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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaactttgttacaacctccaaattttcttaattactgatccccccttactcaaattttcagcaaaatgattttagGGGGAGAATAAAGGTTTCCTTGTCTGCAAGAAAAAGATGGCAACTTCTCCAGAATCTTTGTGTTGCTTTTGCCCACAACCTTTCCGACAATTTATTGAGT

Basic information

species Zea mays
transcript GRMZM2G116151_T03
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 9
gtgaactttgtt-acaacctccaaattttcttaattactgatccc-----------cccttactcaaattttcagcaaaatgattttagGGGGAGAATAAAGGTTTCCTTGTCTGCAAGAAAAAGATGGCAACTTCTCCAGAATCTTTGTGTTGCTTTTGCCCACAACCTTTCCGACAATTTATTGAGT
||||| ||||||  ||      |  |||| |||  |  |  |               ||||| | |  |||      | || ||||||||| |||||||||||||||||||| ||||||||||| ||||| || ||||||||||||||||| ||||| || |||||||||||||| |||||||||||||
gtgaagtttgtttgcagtgcgaatctttttttatctgttcgttttgcaaccttttgtccttagttacctttgtgttgatat-attttagGGAGAGAATAAAGGTTTCCTTGTTTGCAAGAAAAAAATGGCGACCTCTCCAGAATCTTTGTGCTGCTTCTGTCCACAACCTTTCCGGCAATTTATTGAGT

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 9
gtgaactttgttacaacctccaa-attttcttaattactgatccccccttac--tcaaattttcagcaaaatgatttt---agGGGGAGAATAAAGGTTTCCTTGTCTGCAAGAAAAAGATGGCAACTTCTCCAGAATCTTTGTGTTGCTTTTGCCCACAACCTTTCCGACAATTTATTGAGT
       || |||   | || || | |   || | |||| ||      | |   |   ||| | |  |   |  || |   |||| || |||||||| || ||||||||||||||||||||||| |||||||||||| |||||||||||||||| || ||||| || ||||||||| |||| |
------gttattattccttcaaatagtcattttagtactaatggtaaatgaaaatatgattcttatgattttttttgttacagGGAGAAAATAAAGGGTTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCAGAAACTTTGTGTTGCTTTTGTCCTCAACCATTTCGACAATTTGTTGAAT

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 9
gtgaactttgttacaacctccaa-attttcttaattactgatccccccttac--tcaaattttcagcaaaatgatttt---agGGGGAGAATAAAGGTTTCCTTGTCTGCAAGAAAAAGATGGCAACTTCTCCAGAATCTTTGTGTTGCTTTTGCCCACAACCTTTCCGACAATTTATTGAGT
       || |||     || || | |   || | |||| ||      | |   |   | | | |  ||| |  || |   |||| || |||||||| || ||||||||||||||||||||||| || ||||||||| |||||||||||||||| || ||||| || || |||||| | || |
------gttattattgtttcaaatagtcattttagtactaattgtaaatgaaaatatgactcttatgaaactttttgttacagGGAGAAAATAAAGGGTTTCTTGTCTGCAAGAAAAAGATGGCCACGTCTCCAGAAACTTTGTGTTGCTTTTGTCCCCAACCATTTCGGCAATTTGTGGAAT

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 9
gtgaactttgttacaacctccaa-attttcttaattactgatccccccttactcaaat--tttcagcaaaatgattt----tagGGGGAGAATAAAGGTTTCCTTGTCTGCAAGAAAAAGATGGCAACTTCTCCAGAATCTTTGTGTTGCTTTTGCCCACAACCTTTCCGACAATTTATTGAGT
       || |||    ||| || | |   || | |||| ||      | |   | ||  ||      | ||  |||     |||| || |||||||| || ||||||||||||||||||||||| |||||||| ||| ||||||||||||| || || ||||| || || |||||| |||| |
------gttattattgtctcaaatagtcatttgagtactaatggtaagtcaaaaatatgattcttatgagattttttgttacagGGAGAAAATAAAGGATTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCTGAAACTTTGTGTTGCTTGTGTCCTCAACCATTTCGGCAATTTGTTGAAT

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 9
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 9
gtgaactttgttacaacctccaaattttcttaattactgatccccccttactcaaattttcagcaaaatgattttagGGGGAGAATAAAGGTTTCCTTGTCTGCAAGAAAAAGATGGCAACTTCTCCAGAATCTTTGTGTTGCTTTTGCCCACAACCTTTCCGACAATTTATTGAGT------
         ||||     |  |   |||| |    |||  | ||   | | |||     |  |   | |  | |||||| ||||| |||||||||||||| |||||||| |||||||| ||||| |||||| || | || ||||| || || |||||||| || || ||| | ||||      
---------gttatttgtttta---tttcctggcaact--ttccttgtcaatcattaacttggtctatt--tgttagggagagAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGTATGTGG

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 9
lower sequence: AT2G25760.1 (Arabidopsis thaliana), 3'ss of exon 9
---gtgaactttgttacaacctccaaattttcttaattactgatccccccttactcaaattttcagcaaaatgattttagGGGGAGAATAAAGGTTTCCTTGTCTGCAAGAAAAAGATGGCAACTTCTCCAGAATCTTTGTGTTGCTTTTGCCCACAACCTTTCCGACAATTTATTGAGT
   | | ||  |      |  |      |||| |    |||  | ||   | | |||     |  |   | |  | |||||| ||||| |||||||||||||| |||||||| |||||||| ||||| |||||| || | || ||||| || || |||||||| || || ||| | ||||
gttggggacactaaagttatttgttttatttcctggcaact--ttccttgtcaatcattaacttggtctatt--tgttagGGAGAGAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGT

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 9
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 9
-----------------------------------------------gtgaacttt-gttacaacctccaaattttcttaattactgatccccc-cttactcaaattttcagcaaaatgattt---tagGGGGAGAATAAAGGTTTCCTTGTCTGCAAGAAAAAGATGGCAACTTCTCCAGAATCTTTGTGTTGCTTTTGCCCACAACCTTTCCGACAATTTATTGAGT
                                                |||| ||  | || ||  |     || ||||  || |   |      |||  |    || |    |||||    |   ||||| ||||| || || |||||||| |||||||| ||||||||||| ||||| ||| || |||||||||| || |||   |||||| |||| ||| |||| |
gttggctccattcgaagttccgataaaatttgttccttctcttcaatttgaagttccgataaaatttgttccttgtcttcctttcaagtttttgacttgatttttttgttcttaaaatcccatatatagGGAGAGAACAAGGGGTTCCTTGTTTGCAAGAAGAAGATGGCAACATCTCCGGAAGCTCTGTGTTGCTTCTGTCCAATGCCTTTCAGACAGTTTGTTGAAT

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 9
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 9
gtgaactttgttacaacctccaaattttcttaattactgatccccccttactcaaattttcagcaa-aatgattttagGGGGAGAATAAAGGTTTCCTTGTCTGCAAGAAAAAGATGGCAACTTCTCCAGAATCTTTGTGTTGCTTTTGCCCACAACCTTTCCGACAATTTATTGAGT
||  ||  | |   ||| |  | |   | ||  ||  || |    |  |||   | | |  | ||| |     ||||||| ||||||||||| | |||||| ||||| || ||||||||||| ||||||||| |||||||||||||||| || || ||||| || || ||| |||| |
gttgacagtttccaaacttaaataggattttcttttatg-tgattctgtacatcattctgaaccaacagcttctttagGGAGAGAATAAAGGGTACCTTGTTTGCAAAAAGAAGATGGCAACATCTCCAGAAGCTTTGTGTTGCTTTTGTCCTCAGCCTTTTCGGCAGTTTGTTGAAT

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), 46 (downstream exon)
Score: 61

TCATTTGGGGAGAACTGGAAGCAGGAGGGATGACCTTGAATCTCTTGCCTACACACTTGTATTTCTTCTGCGTGGTCGCCTTCCTTGGCAAGGATACCAGgtgaactttg ... atgattttagGGGGAGAATAAAGGTTTCCTTGTCTGCAAGAAAAAGATGGCAACTTCTCCAGAATCTTTGTGTTGCTTTTGCCCACAACCTTTCCGACAATTTATTGAGT


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 31

TCATTTGGGGAGAACTGGAAGCAGGAGGGATGACCTTGAATCTCTTGCCTACACACTTGTATTTCTTCTGCGTGGTCGCCTTCCTTGGCAAGGATACCAGgtgaactttg ... atgattttagGGGGAGAATAAAGGTTTCCTTGTCTGCAAGAAAAAGATGGCAACTTCTCCAGAATCTTTGTGTTGCTTTTGCCCACAACCTTTCCGACAATTTATTGAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 37

TCATTTGGGGAGAACTGGAAGCAGGAGGGATGACCTTGAATCTCTTGCCTACACACTTGTATTTCTTCTGCGTGGTCGCCTTCCTTGGCAAGGATACCAGgtgaactttg ... atgattttagGGGGAGAATAAAGGTTTCCTTGTCTGCAAGAAAAAGATGGCAACTTCTCCAGAATCTTTGTGTTGCTTTTGCCCACAACCTTTCCGACAATTTATTGAGT


Block sizes: 44 (upstream exon), 34 (downstream exon)
Score: 24

TCATTTGGGGAGAACTGGAAGCAGGAGGGATGACCTTGAATCTCTTGCCTACACACTTGTATTTCTTCTGCGTGGTCGCCTTCCTTGGCAAGGATACCAGgtgaactttg ... atgattttagGGGGAGAATAAAGGTTTCCTTGTCTGCAAGAAAAAGATGGCAACTTCTCCAGAATCTTTGTGTTGCTTTTGCCCACAACCTTTCCGACAATTTATTGAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattttcttaattactgatccccccttactcaaattttcagcaaaatgattttagGGGGAGAATAAAGGTTTCCTTGTCTGCAAGAAAAAGATGGCAACTTCTCCAGAATCTTTGTGTTGCTTTTGCCCACAACCTTTCCGACAATTTATTGAGT
                                          aaaatgatttta  TA-rich tract