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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgccgctaggggatcgcttgctttcctcggaccactctgccgaccacatctacaccgcatcaacggtccttccaagtgagctccaatcccctgtctgtagATGGAGAGGGTGCTCAAGGATGACGCCGTCGAGGAGAAGGGCGAGCGCGCCAGGATG

Basic information

species Zea mays
transcript EF517601.1_FGT012
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EF517601.1_FGT012 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g42220.1 (Oryza sativa), 3'ss of exon 1
-----tgccgctaggggatcgcttgctttcctcggaccactctgccgaccacatctacaccgcatcaacggtccttccaagtgagctccaatcccctgtctgtagATGGAGAGGGTGCTCAAGGATGACGCCGTCGAGGAGAAGGGCGAGCGCGCCAGGATG
     ||            |  || |||   | |   |    |||     |  | | ||   | |||  |   |       |||| |        || |  ||| |||||||||||||| |||||||| || || |||||||||||||| || |||||||||
cagtgtgatatccaatctgcatttacttctattgtttctgcgtgctttgtatgttt-cagtacctcagagtgtcacaatcttgagttttttctgtctttagGTAAATGGAGAGGGTGCTGAAGGATGATGCTGTTGAGGAGAAGGGCGAACGTGCCAGGATG

upper sequence: EF517601.1_FGT012 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g42220.2 (Oryza sativa), 3'ss of exon 1
-----tgccgctaggggatcgcttgctttcctcggaccactctgccgaccacatctacaccgcatcaacggtccttccaagtgagctccaatcccctgtctgtagATGGAGAGGGTGCTCAAGGATGACGCCGTCGAGGAGAAGGGCGAGCGCGCCAGGATG---------------------------------------
     ||            |  || |||   | |   |    |||     |  | | ||   | |||  |   |       |||| |        || |  ||| |||||||||||||| |||||||| || || |||||||||||||| || |||||||||                                       
cagtgtgatatccaatctgcatttacttctattgtttctgcgtgctttgtatgttt-cagtacctcagagtgtcacaatcttgagttttttctgtctttagGTAAATGGAGAGGGTGCTGAAGGATGATGCTGTTGAGGAGAAGGGCGAACGTGCCAGGATGGTGTGAAAACCCTTTCTTATCGATTTGACCTTTTTAATT

upper sequence: EF517601.1_FGT012 (Zea mays), 3'ss of exon 8
lower sequence: EFJ28920 (Selaginella moellendorffii), 3'ss of exon 1
tgccgctaggggatcgcttgctttcctcggaccactctgccgaccacatctacaccgcatcaacggtccttccaagtgagctccaatcccctgtctgtagATGGAGAGGGTGCTCAAGGATGACGCCGTCGAGGAGAAGGGCGAGCGCGCCAGGATG
                                                     | ||     ||  |   ||   | |    |  | |   |    | ||   || | | |  ||||||||||||| || || |||||||||||||||||||| |||
--------------------------------------------------gtgagcgttgtgaccatgtatc---gcgtttcctgagcgttttctggcagGCCGATAAGCTCTTCAAGGATGACGCTGTGGAAGAGAAGGGCGAGCGCGCCAGAATG

upper sequence: EF517601.1_FGT012 (Zea mays), 3'ss of exon 8
lower sequence: EFJ13624 (Selaginella moellendorffii), 3'ss of exon 1
tgccgctaggggatcgcttgctttcctcggaccactctgccgaccacatctacaccgcatcaacggtccttccaagtgagctccaatcccctgtctg-tagATGGAGAGGGTGCTCAAGGATGACGCCGTCGAGGAGAAGGGCGAGCGCGCCAGGATG
                                                        || |    | || |     | |    |  | |   | ||||  ||   || | | |  ||||||||||||| || ||||||||||||||||||||||| |||
----------------------------------------------------gtgagcgttg-tgatcatgtatcgcgtttcctgagcgtttttctggcagGCCGATAAGCTCTTCAAGGATGACGCTGTGGAGGAGAAGGGCGAGCGCGCCAGAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatctacaccgcatcaacggtccttccaagtgagctccaatcccctgtctgtagATGGAGAGGGTGCTCAAGGATGACGCCGTCGAGGAGAAGGGCGAGCGCGCCAGGATG
                                         tcccctgtct  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgccgctaggggatcgcttgctttcctcggaccactctgccgaccacatctacaccgcatcaacggtccttccaagtgagctccaatcccctgtctgtagATGGAGAGGGTGCTCAAGGATGACGCCGTCGAGGAGAAGGGCGAGCGCGCCAGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
tgccgct
- - - - - - - - - tgctttc
- - - - - - - - - - - - - - ggaccac
- - - - - - - - - - - - - - - - - -tctgccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - ccgcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agctcca