGGATTTGAGGCAGCTATTGCAGCAGGGGCAAAAGAAATCGCAATATTTGCATCAGCTTCTGAAGGATTTTCCAAGTCAAACATAAACTGCACCATTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 322

TTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAGgtgaagtatg ... cactcatcagGGATTTGAGGCAGCTATTGCAGCAGGGGCAAAAGAAATCGCAATATTTGCATCAGCTTCTGAAGGATTTTCCAAGTCAAACATAAACTGCACCATTAAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 164

TTAGCTGATGCGAAGGATGTTATGGAAGCAGTTCGGACTATGGGGGGTGTACGTTTTCCTGTATTGACTCCAAACCTTAAGgtgaagtatg ... cactcatcagGGATTTGAGGCAGCTATTGCAGCAGGGGCAAAAGAAATCGCAATATTTGCATCAGCTTCTGAAGGATTTTCCAAGTCAAACATAAACTGCACCATTAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatactgtatgtttgcctcatcagtaccttgttatttgtgcgcaccactcatcagGGATTTGAGGCAGCTATTGCAGCAGGGGCAAAAGAAATCGCAATATTTGCATCAGCTTCTGAAGGATTTTCCAAGTCAAACATAAACTGCACCATTAAAG
                            ttgttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaagtatgttcattcaattggcctgtattactatttttatggtattattgtatactgtatgtttgcctcatcagtaccttgttatttgtgcgcaccactcatcagGGATTTGAGGCAGCTATTGCAGCAGGGGCAAAAGAAATCGCAATATTTGCATCAGCTTCTGAAGGATTTTCCAAGTCAAACATAAACTGCACCATTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG