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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatcacatatctattttctgaaataaaaatataactttacattgccctgatttgtcttttacttgaatttcttctgcagGATGTCTGGACTGACTTGGGTCGTCCTTGTGGTATCCATCAGAAGCAG

Basic information

species Zea mays
transcript GRMZM2G116434_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116434_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os06g49990.1 (Oryza sativa), 3'ss of exon 8
-------------------gtacatcacatatctattttctgaaataaaaatataacttta---cattgccctgatttgtcttttacttgaatttcttctgcagGATGTCTGGACTGACTTGGGTCGTCCTTGTGGTATCCATCAGAAGCAG
                      |     || ||| | | ||           |  |||||    |  ||  || |||| | | ||  ||     |||   |||||| || |||||||| ||||||||||| ||||| ||||| |||||||||
gtagcaaattatgccgtctactctctctatctctctctgctttccccttctcaccactttgatgcgatggtcttatttatttcttgatttggcatctctggcagGACGTGTGGACTGAGTTGGGTCGTCCATGTGGCATCCACCAGAAGCAG

upper sequence: GRMZM2G116434_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv04s0023g02970.t01 (Vitis vinifera), 3'ss of exon 8
----gtacatcacatatctattttctgaaataaaaatataactttacattgccc--tgatttgtctttta-----cttgaatttcttctg-------cagGATGTCTGGACTGACTTGGGTCGTCCTTGTGGTATCCATCAGAAGCAG
      | ||| | | |||||| |       |  ||| | |  |||  | |  |  | |||     | ||     ||   ||||||| |        |||||||| |||||||| || || ||||||||||| |||||||| ||||||
tccaaaatatctcgtctctattcttgtgtcaagcaatttgatgttatgtggttcattcattcagtgtataatgatctcatatttcttgttttctattcagGATGTGTGGACTGAATTAGGCCGTCCTTGTGGAATCCATCAAAAGCAG
















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|13126006|gb|BG316681.1|BG316681
EST:     ATAGGGGGGCAACATATTCCTTTTGG-GCATCACCACAG                         GATGTCTGGACTGACTTGGGTCGTCCTTGTGGTATCCATCAGAAGCAG
genomic: ATAGGGGGGCAACATATTCCTTTTGGTGCATCACCACAGgtacatcaca ... tcttctgcagGATGTCTGGACTGACTTGGGTCGTCCTTGTGGTATCCATCAGAAGCAG
EST: gi|67024702|gb|CO453451.1|CO453451
EST:     TTTGGTTCACAATAGGGGGGCAACATATTCCTTTTGGTGCATCACCACAG                         GATGTCTGGACTGACTTAGGTCGTCCTTGTGGTATCCATCAGAAGCAG
genomic: TTTGGTTCACAATAGGGGGGCAACATATTCCTTTTGGTGCATCACCACAGgtacatcaca ... tcttctgcagGATGTCTGGACTGACTTGGGTCGTCCTTGTGGTATCCATCAGAAGCAG
EST: gi|149105604|gb|EE291147.2|EE291147
EST:     TTGGTTTCACA-TAGGGGGGCAACATATTCCTTTTGGTGCATCACCACAG                         GATGTCTGGACTGA
genomic: TTGGTT-CACAATAGGGGGGCAACATATTCCTTTTGGTGCATCACCACAGgtacatcaca ... tcttctgcagGATGTCTGGACTGA
EST: gi|67015496|gb|CO444245.1|CO444245
EST:     TTTGGTTCACAATAGGGGGGCAACATATTCCTTTTGGTGCATCACCACAG                         GATGTCTGGACTGACTTAGGTCGTCCTTGTGGTATCCATCAGAAGCAG
genomic: TTTGGTTCACAATAGGGGGGCAACATATTCCTTTTGGTGCATCACCACAGgtacatcaca ... tcttctgcagGATGTCTGGACTGACTTGGGTCGTCCTTGTGGTATCCATCAGAAGCAG
EST: gi|101393044|gb|EB818453.1|EB818453
EST:     TTTGGTTCACAATAGGGGGGCAACATATTCCTTTTGGTGCATCACCACAG                         GATGTCTGGACTGACTTGGGTCGTCCTTGTGGTATCCATCAGAAGCAG
genomic: TTTGGTTCACAATAGGGGGGCAACATATTCCTTTTGGTGCATCACCACAGgtacatcaca ... tcttctgcagGATGTCTGGACTGACTTGGGTCGTCCTTGTGGTATCCATCAGAAGCAG
EST: gi|78106231|gb|DV524649.1|DV524649
EST:     TTTGGTTCACAATAGGGGGGCAACATATTCCTTTTGGTGCATCACCACAG                         GATGTCTGGACTGACTTGGGTCGTCCTTGTGGTATCCATCAGAAGCAG
genomic: TTTGGTTCACAATAGGGGGGCAACATATTCCTTTTGGTGCATCACCACAGgtacatcaca ... tcttctgcagGATGTCTGGACTGACTTGGGTCGTCCTTGTGGTATCCATCAGAAGCAG
EST: gi|76014245|gb|DT941415.1|DT941415
EST:     TTGGTGCATCACCACAG                         GATGTCTGGACTGACTTGGGTCGTCCTTGTGGTATCCATCAGAAGCAG
genomic: TTGGTGCATCACCACAGgtacatcaca ... tcttctgcagGATGTCTGGACTGACTTGGGTCGTCCTTGTGGTATCCATCAGAAGCAG

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: 42 (upstream exon), 48 (downstream exon)
Score: 43

CTTGGTGAAGAACTTTGGTTCACAATAGGGGGGCAACATATTCCTTTTGGTGCATCACCACAGgtacatcaca ... tcttctgcagGATGTCTGGACTGACTTGGGTCGTCCTTGTGGTATCCATCAGAAGCAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 58

CTTGGTGAAGAACTTTGGTTCACAATAGGGGGGCAACATATTCCTTTTGGTGCATCACCACAGgtacatcaca ... tcttctgcagGATGTCTGGACTGACTTGGGTCGTCCTTGTGGTATCCATCAGAAGCAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 84

CTTGGTGAAGAACTTTGGTTCACAATAGGGGGGCAACATATTCCTTTTGGTGCATCACCACAGgtacatcaca ... tcttctgcagGATGTCTGGACTGACTTGGGTCGTCCTTGTGGTATCCATCAGAAGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 106

CTTGGTGAAGAACTTTGGTTCACAATAGGGGGGCAACATATTCCTTTTGGTGCATCACCACAGgtacatcaca ... tcttctgcagGATGTCTGGACTGACTTGGGTCGTCCTTGTGGTATCCATCAGAAGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaatataactttacattgccctgatttgtcttttacttgaatttcttctgcagGATGTCTGGACTGACTTGGGTCGTCCTTGTGGTATCCATCAGAAGCAG
                                           tttcttctgc  CT-rich tract
     tataactttacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatcacatatctattttctgaaataaaaatataactttacattgccctgatttgtcttttacttgaatttcttctgcagGATGTCTGGACTGACTTGGGTCGTCCTTGTGGTATCCATCAGAAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC