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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtattatttcattttcttgatgttgaccctttgacctattctattgaaaaaatacaactaatttatgtagattaatctgcgatacttctgtatagttgtcgattgtcgtgcatgacactactgtcaattttgaaacagATTCCAGAGGAAGAGAAGAATCTTGGCCCACATGACCGTTTGATTCATGTTTATCATTTTATGAAAGACCCTAATCAGAATCAGCAGATTCAGAATTTCG

Basic information

species Zea mays
transcript GRMZM2G014805_T01
intron # 27
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 27
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 27
gttcgtattatttcattttcttgatgttgaccctttgacctattctattgaaaaaatacaactaatttatgtagattaatctgcgatacttctgtatagttgtcgattgtcgtgcatgacactactgtcaatt-ttgaaacagATTCCAGAGGAAGAGAAGAATCTTGGCCCACATGACCGTTTGATTCATGTTTATCATTTTATGAAAGACCCTAATCAGAATCAGCAGATTCAGAATTTCG
                            |  | ||||| |   | |  |||   |  | |  | |  ||  |  ||| |  |   ||||| ||||     | |  ||||   ||||| ||| |  ||  |    ||||||||||| ||||||||||||||||| |||||||||||||| || |||||||||||||| ||||| |||||||| |||||||| ||||||                
----------------------------gttcgtttgaacatcttttctgactgacgata-ttgacataattccatttagttagtatactactgtcattatatt-attgatttgcataacatttttgctaccaattgaaacagATACCAGAGGAAGAGAAGAACCTTGGCCCACATGATCGGTTGATTCATGTTTACCATTTCATGAAAGATCCTAATCAAAATCAG----------------

upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 27
lower sequence: GLYMA10G23680.1 (Glycine max), 3'ss of exon 23
gttcgtattatttcattttcttgatgttgaccctttgacctattctattgaaaaaatacaactaatttatgtagattaatctgcgatacttctgtatagttgtcgattgtcgtgcatgacactactgtcaattttgaaacagATTCCAGAGGAAGAGAAGAATCTTGGCCCACATGACCGTTTGATTCATGTTTATCATTTTATGAAAGACCCTAATCAGAATCAGCAGATTCAGAATTTCG
                                          || | |    ||  | ||  |  | | | | |  | ||      |      | | | |  ||  || ||  |  | |   |    |   | |||   |||||||| || |||||||| || |||||| | ||||| || ||||| ||||||||||||||  |||||||| | | ||| ||||||                
-----------------------------------------cttttgtcttcaatgt-cattttctgtctatggtgttatacattttttcgtggcacattattcatttttcaagtttcatcttcaatttcctattgctgcagATTCCTGAAGAAGAGAAAAACCTTGGCTCGCATGATCGGTTGATCCATGTTTATCATTTCTTGAAAGACACAACTCAAAATCAG----------------

upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 27
lower sequence: GLYMA13G16040.1 (Glycine max), 3'ss of exon 8
---------------------------------------gttcgtatt-atttcattttcttgatgttgaccctttgacctattctattgaaaaaatacaactaatttatgtagattaatctgcgatacttctgtatagttgtc-------gattgtcgtgcatgacactactgtcaattttgaa----acagATTCCAGAGGAAGAGAAGAATCTTGGCCCACATGACCGTTTGATTCATGTTTATCATTTTATGAAAGACCCTAATCAGAATCAGCAGATTCAGAATTTCG
                                       | | | ||| | || | | | ||  || |     ||   |  ||  |  | | |  |  | |||  | ||  || || | |  |   || |  |||  | ||           ||  | ||   ||  || |  ||||  ||  ||    |||||||||||| |||||||| |||||||| || ||||| ||| | |||||||| || ||||| |  |||||| |   ||| || ||   |             
gtaggaatctctttctgtctgaggggctagatcaagggagatagaatttagtttaatgtattcctgcttttatttgttcaaatgatgataacactacccgactcttctaaatatataattacgttctattcttgttcaattcctctcacaaaataattgtaattgttac-atggtcatattcaaatgtaacagATTCCAGAAGAAGAGAAAAATCTTGGTCCTCATGATCGTCTAATTCATGTGTACCATTTCAATAAAGACGCGGCTCAAAACCAAATG-------------

upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 27
lower sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 19
----------------------------------------------gttcgtattatttcattttcttgatgttgaccctttgacctattctattgaaaaaatacaactaatttatgtagattaatctgcgatacttctgtatagttgtc-----gattgtcgtgcatgacactactgtcaattttgaa----acagATTCCAGAGGAAGAGAAGAATCTTGGCCCACATGACCGTTTGATTCATGTTTATCATTTTATGAAAGACCCTAATCAGAATCAGCAGATTCAGAATTTCG
                                               || || | || |  | |||||| | ||     ||  |   ||  |  | | |     | |||  | ||  || || | | ||   || || |||  | ||         ||  | ||  ||      |  ||||  ||  ||    |||||||||||| |||||||| ||||||||  | ||||| ||| | ||||||||||| ||||| |  |||||  |   ||| || ||   |             
gtaggaatctctttctgtatgtggggctagatcaagggagatagcatttagtgtaatgttgtattcttgcttttatttgttcaa---atgatgataacactgcccgactcttgtaaatatataattatgttctatttttgttcaattcctcacaaaataattgt-tattcttacatggtcatattcaaatgtaacagATTCCAGAAGAAGAGAAAAATCTTGGTTCTCATGATCGTCTAATTCATGTTTACCATTTCAATAAAGAGACAGCTCAAAACCAAATG-------------

upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 27
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 27
gttcgtattatttcattttcttgatgttgaccctttgacctattctattgaaaaaataca-actaatttatgtagattaatctgcgatacttctgtatagttgtcgattgtcgtgcatgacactactgtcaattttgaaacagATTCCAGAGGAAGAGAAGAATCTTGGCCCACATGACCGTTTGATTCATGTTTATCATTTTATGAAAGACCCTAATCAGAATCAGCAGATTCAGAATTTCG
                                           |  ||     || |  | |   || ||   | ||  ||||    |  |  | |   |||| | | | |  |     ||  |  |    || |     ||||||||||| ||||||||||||||||| || ||||| || |||||||||||||| || || |  || ||  ||   |||||||||  |             
-------------------------------------------ttgatcattgaactttagatcgatgtacacaaat--atctttactggtgttctcatgttggctaatcttatcttgaacttttttaatcatct-----cagattccagAAGAAGAGAAGAATCTTGGTCCCCATGATCGCTTGATTCATGTTTACCACTTCACAAAGGAGACTGTACAGAATCAGATG-------------

upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 27
lower sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 27
gttcgtattatttcattttcttgatgttgaccctttgacctattctattgaaaaaatacaactaatttatgtagattaatctgcgatacttctgtatagttgtcgattgtcgtgcatgacacta-ctgtcaattttgaaacagATTCCAGAGGAAGAGAAGAATCTTGGCCCACATGACCGTTTGATTCATGTTTATCATTTTATGAAAGACCCTAATCAGAATCAGCAGATTCAGAATTTCG
                                        ||    ||   ||  || ||  |    | | ||||      ||  |||   |     ||| |  |  | ||  | |      || ||      |||   ||||||||| || || ||||| || || || || ||||| || |||||||||||||||||||||||||||||| | | ||||||||||  |             
---------------------------------------ttaccagatc--aaccatccactttgactctttagacctgattgttata--gcaaatcagtaggagggtttcaagtagttttttaacttgtttctttactacagATTCCTGAAGAGGAGAAAAACCTAGGTCCTCATGATCGGTTGATTCATGTTTATCATTTTATGAAAGACACAACTCAGAATCAGGTG-------------

upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 27
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 27
gttcgtattatttcattttcttgatgttgaccctttgacctattctattgaaaaaatacaactaatttatgt-agattaatctgcgatacttctgtatagttgtcgattgtcgtgcatgacactactgtcaattttgaaacagATTCCAGAGGAAGAGAAGAATCTTGGCCCACATGACCGTTTGATTCATGTTTATCATTTTATGAAAGACCCTAATCAGAATCAGCAGATTCAGAATTTCG
                                  ||     ||| |  |     |||    ||||||||  | | | |||  ||       ||   ||  |  || ||| ||     | ||  |    | ||| |||   |||||||| || |||||||| |||||||| ||||| || || ||||||||||| || || ||||  |||||| |   |||||| ||   |             
----------------------------------ttagttaatttttcttttttaatttt-ctaatttagatgaaagtaaaatgtacatgatccagatt-tgatcaattttccaatttaacttt----taaatattg---cagATTCCTGAAGAAGAGAAAAATCTTGGACCACAGGATCGCTTGATTCATGTATACCACTTTACAAAAGACACAGCTCAGAACCAAATG-------------

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|60354119|gb|DN221092.1|DN221092
EST:     AGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAG                         ATTCCAGAGGAAGAGAAGAATCTTGGCCCACATGACCGTTTGATTCATGTT
genomic: AGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAGgttcgtatta ... tttgaaacagATTCCAGAGGAAGAGAAGAATCTTGGCCCACATGACCGTTTGATTCATGTT
EST: gi|60400323|gb|DN233130.1|DN233130
EST:     GAAGATAGAGAAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAG                         ATTCCAGAGGAAGAGAAGAATCTTGGCCCACATGACCGTTTGATTCATGTT
genomic: GAAGATAGAG-AACATAAATGATCAGTACTGGACATTACGAGCTGAGGAGgttcgtatta ... tttgaaacagATTCCAGAGGAAGAGAAGAATCTTGGCCCACATGACCGTTTGATTCATGTT
EST: gi|76019060|gb|DT946230.1|DT946230
EST:     AGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAG                         ATTCCAGAGGAAGAGAAGAATCTTGGCCCACATGACCGTTTGATTCATGTT
genomic: AGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAGgttcgtatta ... tttgaaacagATTCCAGAGGAAGAGAAGAATCTTGGCCCACATGACCGTTTGATTCATGTT
EST: gi|13178629|gb|BG349887.1|BG349887
EST:     AGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAG                         ATTCCAGAGGAAGAGAAGAATCTTGGCCCACATGACCGTTTGATTCATGTT
genomic: AGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAGgttcgtatta ... tttgaaacagATTCCAGAGGAAGAGAAGAATCTTGGCCCACATGACCGTTTGATTCATGTT
EST: gi|16378289|gb|BI992373.1|BI992373
EST:     AGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAG                         ATTCCAGAGGAAGAGAAGAATCTTGGCCCACATGACC
genomic: AGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAGgttcgtatta ... tttgaaacagATTCCAGAGGAAGAGAAGAATCTTGGCCCACATGACC
EST: gi|94476779|gb|EB705737.1|EB705737
EST:     AGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAG                         ATTCCAGAGGAAGAGAAGAATCTTGGCCCACATGACCGTTTGATTCATGTT
genomic: AGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAGgttcgtatta ... tttgaaacagATTCCAGAGGAAGAGAAGAATCTTGGCCCACATGACCGTTTGATTCATGTT

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: 48 (upstream exon), 49 (downstream exon)
Score: 297

ATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAGgttcgtatta ... tttgaaacagATTCCAGAGGAAGAGAAGAATCTTGGCCCACATGACCGTTTGATTCATGTTTATCATTTTATGAAAGACCCTAATCAGAATCAGCAGATTCAGAATTTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 267

ATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAGgttcgtatta ... tttgaaacagATTCCAGAGGAAGAGAAGAATCTTGGCCCACATGACCGTTTGATTCATGTTTATCATTTTATGAAAGACCCTAATCAGAATCAGCAGATTCAGAATTTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 302

ATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAGgttcgtatta ... tttgaaacagATTCCAGAGGAAGAGAAGAATCTTGGCCCACATGACCGTTTGATTCATGTTTATCATTTTATGAAAGACCCTAATCAGAATCAGCAGATTCAGAATTTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 274

ATTTTTCCGCCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAGgttcgtatta ... tttgaaacagATTCCAGAGGAAGAGAAGAATCTTGGCCCACATGACCGTTTGATTCATGTTTATCATTTTATGAAAGACCCTAATCAGAATCAGCAGATTCAGAATTTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttctgtatagttgtcgattgtcgtgcatgacactactgtcaattttgaaacagATTCCAGAGGAAGAGAAGAATCTTGGCCCACATGACCGTTTGATTCATGTTTATCATTTTATGAAAGACCCTAATCAGAATCAGCAGATTCAGAATTTCG
                                          aattttgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgtattatttcattttcttgatgttgaccctttgacctattctattgaaaaaatacaactaatttatgtagattaatctgcgatacttctgtatagttgtcgattgtcgtgcatgacactactgtcaattttgaaacagATTCCAGAGGAAGAGAAGAATCTTGGCCCACATGACCGTTTGATTCATGTTTATCATTTTATGAAAGACCCTAATCAGAATCAGCAGATTCAGAATTTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT