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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTCAGTATAAGAATGTGGCATTCACTGTGTGGGATGTGGGTGGGCAAGAAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataactattacttgcaagtgcagagacacatgagtagcttcccattatgtctctttggttcccttgtctttctcaactcttgatatggtgtttactt...

Basic information

species Zea mays
transcript GRMZM2G152929_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152929_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g03610.1 (Oryza sativa), 5'ss of exon 3
GGTTCAGTATAAGAATGTGGCATTCACTGTGTGGGATGTGGGTGGGCAAGAAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataactattacttgcaagtgcagagacacatgagtagcttcccattatgtctctttggttcccttgtctttctcaactcttgatatggtgtttactt-
||||||||| |||||||||| ||| |||||||||||||| || || |||||||| |||||| || | |||||||||||||| || ||||||||||||||||||||||||| ||  |   | |  | | |||||||   |  ||    ||    |  | |  ||||    | ||      |  ||  ||   |    | |  
GGTTCAGTACAAGAATGTGGTATTTACTGTGTGGGATGTTGGCGGACAAGAAAAGCTCAGGCCATTATGGAAGATGTACCTCAGCAATTCTGATGCACTGgtaataactagtagat-tgaatttatatacacatgttgatatttagcttggcaccttgtcattccgccctgttatagtgcctttagtactttcccaagtct

upper sequence: GRMZM2G152929_T03 (Zea mays), 5'ss of exon 3
lower sequence: EFJ08154 (Selaginella moellendorffii), 5'ss of exon 3
GGTTCAGTATAAGAATGTGGCATTCACTGTGTGGGATGTGGGTGGGCAAGAAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataactattacttgcaagtgcagagacacatgagtagcttcccattatgtctctttggttcccttgtctttctcaactcttgatatggtgtttactt
||| ||||| ||||||||||  ||||| ||||||||||||||||| || || || || ||  | || ||||||   ||| | || |   | ||||| |||||| |   |   | || |   |       |   || | | || |      ||   |                                            
GGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTGGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAGCAGCACCGATGCTCTGgtactgttttagatttccttctttgttttcgattgtg-atctacaagacgtgctccag------------------------------------------
















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|149099801|gb|EE185853.2|EE185853
EST:     AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTG                         ATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
genomic: AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataacta ... tttgttgcagATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
EST: gi|40335672|gb|CK369742.1|CK369742
EST:     AAAAACTCAGGTCATTGTGGAAGATGTACCTGAGTAATTCTGATGCACTG                         ATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
genomic: AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataacta ... tttgttgcagATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
EST: gi|211169374|gb|FL265646.1|FL265646
EST:     AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTG                         ATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGA
genomic: AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataacta ... tttgttgcagATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGA
EST: gi|149104457|gb|EE289901.2|EE289901
EST:     AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTG                         ATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
genomic: AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataacta ... tttgttgcagATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
EST: gi|18450661|gb|BM428939.1|BM428939
EST:     AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTG                         ATCTATGTCGCTGATTCTCTGGACAGAGAAAGGATCAGAGATGCGAGGCAA
genomic: AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataacta ... tttgttgcagATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
EST: gi|211166028|gb|FL265627.1|FL265627
EST:     AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTG                         ATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
genomic: AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataacta ... tttgttgcagATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
EST: gi|76922611|gb|DV169085.1|DV169085
EST:     AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTG                         ATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
genomic: AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataacta ... tttgttgcagATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
EST: gi|17921469|gb|BM259120.1|BM259120
EST:     AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTG                         ATCTATGTCGGTGATTCTCTGGACAGAGAAAGGATCAGAGATGCGAGGCAA
genomic: AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataacta ... tttgttgcagATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
EST: gi|37418653|gb|CF646998.1|CF646998
EST:     AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTG                         ATCTATGTCGTTGATTCTCTGGACAGAGAAAG
genomic: AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataacta ... tttgttgcagATCTATGTCGTTGATTCTCTGGACAGAGAAAG
EST: gi|149014814|gb|EE044516.2|EE044516
EST:     AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTG                         ATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
genomic: AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataacta ... tttgttgcagATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
EST: gi|149111989|gb|EE191151.2|EE191151
EST:     AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTG                         ATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
genomic: AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataacta ... tttgttgcagATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
EST: gi|211169373|gb|FL265645.1|FL265645
EST:     AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTG                         ATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
genomic: AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataacta ... tttgttgcagATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
EST: gi|20512850|gb|BQ280044.1|BQ280044
EST:     AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTG                         ATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
genomic: AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataacta ... tttgttgcagATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
EST: gi|211167695|gb|FL265632.1|FL265632
EST:     AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTG                         ATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
genomic: AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataacta ... tttgttgcagATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
EST: gi|148956554|gb|EC902394.2|EC902394
EST:     AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTG                         ATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
genomic: AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataacta ... tttgttgcagATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
EST: gi|19057808|gb|BM736475.1|BM736475
EST:     AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTG                         ATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGATGCGAGGCAA
genomic: AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataacta ... tttgttgcagATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
EST: gi|211167699|gb|FL265636.1|FL265636
EST:     AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTS                         ATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
genomic: AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataacta ... tttgttgcagATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
EST: gi|101384105|gb|EB814107.1|EB814107
EST:     AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTG                         ATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
genomic: AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataacta ... tttgttgcagATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
EST: gi|93014208|gb|EB639728.1|EB639728
EST:     AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTG                         ATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
genomic: AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataacta ... tttgttgcagATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
EST: gi|76020452|gb|DT947622.1|DT947622
EST:     AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTG                         ATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
genomic: AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataacta ... tttgttgcagATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
EST: gi|211167698|gb|FL265635.1|FL265635
EST:     AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTG                         ATCTATGTCGTTGATTCTCTGG
genomic: AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataacta ... tttgttgcagATCTATGTCGTTGATTCTCTGG
EST: gi|17921794|gb|BM259445.1|BM259445
EST:     AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTG                         ATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGATGCGAGGCAA
genomic: AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataacta ... tttgttgcagATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAA
EST: gi|211166029|gb|FL265628.1|FL265628
EST:     AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTG                         ATCTATGTCGTTG
genomic: AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataacta ... tttgttgcagATCTATGTCGTTG
EST: gi|211166023|gb|FL265622.1|FL265622
EST:     AAAAACTCAGGTCACTGTGGGAGATGTACCTGAGTAATTCTGATGCACTG                         ATCTATGTCGTTGATTCTCTGGACAGA-AAAGGA
genomic: AAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataacta ... tttgttgcagATCTATGTCGTTGATTCTCTGGACAGAGAAAGGA

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: 141

GGTTCAGTATAAGAATGTGGCATTCACTGTGTGGGATGTGGGTGGGCAAGAAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataacta ... tttgttgcagATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAAGAGTTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 288

GGTTCAGTATAAGAATGTGGCATTCACTGTGTGGGATGTGGGTGGGCAAGAAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataacta ... tttgttgcagATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAAGAGTTCCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 224

GGTTCAGTATAAGAATGTGGCATTCACTGTGTGGGATGTGGGTGGGCAAGAAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataacta ... tttgttgcagATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAAGAGTTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 177

GGTTCAGTATAAGAATGTGGCATTCACTGTGTGGGATGTGGGTGGGCAAGAAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataacta ... tttgttgcagATCTATGTCGTTGATTCTCTGGACAGAGAAAGGATCAGAGACGCGAGGCAAGAGTTCCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTCAGTATAAGAATGTGGCATTCACTGTGTGGGATGTGGGTGGGCAAGAAAAACTCAGGTCACTGTGGAAGATGTACCTGAGTAATTCTGATGCACTGgtaataactattacttgcaagtgcagagacacatgagtagcttcccattatgtctctttggttcccttgtctttctcaactcttgatatggtgtttactt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG