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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttgatcataattaattaaattgtttacaaatgttgtttgctttagcagtttttccattatgattacattatattttggctcttcttgtccctaaagTTGAAATATCACGACACTGGAAGAGAGAAAGAATACTTGCCACAAGTTGGTCAGTGGAATATGATGAACAAG

Basic information

species Glycine max
transcript GLYMA04G21450.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G21450.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 9
gtaatttgatcataattaattaaattgtttacaaatgttgtttgctttagcagtttttccattatgattacattatattttggctct----tcttgtc-cctaaagTTGAAATATCACGACACTGGAAGAGAGAAAGAATACTTGCCACAAGTTGGTCAGTGGAATATGATGAACAAG
                       ||  ||| |     |||||    | || ||||     | |    | |  | ||| ||||| | |    | ||||  | |  || |||||||||| || ||||| |  || || || | |||||||||||||||||||||||| ||| ||||||||
---------------------gtatgatttgc---ctttgttaatctcagtagttggctaactgctctcagctaataatttgggtatgaaattttgtggctttcagCTGAAATATCATGATACTGGGAAGGAAAAGGAGTGCTTGCCACAAGTTGGTCAGTGGAACATGGTGAACAAG

upper sequence: GLYMA04G21450.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G079080_T01 (Zea mays), 3'ss of exon 9
gtaatt-tgatcataattaattaaattgtttacaaatgttgtttgctttagcagtttttccattatgattacattat--at---tttggctcttcttgtccctaaagTTGAAATATCACGACACTGGAAGAGAGAAAGAATACTTGCCACAAGTTGGTCAGTGGAATATGATGAACAAG
||||   | ||  ||  | | |   ||  || ||   |    || |  ||  |    |    |||      |||| |  ||   |    |  || || |   |  ||||||| ||||| |||||||||| ||||||||| | ||| ||||| |||||||||||||| ||| | ||||||
gtaagaataattttatgtcacttttttcctttcaggagcaccttacactattatccatgaggttagttgctcattgttgatgcatcgaacaatttttttgaattcagTTGAAGTATCATGACACTGGAAAAGAGAAAGAGTGCTTACCACAGGTTGGTCAGTGGAACATGGTAAACAAG

upper sequence: GLYMA04G21450.1 (Glycine max), 3'ss of exon 10
lower sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 8
-----------gtaatttgatcataattaattaaattgtttacaaatgttgtttgctttagcagtttttccattatgattacatt----atattttggctc-ttcttgtccctaaagTTGAAATATCACGACACTGGAAGAGAGAAAGAATACTTGCCACAAGTTGGTCAGTGGAATATGATGAACAAG
            | || | |   | ||| |||   ||  ||      |    || |  ||  | || |  |  ||  |   ||||    || |  ||  |   | ||||   |  || |||| ||||| |||||||||| ||||||||| | ||| ||||| |||||||||||||| ||| | ||||||
gtgaggataatcttatgtcactgttattcattttttttcttttgggagcaccttacactattatttatgacgctagtagctcattgttgatgtgctgaataacttttgtgaattcagCTGAAGTATCATGACACTGGAAAAGAGAAAGAGTGCTTACCACAGGTTGGTCAGTGGAACATGGTAAACAAG

upper sequence: GLYMA04G21450.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 9
gtaatttgatcataattaattaaattgtttacaaatgttgtttgctttagcagtttttccattatgattacat-tatattttggctct---tcttgtccct--aaagTTGAAATATCACGACACTGGAAGAGAGAAAGAATACTTGCCACAAGTTGGTCAGTGGAATATGATGAACAAG
                       | ||||||  |      |||   |||   | | ||  |  ||| |   || || | ||||   ||   | |||| |||  | || | ||||||||||| || |||| ||| |||||||| ||||| ||||||||||| ||||||||||  ||||||
---------------------gtaatgtttaacatccccttttctcttattggatattttaacatggtctgatctaaaatttgttcctctattttgttccttgatagCTTAAATATCACGATACCGGAAAAGAAAAAGAATATTTGCCGCAAGTTGGTCAATGGAATATGACAAACAAG

upper sequence: GLYMA04G21450.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ15357 (Selaginella moellendorffii), 3'ss of exon 10
gtaatttgatcataattaattaaattgtttacaaatgttgtttgctttagca-gtttttccattatgattacattatattttggctcttcttgtccctaaagTTGAAATATCACGACACTGGAAGAGAGAAAGAATACTTGCCACAAGTTGGTCAGTGGAATATGATGAACAAG
                                                 | | || || | |  ||  |||  | |   | |  |  ||  || |     ||||||| ||||| || |||||| | |||||||| | | | || |||||||| |||||||||||||||||||||
-------------------------------------------------gtatgtcttccgaagatcgttaattcaagctctaacgttttctgac-----agTTGAAGTATCATGATACTGGACGGGAGAAAGACTGCCTTCCTCAAGTTGGGCAGTGGAATATGATGAACAAG

upper sequence: GLYMA04G21450.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ24991 (Selaginella moellendorffii), 3'ss of exon 10
gtaatttgatcataattaattaaattgtttacaaatgttgtttgctttagca-gtttttccattatgattacattatattttggctcttcttgtccctaaagTTGAAATATCACGACACTGGAAGAGAGAAAGAATACTTGCCACAAGTTGGTCAGTGGAATATGATGAACAAG
                                                 | | || || | |  |   |||  | |   |    |  ||  || |     ||||||| ||||| || |||||| | |||||||| | | | || |||||||| |||||||||||||||||||||
-------------------------------------------------gtatgtcttccgaagaccgttaattcaagctcaaacgttttctgac-----agTTGAAGTATCATGATACTGGACGGGAGAAAGACTGCCTTCCTCAAGTTGGGCAGTGGAATATGATGAACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagcagtttttccattatgattacattatattttggctcttcttgtccctaaagTTGAAATATCACGACACTGGAAGAGAGAAAGAATACTTGCCACAAGTTGGTCAGTGGAATATGATGAACAAG
                                     ctcttcttgtccct  CT-rich tract
       tttttccattatgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttgatcataattaattaaattgtttacaaatgttgtttgctttagcagtttttccattatgattacattatattttggctcttcttgtccctaaagTTGAAATATCACGACACTGGAAGAGAGAAAGAATACTTGCCACAAGTTGGTCAGTGGAATATGATGAACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA