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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaggcagccagatttttcttttgtttaaatcgcattacattgaagcaagatgtaacaccctacatttttcttttgactgctcacaagttgattgaaacagGAACCGTTGTTGATTCTAAGATATGCCACCCAACGGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAG

Basic information

species Zea mays
transcript GRMZM2G079080_T02
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 18
-----gaggcagccagatttttcttttgtttaaatcgcattacattgaagcaagatgtaacaccctacatttttcttttgactgctcacaagttgattgaaa--cagGAACCGTTGTTGATTCTAAGATATGCCACCCAACGGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAG
       |      |   | |   ||||  | ||       || || |       ||| |  | ||  |||| | |    | ||||||   |||   | |||  ||||||| ||||||||||| ||||| ||||||||| | ||||||||||||||||||||||| ||||||||||| |||
tttcttggattattaaggtatcactttgggtgaacta----acttttatatttactgttattcacttgatttctgt---aattgctcatgtgtttgctaaaaaacagGAACTGTTGTTGATTCAAAGATCTGCCACCCATCAGAGTTTGATTTCTACCTCTGTAGCCATGCTGGAATTCAG

upper sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA10G00530.1 (Glycine max), 3'ss of exon 10
-------gag-gcagccagatttttcttttgtttaaatcg------cattacattgaagcaagatgtaacaccctac---atttttcttttgactgctcacaagttgattgaaacagGAACCGTTGTTGATTCTAAGATATGCCACCCAACGGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAG
       ||| |   |   |||  || | |    ||||        ||||   ||     || |   |    |  |    | |    |||| | |  |    |  || ||    |||| || || |||||||| || || || || ||||| || |||||||| || ||||||||||||||||| ||||||
gtacaatgagtgttcctgaattgctcgtgtacacaaataaatgtgtcattttttttgtttaaaactgattgtctaattggactaactttttaaataattttcatctgtttt---cagGGACTGTAGTTGATTCCAAAATCTGTCATCCAACAGAATTTGATTTTTATCTCTGTAGTCATGCTGGCATCCAG

upper sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 18
lower sequence: EFJ15357 (Selaginella moellendorffii), 3'ss of exon 19
gaggcagccagatttttcttttgtttaaatcgcattacattgaagcaagatgtaacaccctacatttttcttttgactgctcacaagttgattgaaacagGAACCGTTGTTGATTCTAAGATATGCCACCCAACGGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAG
                                       ||| || ||  | |       | || | | |||   ||  ||   ||   | ||     ||| || || || ||| | ||||| || || || ||||| ||||||||||||||||| ||||| |||||||| |||
-------------------------------------gtttgtaggaaagtttg------ttcaatgtgcttc--acaact---aaaacgcttttgctagGTACTGTGGTGGATACGAAGATCTGTCATCCCACGGAATTTGATTTCTACCTCTGCAGTCACGCTGGAATACAG

upper sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 18
lower sequence: EFJ19862 (Selaginella moellendorffii), 3'ss of exon 17
gaggcagccagatttttcttttgtttaaatcgcattacattgaagcaagatgtaacaccctacatttttcttttgactgctcacaagttgattgaaacagGAACCGTTGTTGATTCTAAGATATGCCACCCAACGGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAG
                                        ||  ||    | |||        ||||   |    | ||       |||       ||||| || || || ||||| ||||| ||||| |||||||||||||| |||||||| || || ||||| || || |||
------------------------------------gtgctgttgccgtttataa-gtggcgaatttagataactaatgagagaccgttttccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG

upper sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 18
lower sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 17
gaggcagccagatttttcttttgtttaaatcgcattacattgaag-caagatgtaacaccctacatttttcttttgactgctcacaagttgattgaaacagGAACCGTTGTTGATTCTAAGATATGCCACCCAACGGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAG
                                  |    |||  | ||| | ||  |    |  |  |  ||  |||  |  |    |||       ||||| || || || ||||| ||||| ||||| |||||||||||||| |||||||| || || ||||| || || |||
---------------------------------gtgctgttgccgtcaataagtggcgaatt-tagataactaatgagagacc----gttttccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG

upper sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 18
lower sequence: EFJ24991 (Selaginella moellendorffii), 3'ss of exon 19
gaggcagccagatttttcttttgtttaaatcgcattacattgaagcaagatgtaacaccctacatttttcttttgactgctcacaagttgattgaaacagGAACCGTTGTTGATTCTAAGATATGCCACCCAACGGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAG
                                       ||| |||||  | |       | || | | ||  ||||  ||   ||   | ||     ||| || || || ||| | ||||| || || || ||||| ||||||||||||||||| ||||| |||||||| |||
-------------------------------------gtttgtagcaaagtttg------ttcaatgtgct--tgacaact---aaaacgcttttgctagGTACTGTGGTGGATACGAAGATCTGTCATCCCACGGAATTTGATTTCTACCTCTGCAGTCACGCTGGAATACAG

upper sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 18
lower sequence: EFJ19863 (Selaginella moellendorffii), 3'ss of exon 17
gaggcagccagatttttcttttgtttaaatcgcattacattgaagcaagatgtaacaccctacatttttcttttgactgctcacaagttgattgaaacagGAACCGTTGTTGATTCTAAGATATGCCACCCAACGGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAG
                             |    || |  | ||  |||  |  |      | |  |       ||| | |      ||  ||||  |||| || || || ||||| ||||| ||||| |||||||||||||| |||||||| || || ||||  || || |||
----------------------------gtgctgttgccgttaa-taagtggcgaatttagataactaatgagagaccgtt------ttccttga--cagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGGCGGCATTCAG

upper sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 18
lower sequence: EFJ14096 (Selaginella moellendorffii), 3'ss of exon 17
gaggcagccagatttttcttttgtttaaatcgcattacattgaagc-aagatgtaacaccctacatttttcttttgactgctcacaagttgattgaaacagGAACCGTTGTTGATTCTAAGATATGCCACCCAACGGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAG
                                  |    |||  |  || | ||  |    |  |  |  ||  |||  |  |    |||       ||||| || || || ||||| ||||| ||||| |||||||||||||| |||||||| || || ||||| || || |||
---------------------------------gtgctgttgccgttaataagtggcgaatt-tagataactaatgagagacc----gttttccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagatgtaacaccctacatttttcttttgactgctcacaagttgattgaaacagGAACCGTTGTTGATTCTAAGATATGCCACCCAACGGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAG
               tacatttttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaggcagccagatttttcttttgtttaaatcgcattacattgaagcaagatgtaacaccctacatttttcttttgactgctcacaagttgattgaaacagGAACCGTTGTTGATTCTAAGATATGCCACCCAACGGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA