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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgttgagtcttattcttgagtgtttgttcattattatgactattattttgaatgatgattccatatttcctttgtgcagGTTATGGATATGCTGGGACCTAGCCTCTGGGACGTTTGGAATAATAGCAATCATCA

Basic information

species Glycine max
transcript GLYMA08G21570.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G21570.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 4
-------------------------------gtatgttgttgagtcttattcttgagtgtttgttcattattatgactattattttgaatgatgattcca------tatttcctttgtgcagGTTATGGATATGCTGGGACCTAGCCTCTGGGACGTTTGGAATAATAGCAATCATCA
                                | || | |   || |     |||| || ||  |  || |  | |  |||||     | | |  ||| |       |  |  ||  ||||||||||||||||| ||||||| ||||| ||||| ||||||||||| |     ||   
gtaatggagcatgaactagatttttttttttttttgctttccggtttatggtttgattggtttctttttctcttaagaattatcaactacgttttttctaaccatacacatttttcatgcagGTTATGGATATGTTGGGACCGAGCCTGTGGGATGTTTGGAATAACAATTCCCACTC

upper sequence: GLYMA08G21570.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g54100.1 (Oryza sativa), 3'ss of exon 4
------gtatgttgttgagtcttattcttgag----tgtttgttcattattatgactattattttgaatgatgattccatatttcctttgtgcagGTTATGGATATGCTGGGACCTAGCCTCTGGGACGTTTGGAATAATAGCAATCATCA
        |  |  ||  | ||  | |  |||    |||||  |  ||    |  | |  ||||| | | |    |   | | |      || |||||||||||||||||||||| || || ||||| |||||||||||||    |||   
gtaatgacacctcattttgactactacgagagaaactgttttctttttgccctttccaaaattttaattaac---ttggtttatgaaaaatgtagGTTATGGATATGCTGGGACCCAGTCTTTGGGATGTTTGGAATAATAATTCTCACAC

upper sequence: GLYMA08G21570.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G045259_T01 (Zea mays), 3'ss of exon 4
----------------------------------------------------------------------gtatgttgttgagtcttattcttgagtgtttgttcattatt-atgactattatt----ttgaa---tgatgattccatatttcctttgtgcagGTTATGGATATGCTGGGACCTAGCCTCTGGGACGTTTGGAATAATAGCAATCATCA
                                                                        ||| | |||   |  ||  |    || |  |   |  || |  |||||||      |||     || | || | || |    |   || |||||||||||||  ||||||| ||||| ||||| |||||||||||||     ||   
gtttgggcaatgaaccttcttatatttgtttcacttgttatgcacatgttaatatagatattagataggcagatggtattggtgcaaatcttcttttggtcctctttcgttgacaactattaacaaacttggttcttgttaatccgatttggtttgcatgtagGTTATGGATATTTTGGGACCAAGCCTATGGGATGTTTGGAATAATAATTCCCACTC

upper sequence: GLYMA08G21570.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G120951_T01 (Zea mays), 3'ss of exon 4
gtatgttgttgagtcttattcttgagtgtttgttcattattatgact-attattttgaatgatgatt--ccatatttcctttgtgcagGTTATGGATATGCTGGGACCTAGCCTCTGGGACGTTTGGAATAATAGCAATCATCA
||||     |  |  || ||   |||| || | | |||  |||  || ||  ||||  ||| |  ||  |    | |      | ||||||||||||||||| ||||| || || ||||| || ||||||||||    |||   
gtataacactctggattgttg--gagtattagcttatt--tatttctgatcgttttagatgctagttaacttggtcttaaaaattcagGTTATGGATATGCTCGGACCCAGTCTGTGGGATGTCTGGAATAATAAATCTCACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttcattattatgactattattttgaatgatgattccatatttcctttgtgcagGTTATGGATATGCTGGGACCTAGCCTCTGGGACGTTTGGAATAATAGCAATCATCA
                                  ttccatatttccttt  CT-rich tract
     attattatgactatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttgttgagtcttattcttgagtgtttgttcattattatgactattattttgaatgatgattccatatttcctttgtgcagGTTATGGATATGCTGGGACCTAGCCTCTGGGACGTTTGGAATAATAGCAATCATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG