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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttctggaatacttctcttcataagaaatgccatcattgggttgaattgagtccctttttttgtctagccttaatggtttattgtgtttggctttcagGTTAAGCAGATGGTTGTTGCAACACTTGCCGAGTCAGGAATGAATCTTTCGGATGAAATTGTAGAGAGTATAATTGACAAG

Basic information

species Zea mays
transcript GRMZM2G173424_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G173424_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g40510.1 (Oryza sativa), 3'ss of exon 6
tttttctggaatacttc-----tcttcataagaaatgccatcattgggttgaattgagtccctttttttgtctagccttaatggtttattgtgtttggctttcagGTTAAGCAGATGGTTGTTGCAACACTTGCCGAGTCAGGAATGAATCTTTCGGATGAAATTGTAGAGAGTATAATTGACAAG
|        |||| ||        ||  |     ||| |||  ||   |||  | |  |   |  ||||   |   ||  || ||||||    ||    | |||||||||||||||||||||||| |||||||| ||||| |||||||||||||| ||||||||| ||||||| ||||| || |||
tcaaagctaaatattttaaatagttttgttgtggatgtcattctt---ttgggtaggatatttccttttacttcatct--atagtttataaaattgatttatcagGTTAAGCAGATGGTTGTTGCTACACTTGCTGAGTCTGGAATGAATCTTTCTGATGAAATTATAGAGAGCATAATCGATAAG

upper sequence: GRMZM2G173424_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 3'ss of exon 5
tttttctggaatacttctcttcataagaaatgccatcattgggttgaattgagtccctttttttg--tctagccttaatggtttattgtgtttggctttcagGTTAAGCAGATGGTTGTTGCAACACTTGCCGAGTCAGGAATGAATCTTTCGGATGAAATTGTAGAGAGTATAATTGACAAG
  ||| | |  | |||   || ||      |    || | |  ||    | | | |  |||| |   | |||   |  | || | |    |      || |||| ||||| ||||| || || |||||||| || || || |||||||||||||||||  || |||| ||||| |||||||||
-atttgtaggttgcttggttttatccctc-tattttcttggactttctataatttctcttttgtcattttagttcttcttgtatgtgacctcctatatttagGTGAAGCAAATGGTAGTGGCCACACTTGCTGAATCTGGTATGAATCTTTCGGATGATGTTATAGAAAGTATCATTGACAAG
















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|211209490|gb|FL043658.1|FL043658
EST:     CATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAGAG                         GTTAAGCAGATGGTTGNTGCAACACTTGCCGAGTCAGGAATGAATCTTTCG
genomic: CATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAGAGgtatggtact ... tggctttcagGTTAAGCAGATGGTTGTTGCAACACTTGCCGAGTCAGGAATGAATCTTTCG
EST: gi|211119821|gb|FL462978.1|FL462978
EST:     CATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAGAG                         GTTAAGCAGATGGTTGTTGCAACACTTGCCGAGTCAGGAATGAATCTTTCG
genomic: CATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAGAGgtatggtact ... tggctttcagGTTAAGCAGATGGTTGTTGCAACACTTGCCGAGTCAGGAATGAATCTTTCG
EST: gi|211209489|gb|FL043657.1|FL043657
EST:     CATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAGAG                         GTTAAGCAGATGGTTGTTGCAACACTTGCCGAGTCAGGAATGAATCTTTCG
genomic: CATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAGAGgtatggtact ... tggctttcagGTTAAGCAGATGGTTGTTGCAACACTTGCCGAGTCAGGAATGAATCTTTCG
EST: gi|74244689|gb|DT652603.1|DT652603
EST:     CATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAGAG                         GTTAAGCAGATGGTTGTTGCAACACTTGCCGAGTCAGGAATGAATCTTTCG
genomic: CATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAGAGgtatggtact ... tggctttcagGTTAAGCAGATGGTTGTTGCAACACTTGCCGAGTCAGGAATGAATCTTTCG
EST: gi|71307467|gb|DR789938.1|DR789938
EST:     CATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAGAG                         GTTAAGCAGATGGTTGTTGCAACACTTGCCGAGTCAGGAATGAATCTTTCG
genomic: CATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAGAGgtatggtact ... tggctttcagGTTAAGCAGATGGTTGTTGCAACACTTGCCGAGTCAGGAATGAATCTTTCG

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: 45 (upstream exon), 48 (downstream exon)
Score: 68

TTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAGAGgtatggtact ... tggctttcagGTTAAGCAGATGGTTGTTGCAACACTTGCCGAGTCAGGAATGAATCTTTCGGATGAAATTGTAGAGAGTATAATTGACAAG


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 33

TTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAGAGgtatggtact ... tggctttcagGTTAAGCAGATGGTTGTTGCAACACTTGCCGAGTCAGGAATGAATCTTTCGGATGAAATTGTAGAGAGTATAATTGACAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 67

TTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAGAGgtatggtact ... tggctttcagGTTAAGCAGATGGTTGTTGCAACACTTGCCGAGTCAGGAATGAATCTTTCGGATGAAATTGTAGAGAGTATAATTGACAAG


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 71

TTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAGAGgtatggtact ... tggctttcagGTTAAGCAGATGGTTGTTGCAACACTTGCCGAGTCAGGAATGAATCTTTCGGATGAAATTGTAGAGAGTATAATTGACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaattgagtccctttttttgtctagccttaatggtttattgtgtttggctttcagGTTAAGCAGATGGTTGTTGCAACACTTGCCGAGTCAGGAATGAATCTTTCGGATGAAATTGTAGAGAGTATAATTGACAAG
                         ccttaat  putative branch site (score: 71)
                                                ctttc  putative PPT
            tttttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttctggaatacttctcttcataagaaatgccatcattgggttgaattgagtccctttttttgtctagccttaatggtttattgtgtttggctttcagGTTAAGCAGATGGTTGTTGCAACACTTGCCGAGTCAGGAATGAATCTTTCGGATGAAATTGTAGAGAGTATAATTGACAAG

-ttttctg
- - - - - - - - - - - ataagaaa
- - - - - - - - - - - - - - - -gccatca
- - - - - - - - - - - - - - - - - - - - - - tgaattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtgtt