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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgagactatgctaaacttgattctgttgcttaccctaagaatgaatctaatgcctctgttatttctgtgcctccagGAATCCACAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGGATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG

Basic information

species Zea mays
transcript AC235535.1_FGT001
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 11
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 11
gtatgagactatgctaaacttgattctgttgcttaccctaagaatgaatct--aatgcct----ctgttatttctgtgcctccagGAATCCACAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGGATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG
|||||    ||||   || ||| ||   |      || | |  ||| || |  |||   |     |  | | |   || || |||||||||||||||||||||||||||||| ||||||||||||||||||||||| ||||||||||||||||| ||||| ||||||||||||
gtatgctgttatgtgcaaattgttttcttctgaacccatgaatatgtatgttgaatatttagtgttaatgtgttgatgtcttcagGAATCCACAAGCTGATCTGCAAGCTCAAGACCGTGCACATAGGATAGGTCAGAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 11
gtatgagactatgctaaacttgattctgttgcttaccctaaga-atgaatctaatgcctctgttatttctgtgcctccagGAATCCACAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGGATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG
|||||   || | | || | | ||| | |  | | |   ||    ||||  ||| |  | || |  ||  ||  | | |||||||| ||||  ||||||||||| || || ||||||||||| || ||||||||||||||||||||||| || || || |||||||||
gtatgtc-cttttcaaatcgtaattttttctcattctacaatttgtgaagttaaaggttatggttatttggtttcac-agGAATCCTCAAGTGGATCTGCAAGCGCAAGATCGTGCACATAGAATTGGTCAAAAGAAAGAAGTTCAAGTTTTTCGTTTCTGCACTGAG

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 11
-----------------gtatgagactatgctaaacttgattctgttgcttaccctaagaatgaatctaatgcctctgttatttctgtgcctc-cagGAATCCACAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGGATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG
                  | | ||         ||||||   | ||  | ||   | |  |  |||    |   |   | |||  ||    |  |||||| ||||||| ||| |||||||||||||| ||||| |||||||| ||||||||||||||||||||||| ||||| ||||||||||||
gcaagtattcatattgattgtcagcagccttctaacttgcagcggtgccataagttcatgactaattctttttgttgataattggtggttataacagGAACCCACAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 11
------gtatgagactatgctaaacttgattctgttgcttaccctaagaatgaatctaatgcctctgttatttctgtgcctcca---gGAATCCACAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGGATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG
       | | |     |  |  |||      | |   |||       |   ||  || |   |   |  ||  ||    | ||   |||| ||||||| |||  |||| |||||||| ||||| |||||||| ||||||||||||||||||||||| ||||| ||||| ||||||
gtcagtatttcaagtagttatggactcagccatctgatttatatctgtaccaaaattattttgttgatggttggtgcttttacaacagGAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGTACTGAG

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 11
------------gtatgagactatgctaaacttgattctgttgct-taccctaagaatgaatctaat-gcctctgttatt--tctgtgcctc---cagGAATCCACAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGGATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG
            || |||   |  ||     |  |   ||  |   | || ||||       ||||| |  | ||||  |  |  |||  |    |||||| || |||| ||| |||||||||||||| ||||| |||||||| ||||||||||||||||||||||| ||||| ||||||||||||
gttagtattcttgt-tgattgtcagcagccttctaacttgcagtgatgccataagttcatgactaattgtttttgttgataattggtggttataacagGAACCCTCAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 11
------gtatgagactatgctaaacttgattctgttgcttaccctaagaatgaatctaatgcctctgttatttctgtgcctcca---gGAATCCACAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGGATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG
       | |       |  | |||       ||||  |||       |   ||  || |   |   |  ||  ||    | ||   |||| ||||||| |||  |||| |||||||| ||||| |||||||| ||||||||||||||||||||||| ||||| ||||| ||||||
gtcagtatttctagtagttttgaacacagccatgttatttatatctgtacccaaattattttgttgatggttggtgcttttacaacagGAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGTTTTTGTACTGAG

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 11
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 11
gtatgagactatgctaaacttgattctgttgcttaccctaagaatgaatc---taatgcctc-tgttatttctgtgcctc--cagGAATCCACAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGGATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG
          | |||    |||  ||  |||  ||   || || ||  |    | ||||||  ||   |   ||        |||||| || |||| |||  ||||||||||||| |||||||||||||| |||||||| |||||||||||||||||||| || ||||| |||
-------gtaaggctctttttgtgtccattg--taatttatgagtgttttcttttatgcctaatgaggtgggtggattatggcagGAACCCTCAAGTTGACTTGCAAGCTCAGGATCGTGCACATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTCCGGTTCTGCACCGAG

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 11
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 11
gtatgag-actatgctaaacttgattctgttgctt-----accctaag-aatgaatctaatgcct----------ctgttatttctgtgcctcc--agGAATCCACAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGGATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG
   |||| | |   | |   ||  |||| || |||     |  ||| | |||   | || |   |           || | | | | |  | ||  ||||| || |||| |||| ||||||| || || ||||| ||| |||| |||||||||||||||||||||||||| || || ||||| |||
--gtgagcatttctccatttttttttctttttcttttagaatgctagggaattgttatattatttaccaatctggttgatctctttattgcaccgtagGAACCCCCAAGTTGATTTGCAAGCACAAGATCGTGCTCATCGGATTGGTCAAAAGAAAGAAGTTCAAGTGTTTCGATTCTGCACAGAG

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 11
lower sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 11
gtatgagactatgctaaacttgattctgttgcttaccctaagaatgaatctaatgcctctgttatttctgtgcctccagGAATCCACAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGGATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG
                    | ||  |  || ||          ||| |   |||  | |   | || ||   || ||||||||| ||||  ||| ||||||| || || || |||||| |||| || || || |||||||||||||| ||||| ||||||||  ||
-------------------gtaataataatgatttgttc-----tgagtggcatgtttttagaaattatg---ctgcagGAATCCTCAAGTCGATTTGCAAGCGCAAGATCGAGCACATCGGATTGGACAGAAAAAAGAAGTTCAAGTTTTCCGATTTTGCACGCAG

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 11
lower sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 11
gtatgagactatgctaaacttgattctgttgcttaccctaagaatgaatctaatgcctctgttatttctgtgcctccagGAATCCACAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGGATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG
                    | ||  |  || ||          ||| |   |||  |  |  |||    ||| | ||||||||| ||||  ||| ||||||| || || || |||||| |||| || || || |||||||||||||| ||||| ||||||||  ||
-------------------gtaatagtaatgatttgttc-----tgagtggcatgttttagaaatt---atgc-tgcagGAATCCTCAAGTCGATTTGCAAGCGCAAGATCGAGCACATCGGATTGGACAGAAAAAAGAAGTTCAAGTTTTCCGATTTTGCACGCAG

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: 370

CAGGAAGTGAAAAGTTTGTTTTCTTACTTTCAACTAGGGCAGGTGGCCTTGGTATCAACTTGGCCACTGCTGATGTTGTGGTTCTTTATGACAGCGATTGgtatgagact ... gtgcctccagGAATCCACAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGGATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 156

CAGGAAGTGAAAAGTTTGTTTTCTTACTTTCAACTAGGGCAGGTGGCCTTGGTATCAACTTGGCCACTGCTGATGTTGTGGTTCTTTATGACAGCGATTGgtatgagact ... gtgcctccagGAATCCACAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGGATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 166

CAGGAAGTGAAAAGTTTGTTTTCTTACTTTCAACTAGGGCAGGTGGCCTTGGTATCAACTTGGCCACTGCTGATGTTGTGGTTCTTTATGACAGCGATTGgtatgagact ... gtgcctccagGAATCCACAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGGATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 225

CAGGAAGTGAAAAGTTTGTTTTCTTACTTTCAACTAGGGCAGGTGGCCTTGGTATCAACTTGGCCACTGCTGATGTTGTGGTTCTTTATGACAGCGATTGgtatgagact ... gtgcctccagGAATCCACAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGGATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgttgcttaccctaagaatgaatctaatgcctctgttatttctgtgcctccagGAATCCACAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGGATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG
                                        tttctgt  CT-rich tract
                      aatctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgagactatgctaaacttgattctgttgcttaccctaagaatgaatctaatgcctctgttatttctgtgcctccagGAATCCACAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGGATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT