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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttccttaattagcaaacattttatttaaaaatattttaaggtttacaatcaaattggttggttttgtattcttgtaattcatttttatatggctgatattgtaatcgatgttatcagtgtttgtttctgacatttctctttgtgtgtttagCACGGCTGGGATGGAAGCCAGTGGAACAAGCAACATGAAATTTGCAATGAATGGATGCATAGTTATTGGAACTCTTGATGGAGCTAATGTTGAAATAAGA

Basic information

species Glycine max
transcript GLYMA20G03250.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G03250.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os03g55090.1 (Oryza sativa), 3'ss of exon 12
gtactttccttaattagcaaacattttatttaaaaatattttaaggtttacaatcaaattggttggttttgtattcttgtaattcatttttatatggctgatattgtaatcgatgttatcagtgtttgtttctgacatttctctttgtgtgtttagCACGGCTGGGATGGAAGCCAGTGGAACAAGCAACATGAAATTTGCAATGAATGGATGCATAGTTATTGGAACTCTTGATGGAGCTAATGTTGAAATAAGA
                              ||| ||| |    |  ||| || || |   | ||        |    |       |||   || | |  | | |||  |    ||  | | ||   |||||||   | ||   |||        || || ||||| |||||||| |||||||| ||||||||||| ||||||||||||||||| ||  ||||||||||| | ||||| |||||||| ||||| |||
-----------------------------gtaataatctggctacattt-cagtcta-cagattcacagaaaaactctcctgcctattagaatgtaga-gtttttgccag-actgccaactgtaagtgtttctacaaatttaattt---cacgcagTACTGCTGGAATGGAAGCTAGTGGAACCAGCAACATGAAGTTTGCAATGAATGGATGTATCCTTATTGGAACTTTGGATGGTGCTAATGTGGAAATCAGA

upper sequence: GLYMA20G03250.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G074158_T01 (Zea mays), 3'ss of exon 12
gtactttccttaattagcaaacattttatttaaaaatattttaaggtttacaatcaaattggttggttttgtattcttgtaattcatttttatatggctgatattgtaatcgatgttatcagtgtttgtttctgacatttctctttgtgtgtttagCACGGCTGGGATGGAAGCCAGTGGAACAAGCAACATGAAATTTGCAATGAATGGATGCATAGTTATTGGAACTCTTGATGGAGCTAATGTTGAAATAAGA
                                                                              |||||    |          |  | ||    |||||   ||  |||||| |   | ||||  |   || |  ||| || || ||||| |||||||| ||||| || || |||||||| ||||||||||| || |||||  ||||||||||| | ||||| || ||||| ||||| |||
------------------------------------------------------------------------------gtaatagtgtacctgccactttttttttctctcgataggatttgtgttt-tcgttaacat--catattatcggttcagTACTGCTGGAATGGAAGCTAGTGGGACCAGTAACATGAAGTTTGCAATGAACGGTTGCATTCTTATTGGAACTTTAGATGGTGCAAATGTGGAAATCAGA

upper sequence: GLYMA20G03250.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv01s0011g00730.t01 (Vitis vinifera), 3'ss of exon 12
gtactttccttaattagcaaacattttatttaaaaatattttaa-ggtttacaatcaaattggttggttttgtattcttgtaattcatttttatatggct-gatattgtaatcgatgttatcagtgtttgtttctgacatttctctttgtgtgtttagCACGGCTGGGATGGAAGCCAGTGGAACAAGCAACATGAAATTTGCAATGAATGGATGCATAGTTATTGGAACTCTTGATGGAGCTAATGTTGAAATAAGA
                      | |||  || |    ||   |  ||  ||    ||||    |  | |  |  ||    |      ||| |  |||  | |||| ||  ||||   || | | |         | ||||||   ||    || ||||||||||||| ||||||||||||||||| ||||||||||| ||||| |||||||| |||||  | ||||||||  | ||||| ||||||||||| ||||| 
--------------------gtactttgatttagctcataaaagtggcctaacgccaaagctctctgctaagagttagactggcaagtttcttaatgttttgatactg--atcgtctttcttaat--------ttaacattttctttccactggttagCACGGCTGGAATGGAAGCCAGTGGAACCAGCAACATGAAGTTTGCTATGAATGGCTGCATCCTGATTGGAACCTTAGATGGTGCTAATGTTGAGATAAGG

upper sequence: GLYMA20G03250.1 (Glycine max), 3'ss of exon 12
lower sequence: PP1S53_212V6.1 (Physcomitrella patens), 3'ss of exon 12
gtactttccttaattagcaaacattttatttaaaaatattttaaggtttacaatcaaattggttggttttgtattcttgtaattcatttttatatggctgatattgtaatcgatgttatcagtgtttgtttctgacatttctctttgtgtgtttagCACGGCTGGGATGGAAGCCAGTGGAACAAGCAACATGAAATTTGCAATGAATGGATGCATAGTTATTGGAACTCTTGATGGAGCTAATGTTGAAATAAGA
                              || | |  |   ||  |   ||  |       ||| |||| | | ||  |  |   |       |||  ||| | || |  ||||  ||| |||| ||   |    |||    | ||  ||   || || || || ||||||||||||||||||||||||||||| ||  |||||||||| ||  |  | ||||| ||| | || || || ||||| || || || 
-----------------------------gtatagagttgcaaaaatcggcagaccgtaatcttgattttatctactcctggtaggtaccagcttggtagat-tagtgagtgatg--atc-gtgtctgaccccatgattgagatgtgactgc--agTACTGCGGGAATGGAAGCCAGTGGAACAAGCAACATGAAGTTCTCAATGAATGGGTGTGTCTTGATTGGCACTTTGGACGGTGCAAATGTCGAGATTAGG

upper sequence: GLYMA20G03250.1 (Glycine max), 3'ss of exon 12
lower sequence: PP1S86_213V6.1 (Physcomitrella patens), 3'ss of exon 11
gtactttccttaattagcaaacattttatttaaaaatattttaaggtttacaatcaaattggttggttttgtattcttgtaattcatttttatatggctgatattgtaatcgatgttatcagtgtttgtttctgacatttctctttgtgtgtttagCACGGCTGGGATGGAAGCCAGTGGAACAAGCAACATGAAATTTGCAATGAATGGATGCATAGTTATTGGAACTCTTGATGGAGCTAATGTTGAAATAAGA
                              | | ||      ||||  || | |||    ||     |  || || ||| |  |    |    ||       ||   | ||  ||  |||||   ||      || | || ||||    |||  |||||||| ||||||||||| |||||||| ||||||||||| || || ||||| || ||| |  | |||||||| || |||||||| || ||||| ||  ||
-----------------------------gtgacaacg----aaggactatactca---cggactaatcagtcttattgcatctacaatcaccataatcagcat--cagtctttgaaatcagatcttacagaagaaaattatcttgcattgtgcagCACGGCAGGGATGGAAGCTAGTGGAACGAGCAACATGAAGTTCGCCATGAACGGCTGCGTGCTGATTGGAACCCTGGATGGAGCCAACGTTGAGATCCGA

upper sequence: GLYMA20G03250.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ09932 (Selaginella moellendorffii), 3'ss of exon 11
gtactttccttaattagcaaacattttatttaaaaatattttaaggtttacaatcaaattggttggttttgtattcttgtaattcatttttatatggctgatattgtaatcgatgttatcag-tgtttgtttctgacatttctctttgtgtgtt-tagCACGGCTGGGATGGAAGCCAGTGGAACAAGCAACATGAAATTTGCAATGAATGGATGCATAGTTATTGGAACTCTTGATGGAGCTAATGTTGAAATAAGA
                                                                                                    | ||   | ||| | || ||   ||||||     || || |  ||||   || | ||| ||||| || |||||||| |||||||| ||||||||||||||  | ||||| |||    |  | ||||| ||||| ||||| || || || || ||  | 
--------------------------------------------------------------------------------------------------gtacataccattcgctcttttcttctgtttgaactggatatcttccttttgatgatgtagTACGGCGGGAATGGAAGCTAGTGGAACCAGCAACATGAAATTCTCGATGAACGGAGCTGTTTTGATTGGCACTCTCGATGGTGCCAACGTCGAGATCCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgtaatcgatgttatcagtgtttgtttctgacatttctctttgtgtgtttagCACGGCTGGGATGGAAGCCAGTGGAACAAGCAACATGAAATTTGCAATGAATGGATGCATAGTTATTGGAACTCTTGATGGAGCTAATGTTGAAATAAGA
                            ttctgac  putative branch site (score: 2)
                                    tttctctttgt  CT-rich tract
           atgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactttccttaattagcaaacattttatttaaaaatattttaaggtttacaatcaaattggttggttttgtattcttgtaattcatttttatatggctgatattgtaatcgatgttatcagtgtttgtttctgacatttctctttgtgtgtttagCACGGCTGGGATGGAAGCCAGTGGAACAAGCAACATGAAATTTGCAATGAATGGATGCATAGTTATTGGAACTCTTGATGGAGCTAATGTTGAAATAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT