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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcgcatgatttatgtgaagtatttaccgaatgaagagtcctggctctttctaatccaatgttctagaatttctgaatttgtaaaattagtgttatttttttccttaaacttggcattgttagtatgatataattattttctgcagATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAG

Basic information

species Zea mays
transcript GRMZM2G014805_T01
intron # 26
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 26
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 26
gtttgcgcatgatttatgtgaagtatttaccgaatgaagagtcctggctctttctaatccaatgttctagaatttctgaatttgtaaaattagtgttatttttttccttaaacttggcattgttagtatg-atataattattttctgcagATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAG
                          |    | |||    |   ||  | ||  || ||     ||   |||   |    ||||  |||||||| |||| |||| | |  |   |       ||  | || | ||||||  | |||| |||| ||||| ||||| ||||| |||||||||||||||||||||||||||||| |||| |||||||||
-------------------------gtccttggatgttctgctttgcattttgatagtctttattttctgaagacc---gtttg-gaaattagtattatattttccttacattattaaccccttgttgtgtaaataatt--tatctgtagATATTTCCACCTCACGAGAAAATAGAGAACATAAATGATCAGTACTGGACACTACGTGCTGAGGAG

upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 26
lower sequence: GLYMA13G16040.1 (Glycine max), 3'ss of exon 7
gtttgcgcatgatttatgtgaagtatttaccgaatgaagagtcctggctctttctaatccaatgttctagaatttctgaatttgtaaaattagtgttatttttttccttaaacttggcattgttagtatgatataattattttctgcagATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAG
                                              || || |||       |||| | |  | |  |   ||| |  || |      |  ||||  || || ||    ||   | |    |    |  |  | ||||| | || || ||  |||| ||||| || ||||| |||||||| ||||||||||||||||| ||||||
----------------------------------------------gccctctctgcctgtctgtttttgcttgtgcgctattg-actatcacaaaactcatttttgttgaattt--tttttacacttccctgccctcttcctgtgcagGTCTTCCCTCCCAATGAAAAGATTGAAAACATTAATGATCAATACTGGACATTACGAGCAGAGGAG

upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 26
lower sequence: AT5G06600.2 (Arabidopsis thaliana), 3'ss of exon 26
gtttgcgcatgatttatgtgaagtatttaccgaatgaagagtcctggc-tctttctaatccaatgttctagaatttctgaattt----gtaaaattagtgttatttttttccttaaacttggcattgttagtatgatataat--tattttctgcagATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAG
  |  |     | || |    |   |||||   ||    | || |  | |  | ||||    |||   |     | | | || |     | |||||  ||  |   |||    || | |   ||   ||| |   || |  |  |||    |||||||||| ||  |   ||| |  || ||||| |||||||| ||||||||||| |||||||||||||||
-gtaacaagcaacttctt---atcttttacattatagtcaatcttttcatggtcctaagatgatggcttcttgataccgtatctcctgatgaaattcttgcaaccctttgaagtataatgacca--attaatccaatgtgctggtatgccttgcagATTTTCCCATCAACTGAAAGAATTGAGAATATAAATGACCAGTACTGGACTTTACGAGCTGAGGAG

upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 26
lower sequence: AT5G06600.3 (Arabidopsis thaliana), 3'ss of exon 26
gtttgcgcatgatttatgtgaagtatttaccgaatgaagagtcctggc-tctttctaatccaatgttctagaatttctgaattt----gtaaaattagtgttatttttttccttaaacttggcattgttagtatgatataat--tattttctgcagATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAG----------------------------------
  |  |     | || |    |   |||||   ||    | || |  | |  | ||||    |||   |     | | | || |     | |||||  ||  |   |||    || | |   ||   ||| |   || |  |  |||    |||||||||| ||  |   ||| |  || ||||| |||||||| ||||||||||| |||||||||||||||                                  
-gtaacaagcaacttctt---atcttttacattatagtcaatcttttcatggtcctaagatgatggcttcttgataccgtatctcctgatgaaattcttgcaaccctttgaagtataatgacca--attaatccaatgtgctggtatgccttgcagATTTTCCCATCAACTGAAAGAATTGAGAATATAAATGACCAGTACTGGACTTTACGAGCTGAGGAGGTATATTACTAGGCTGCACCTTGTATTTTTCTTA

upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 26
lower sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 26
gtttgcgcatgatttatgtgaagtatttaccgaatgaagagtcctggctctttctaatccaatgttctagaatttctgaatttgtaaaattagtgttatttttttccttaaacttggcattgttagtatgatataattattttctgcagATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAG
                                           |      || | | | |  | ||  |||   |    ||   || |  |  | |  || | || ||||   ||  | |  ||   ||  | | | |||   ||||||||||| || |   |||||||||| |||||||| |||||||| |||||||||||||| || ||||||
-------------------------------------------cacaggattccgagttc--tattaaagatagtagagatcattagagatcctttgtttgtgtttctta---ttatcctgcttgtaattctgtgactatcc-ctgcagATTTTCCCACTCAATGAGAAGATTGAGAACATTAATGATCAATACTGGACATTACGTGCAGAGGAG

upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 26
lower sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 26
--------------------------------gtttgcgcatgatttat-------gtgaagtatttaccgaat---gaagagtcctggctctttctaatcc--aatgttctagaatttctgaatttgtaaaattagtgttatttttttccttaaacttggcat-tgttagtatgatataatt---attttctgcagATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAG
                                 |||| || || | | |       | || |   | |  || |   | ||| |  | ||  | |   ||    ||||  |||   ||||||| || || |  ||| |||   |  |    | |||      || | ||     || ||  ||     | | | ||||| || ||       |||||||| |||||||| |||||||| ||||||||  | ||||||||||||
gttatttgcagacttcagtctatttggatcgcatttgagcttggtattttgggggggagagggggtcattgattctagtagaatggtagcgttatactatttttaatgcccta---tttctgatttcgtgattttattgtcggtaataagttgaaatgataaatgtattttcgcgacatcttttgggatctttccagATCTTCCCCTTGAGCGAGAAGATTGAGAACATCAATGATCAATACTGGACGCTTCGAGCTGAGGAG

upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 26
lower sequence: PP1S42_181V6.1 (Physcomitrella patens), 3'ss of exon 26
-----------------------------------------gtttgcgcatgatttatgtgaagtattta-ccgaatgaagagtcctggctctttctaatccaatgttctagaatttctgaatttgtaaaattagtgttatttttttcc--ttaaacttggca-ttgttagtatgatataattattttctgcagATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAG
                                         | |||  ||     || ||||| | || | || ||||||   | ||   | ||    ||    | |  ||  |||   || ||  | | | |  | |||    |   |  |   | ||   | || |  || | ||| | || | || | ||||| ||||| | | ||||||| |||||||| || |||||||||||||||||  | |||||||| |||
gtttgctacaacttgttttcttttatgggattggtaatttagattgacca-atcctaggtgaaattttgaacctaatgaaa--ttctcaatattag-gatattgtatagtactattcgagatttcttgatagtgtttttagacataatcaatagcatttaatagttttctgtgtaata-atttgtctttttcagATCTTTCCTCTTAATGAGAAAATAGAGAATATCAATGATCAGTACTGGACCCTGCGAGCTGAAGAG

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|32933255|gb|CF038067.1|CF038067
EST:     CTGATACTGAGCTCCGCTTGCTTGAAGTATTTTACCACAAGATTTATAAG                         ATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTAC
genomic: CTGATACTGAGCTCCGCTTGCTTGAAGTATTTTACCACAAGATTTATAAGgtttgcgcat ... ttttctgcagATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTAC
EST: gi|32934023|gb|CF038835.1|CF038835
EST:     CTGATACTGAGCTCCGCTTGCTTGAAGTATTTTACCACAAGATTTATAAG                         ATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTAC
genomic: CTGATACTGAGCTCCGCTTGCTTGAAGTATTTTACCACAAGATTTATAAGgtttgcgcat ... ttttctgcagATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTAC
EST: gi|60354119|gb|DN221092.1|DN221092
EST:     CTGATACTGAGCTCCGCTTGCTTGAAGTATTTTACCACAAGATTTATAAG                         ATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACA
genomic: CTGATACTGAGCTCCGCTTGCTTGAAGTATTTTACCACAAGATTTATAAGgtttgcgcat ... ttttctgcagATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACA
EST: gi|76019060|gb|DT946230.1|DT946230
EST:     CTGATACTGAGCTCCGCTTGCTTGAAGTATTTTACCACAAGATTTATAAG                         ATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACA
genomic: CTGATACTGAGCTCCGCTTGCTTGAAGTATTTTACCACAAGATTTATAAGgtttgcgcat ... ttttctgcagATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACA
EST: gi|13178629|gb|BG349887.1|BG349887
EST:     CTGATACTGAGCTCCGCTTGCTTGAAGTATTTTACCACAAGATTTATAAG                         ATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACA
genomic: CTGATACTGAGCTCCGCTTGCTTGAAGTATTTTACCACAAGATTTATAAGgtttgcgcat ... ttttctgcagATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACA
EST: gi|16378289|gb|BI992373.1|BI992373
EST:     CTGATACTGAGCTCCGCTTGCTTGAAGTATTTTACCACAAGATTTATAAG                         ATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACA
genomic: CTGATACTGAGCTCCGCTTGCTTGAAGTATTTTACCACAAGATTTATAAGgtttgcgcat ... ttttctgcagATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACA
EST: gi|94476779|gb|EB705737.1|EB705737
EST:     CTGATACTGAGCTCCGCTTGCTTGAAGTATTTTACCACAAGATTTATAAG                         ATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACA
genomic: CTGATACTGAGCTCCGCTTGCTTGAAGTATTTTACCACAAGATTTATAAGgtttgcgcat ... ttttctgcagATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACA

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: 46 (upstream exon), 49 (downstream exon)
Score: 204

GTTGAACTATCAAATCCTGATACTGAGCTCCGCTTGCTTGAAGTATTTTACCACAAGATTTATAAGgtttgcgcat ... ttttctgcagATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 181

GTTGAACTATCAAATCCTGATACTGAGCTCCGCTTGCTTGAAGTATTTTACCACAAGATTTATAAGgtttgcgcat ... ttttctgcagATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 176

GTTGAACTATCAAATCCTGATACTGAGCTCCGCTTGCTTGAAGTATTTTACCACAAGATTTATAAGgtttgcgcat ... ttttctgcagATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 142

GTTGAACTATCAAATCCTGATACTGAGCTCCGCTTGCTTGAAGTATTTTACCACAAGATTTATAAGgtttgcgcat ... ttttctgcagATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttatttttttccttaaacttggcattgttagtatgatataattattttctgcagATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAG
                                          ttattttct  CT-rich tract
                        attgttagtatgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcgcatgatttatgtgaagtatttaccgaatgaagagtcctggctctttctaatccaatgttctagaatttctgaatttgtaaaattagtgttatttttttccttaaacttggcattgttagtatgatataattattttctgcagATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG