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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttggatgaatagtgcgctttttagtctgccatatttgcttaatttgaatgcaactactttgtctctactgttaaaactgggatgtacactatttgccagGTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAGTACTGGAAGAAGTCTAAATTGCCACACGCAACAATATTCAAACCTCAAC

Basic information

species Zea mays
transcript GRMZM2G156251_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G156251_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g27020.2 (Oryza sativa), 3'ss of exon 3
cttggatgaatagtgcgctttttagtctgccatatttgcttaatttgaatgcaactactttgtctctactgt-taaaactgggatgtacactat----ttgccagGTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAGTACTGGAAGAAGTCTAAATTGCCACACGCAACAATATTCAAACCTCAAC
     ||  || ||     | ||    ||| |||| ||||| | |||  | ||   | ||  |  | | | | |||   |   |||| || |||    |   ||||| |||||||||||||||||||||||||||||||| ||||| || |||||||| ||||| ||||| ||  ||||||| || ||||||||||||||||| |
-----atttattgtttttatcttgtgttgctatatatgctttagttgcttacataaaattgattgccattttctaattttaatatgtgcaatatgaactgatcagGTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAGTATTGGAAAAAGTCCAAGCTGCCACATGCTACAATATTCAAACCTCAGC

upper sequence: GRMZM2G156251_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G10470.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------------------------------------cttggatg---aatagtgcgctttttagtctgccatatttgcttaatttgaatgcaac-----tactttgt-ctctactgttaaaactgggatgtacactatttgccagGTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAGTACTGGAAGAAGTCTAAATTGCCACACGCAACAATATTCAAACCTCAAC
                                                                             ||  | ||    ||  ||   |   | | ||  ||  |||     | |||| ||  |      | |||||   | ||||  || || | | ||    | | | |   ||||||| ||| | |||||||| ||||| ||||||||||| |||||||| || || ||||| ||||| || ||||| || || || || || || || ||||
gtaatctatgatggatacattatatagggtctatagttgcatcttttaagggcataatgtgtattcagtttactagtctaaggtgcaagattttgttgtccatggcctctcaattttctgctacttgattgtgaaatttgtgctttggattttacttctataattagcatcctta-tgtgttgtagGTGGAGCAGCTACACAAGATATTCAAACTATGTGGTTCTCCTTCTGATGAATATTGGAAAAAGTCAAAGTTGCCTCATGCTACCATTTTTAAGCCCCAAC

upper sequence: GRMZM2G156251_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G30030.1 (Glycine max), 3'ss of exon 3
cttggatga-atagtgcgctttttagtc-tgccatatttgct--taatttgaatgcaactactttgtctctactgttaaaactgggatgtacactatttgc-cagGTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAGTACTGGAAGAAGTCTAAATTGCCACACGCAACAATATTCAAACCTCAAC
 |||  | | ||   |    | | | |    |  ||||||||  | |||||||     | | |   | | | |||  |    |    | |  |  | || |  ||||||||||  |||| ||||| | ||| || |||||||| |||||||| ||||| ||||||||||| ||  ||||  | || ||  | || ||||||| ||
tttgcgtcacattaaggatatatcacttgcactttatttgctggttatttgaa-atttccattggatattttctgacactttt----tcttgatgacttacatagGTGGAACAACTGCATAAGATATACAAACTTTGTGGTTCGCCTTCTGATGAGTATTGGAAGAAGTCAAAGATGCCTAATGCTACTTTGTTTAAACCTCGAC

upper sequence: GRMZM2G156251_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G37360.1 (Glycine max), 3'ss of exon 3
cttggat-gaatagtgcgctttttagtc-tgccatatttgct--taatttgaatgcaactactttgtctctactgttaaaactgggatgtacactatttgccagGTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAGTACTGGAAGAAGTCTAAATTGCCACACGCAACAATATTCAAACCTCAAC
 ||| || | ||   |    | | | |    |  ||||||||  | |||||||   |  | | |||  | |  | | | |  |    || |     | |   ||||||||||  |||| ||||| | ||| || |||||||| |||||||| ||||| ||||||||||| ||  ||||  | || ||  | || ||||||| | 
tttgtatcgcattaaggatatatcacttgcactttatttgctggttatttgaa---attttcattggatattttctgacactttttctggatgacttatat-agGTGGAACAACTGCATAAGATATACAAACTTTGTGGTTCGCCTTCTGATGAGTATTGGAAGAAGTCAAAGATGCCTAATGCTACCTTGTTTAAACCTCGAG

upper sequence: GRMZM2G156251_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G28650.1 (Glycine max), 3'ss of exon 3
--------------------------------------------------------------------------------------cttggatgaatagtgcgctttt---tagtctgccatatttgcttaatttgaatgcaactactttgtctc------tactgttaaaactgggatgtacactatttgccagGTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAGTACTGGAAGAAGTCTAAATTGCCACACGCAACAATATTCAAACCTCAAC
                                                                                      ||  | || |  ||    || |   | |  |  ||  |||     | |||| ||  |    | ||  ||      ||||| || || | | ||      | | |   |||| || ||| | |||||||| ||||| ||||||||||| |||||||| || || ||||| ||||| || |||||||| || || || || || || ||||
gtaatctctatgatggatacactatatagggcttaatgtctatagttgcatcttttaagggcttaatgtgtattcagtttactagtctaaggtgcaaggttttgttgtcgatggcttctcaattttctgctacttgattgtgaaatttgtgcttcagattttactgctataattagcatcctttatgtgttatagGTAGAGCAGCTACACAAGATATTCAAACTATGTGGTTCTCCTTCTGACGAATATTGGAAAAAGTCAAAGTTGCCACATGCTACCATTTTTAAGCCCCAAC

upper sequence: GRMZM2G156251_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA03G40330.1 (Glycine max), 3'ss of exon 3
cttggatga-atagtgcgctttttag-tctgccatatttgcttaatttgaatgcaactactttgtctctactgttaaaactgggatgtacact-atttgc-cagGTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAGTACTGGAAGAAGTCTAAATTGCCACACGCAACAATATTCAAACCTCAAC
 ||| |||  |||||  |  ||| || | |  || |||   || ||||||     | || |  |     ||  ||| |  |    |      | | | ||  |||||||||| ||||||||||| | ||| ||||||||||| ||||| || ||||| ||||||||||| || |||||  | || ||    || ||||| | | 
tttgcatggtatagtttgaatttaagatatatcaaattgcatttatttga---tgatta-taagaaaacacaattagattttttctaagtcttcactcgcatagGTGGAACAATTGCACAAGATATACAAACTATGTGGTTCACCTTCAGATGAGTATTGGAAGAAGTCAAAGTTGCCTAATGCTACCTCGTTTAAACCACGAG

upper sequence: GRMZM2G156251_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 3
cttggatgaatagtgcgctttttagtctgccatatttg-cttaatttgaatgcaactactttgtctctactgttaaaactggga--tgtacactatttgc-cagGTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAGTACTGGAAGAAGTCTAAATTGCCACACGCAACAATATTCAAACCTCAAC
       |  |  ||   ||| |||       |  | | |  |||||  |  |||       |   || || ||    ||   |  | |    | | ||| |||||||| ||| | |||||||| || ||||||||||| || |||||||| || |||||||| || || || ||||| || ||||| ||||| || |||||||
----agggtttgttgaattttctaggtgtttgtggtggacccaattttgaaacaagagtacagctgcttctattgctgctaaaaattttcttttgtgtgctcagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAATACTGGAAAAAATCAAAGTTGCCGCATGCAACCATATTTAAGCCTCAAC

upper sequence: GRMZM2G156251_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S89_168V6.1 (Physcomitrella patens), 3'ss of exon 4
cttggatgaatagtgcgctttttagtctgccatatttgcttaatttgaatgcaactactttgtctctactgttaaaactgggatgtacactatttgc-cagGTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAGTACTGGAAGAAGTCTAAATTGCCACACGCAACAATATTCAAACCTCAAC
 ||   |     ||  | |    ||  ||     ||||         | |        |  | |  || |   |    |  |    |  ||  |     |||||||||| ||||||||||| || ||| | || |||||||| || |||||||| ||||||||||| |||||||| || || || |||||||| |||||||
tttacctccggcgtttggtaac-agattgtagggtttgtagggcccaagttgtggggttgaggccgtaattggaggggtttggcacattcttgtgatgtagGTGGAACAATTGCACAAGATCTTTAAGTTGTGCGGTTCCCCATCCGAGGAGTATTGGAAGAAGTCGAAATTGCCGCATGCGACGATATTCAAGCCTCAAC

upper sequence: GRMZM2G156251_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S271_84V6.1 (Physcomitrella patens), 3'ss of exon 3
cttggatgaatagtgcgctttttagtctgccatatttgcttaatttgaatgcaactactttgtctc--tactgttaaaactgggatgtacactatttgccagGTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAGTACTGGAAGAAGTCTAAATTGCCACACGCAACAATATTCAAACCTCAAC
    |  |    | | |  |  |              |  |   | |||||  |      ||      |   |||     ||| |||         || |||||||||||| ||||||||||||||||| | || ||||| || || |||||||| ||||||||||| ||  |||| ||||| || |||||||| ||||| |
--cagtcgcggcgagtgtgtggtgagtgatggggggggggtgtgtggaatgtgaggcgcgtgctgaagtggggttggttgtggcatgggtgtgtggtggcagGTGGAACAGCTGCACAAGATTTTCAAGTTGTGCGGTTCGCCGTCGGAGGAGTATTGGAAGAAGTCGAAGCTGCCGCACGCGACGATATTCAAGCCTCAGC

upper sequence: GRMZM2G156251_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S428_20V6.1 (Physcomitrella patens), 3'ss of exon 3
--cttggatgaatagtgcgctttttagtctgccatatttgcttaatttgaatgcaactactttgtctctactgttaaaactgggatgtacactatttgccagGTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAGTACTGGAAGAAGTCTAAATTGCCACACGCAACAATATTCAAACCTCAAC
   |          ||| |||    | |     | ||  | ||   ||| | |    || ||  | |  |          ||| | |   |     || |||||||||||  | || ||||| |||||| |||| ||||| || || |||||||| ||||| ||||| |||||||| ||||| || |||||||| |||||||
ttttccctcttgcggtg-gctacagattggagtagatgcgtttgggttgtaagatggtatttaatttagagaac-gggtttggtacgggaatatggtggcagGTGGAACAACTTCATAAGATCTTCAAGTTATGCGGTTCTCCGTCCGAGGAGTATTGGAAAAAGTCAAAATTGCCGCACGCTACGATATTCAAGCCTCAAC

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|31353665|gb|CD438022.1|CD438022
EST:     TTCTTGCAGAGCTCCTGTATGGAAAGCCCATAATGCCTGGGCGCACTGAG                         GTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAG
genomic: TTCTTGCAGAGCTCCTGTATGGAAAGCCCATAATGCCTGGGCGCACTGAGgtgagtcttg ... tatttgccagGTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAG
EST: gi|19351019|gb|BM895551.1|BM895551
EST:     TTCTTGCAGAGCTCCTGTATGGAAAGCCCATAATGCCTGGGCGCACTGAG                         GTGGAACAGTTGCACAAGATTTTCNAGCTATGTGGTTCCCCTTCTGAGGAG
genomic: TTCTTGCAGAGCTCCTGTATGGAAAGCCCATAATGCCTGGGCGCACTGAGgtgagtcttg ... tatttgccagGTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAG
EST: gi|13178081|gb|BG349339.1|BG349339
EST:     TTCTTGCAGAGCTCCTGTATGGAAAGCCCATAATGCCTGGGCGCACTGAG                         GTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAG
genomic: TTCTTGCAGAGCTCCTGTATGGAAAGCCCATAATGCCTGGGCGCACTGAGgtgagtcttg ... tatttgccagGTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAG
EST: gi|19436114|gb|BM952524.1|BM952524
EST:     TTCTTGCAGAGCTCCTGTATGGAAAGCCCATAATGCCTGGGCGCACTGAG                         GTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAG
genomic: TTCTTGCAGAGCTCCTGTATGGAAAGCCCATAATGCCTGGGCGCACTGAGgtgagtcttg ... tatttgccagGTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAG
EST: gi|67028072|gb|CO456821.1|CO456821
EST:     TTCTTGCAGAGCTCCTGTATGGAAAGCCCATAATGCCTGGGCGCACTGAG                         GTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAG
genomic: TTCTTGCAGAGCTCCTGTATGGAAAGCCCATAATGCCTGGGCGCACTGAGgtgagtcttg ... tatttgccagGTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAG

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: 134

TGGTGCCACTGAGTATAGTGTAGGTGTTGATTTGTGGAGTGCTGGATGCATTCTTGCAGAGCTCCTGTATGGAAAGCCCATAATGCCTGGGCGCACTGAGgtgagtcttg ... tatttgccagGTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAGTACTGGAAGAAGTCTAAATTGCCACACGCAACAATATTCAAACCTCAAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 152

TGGTGCCACTGAGTATAGTGTAGGTGTTGATTTGTGGAGTGCTGGATGCATTCTTGCAGAGCTCCTGTATGGAAAGCCCATAATGCCTGGGCGCACTGAGgtgagtcttg ... tatttgccagGTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAGTACTGGAAGAAGTCTAAATTGCCACACGCAACAATATTCAAACCTCAAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 132

TGGTGCCACTGAGTATAGTGTAGGTGTTGATTTGTGGAGTGCTGGATGCATTCTTGCAGAGCTCCTGTATGGAAAGCCCATAATGCCTGGGCGCACTGAGgtgagtcttg ... tatttgccagGTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAGTACTGGAAGAAGTCTAAATTGCCACACGCAACAATATTCAAACCTCAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

TGGTGCCACTGAGTATAGTGTAGGTGTTGATTTGTGGAGTGCTGGATGCATTCTTGCAGAGCTCCTGTATGGAAAGCCCATAATGCCTGGGCGCACTGAGgtgagtcttg ... tatttgccagGTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAGTACTGGAAGAAGTCTAAATTGCCACACGCAACAATATTCAAACCTCAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatgcaactactttgtctctactgttaaaactgggatgtacactatttgccagGTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAGTACTGGAAGAAGTCTAAATTGCCACACGCAACAATATTCAAACCTCAAC
                        tgttaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttggatgaatagtgcgctttttagtctgccatatttgcttaatttgaatgcaactactttgtctctactgttaaaactgggatgtacactatttgccagGTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAGTACTGGAAGAAGTCTAAATTGCCACACGCAACAATATTCAAACCTCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
-ttggatg
- - - - - - - - - - - - -tctgcca
- - - - - - - - - - - - - - - - - tttgctt
- - - - - - - - - - - - - - - - - - - - - - -tgaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgtac