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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccttgtaattaagtccttgactgttgctgatagtgataataaactaaaataacattttttcttgcagCAAATGTGTTTCATCGTGACTTGAAGCCAAAAAATATTCTAGCTAATGCTGATTGCAAGCTAAAATTATGTGATTTTGGACTTGCTCGAGTTTCATTTAA

Basic information

species Glycine max
transcript GLYMA07G11470.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G11470.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g50120.1 (Oryza sativa), 3'ss of exon 2
------gtatccttgtaatt--aagtccttga---ctgttgctgatagtgataataaactaaaataaca-ttttttcttgcagCAAATGTGTTTCATCGTGACTTGAAGCCAAAAAATATTCTAGCTAATGCTGATTGCAAGCTAAAATTATGTGATTTTGGACTTGCTCGAGTTTCATTTAA
      |  ||| | || |   || ||  | |   || ||||| ||   | | | |  || |  |     ||| |  ||||||||| ||| || ||||| ||  | ||||| || ||||||||||| ||||||||||||||||| ||  | || ||||| || ||||| ||||| ||||||||
gtagtagattccatatagtaggaaatcggtaatttcttttgcttatgtggttgacacgctcactttctggtttctctttgcagCAAGTGTTTTCCATCGGGATCTTAAGCCCAAGAATATTCTAGCCAATGCTGATTGCAAGCTGAAGGTTTGCGATTTCGGCCTTGCCCGAGTGTCATTTAA

upper sequence: GLYMA07G11470.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G062761_T02 (Zea mays), 3'ss of exon 2
--------------------gtatccttgtaattaagtccttgactgttgctgatagtgataataaa---ctaaaataacattttttcttgcagCAAATGTGTTTCATCGTGACTTGAAGCCAAAAAATATTCTAGCTAATGCTGATTGCAAGCTAAAATTATGTGATTTTGGACTTGCTCGAGTTTCATTTAA
                    ||   ||||| | |   |  ||    ||| ||  | ||||   | |    |||   |     ||  | |||||||||  || || ||||| ||  | ||||| || ||||||||||| |||||||| |||||||| ||  | ||||||||||| ||||| || |||||||| ||
gttgttagactccacattgagtggacttgttaatggtttgtta--cgttacttcttgtgagcttcagtttctatgcttgttcttggttttgcagCAAGCGTCTTCCATCGGGATCTTAAGCCCAAGAATATTCTAGCCAATGCTGACTGCAAGCTGAAGATTTGTGATTTTGGCCTTGCCCGCGTTTCATTCAA

upper sequence: GLYMA07G11470.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G18150.3 (Arabidopsis thaliana), 3'ss of exon 3
------------------gtatccttgtaattaagtcct--tgactgttgctgatagtgataataaactaaaataacatttttt-cttgcagCAAATGTGTTTCATCGTGACTTGAAGCCAAAAAATATTCTAGCTAATGCTGATTGCAAGCTAAAATTATGTGATTTTGGACTTGCTCGAGTTTCATTTAA
                    ||   | |  ||   ||||  ||| | ||| |     | ||| | ||  |    |   || | |  || |||| |||||||||||||| || ||||| || || || |||||||||||||||||||||||  | ||  | ||||||||||| || ||||| ||||| |||||
gttagtttctggttttacacattggtctctttcgatcctcatgatttttgttatagataatattgaaacacttaagggttctctgttttcagCTAATGTGTTTCATCGGGATTTGAAACCGAAGAACATTCTAGCTAATGCTGATTGCAAATTGAAGATCTGTGATTTTGGGCTGGCTCGCGTTTCTTTTAA

upper sequence: GLYMA07G11470.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 1
-------------------gtatccttgtaa--ttaagtccttgactgttgctgatagtgataataaactaaaataacattttttcttgcagCAAATGTGTTTCATCGTGACTTGAAGCCAAAAAATATTCTAGCTAATGCTGATTGCAAGCTAAAATTATGTGATTTTGGACTTGCTCGAGTTTCATTTAA
                     || | |||    ||  |||| | |||| |  | | | | |   | |   ||||     || ||   | |||| ||||||||||||||||| |||||||| |||||||||||||| ||  ||||||||||| | ||  | || || ||||| ||||||||||| || |||||
gcgagtgccttggcttgagaaattcgtgtttccttttgtccattactgcttttcaaactcaatctgatggaaaacttttttattcgatacagCTAATGTGTTTCATCGTGATTTGAAGCCTAAAAATATTCTAGCCAACTCTGATTGCAAGTTGAAGATTTGCGACTTTGGGCTTGCTCGAGTGTCCTTTAA

upper sequence: GLYMA07G11470.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G73670.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatccttgtaattaag-tccttgactgttgctg--atagtgataataaacta-----aaataacattt----tttcttgcagCAAATGTGTTTCATCGTGACTTGAAGCCAAAAAATATTCTAGCTAATGCTGATTGCAAGCTAAAATTATGTGATTTTGGACTTGCTCGAGTTTCATTTAA
||    || |||  |   || || |||  || |   ||  |||||  |   ||      |   || | |    ||  ||||||| |||||||||||||| || ||||| ||||| || ||||| |||||||||||||||||| | ||  | ||||| ||||| || ||||| || || |||||
gttagtttctaaacagtctctttcacttgtgttatcattatgatataaggttattgaagagctacgtctctgtttgtttgcagCGAATGTGTTTCATCGGGATTTGAAACCAAAGAACATTCTTGCTAATGCTGATTGCAAGTTGAAGATTTGTGACTTTGGTCTAGCTCGTGTATCTTTTAA

upper sequence: GLYMA07G11470.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 2
-----------------gtatccttg--taattaagtccttgactgt-tgctgatagtgataataaactaaaataacattttttcttgcagCAAATGTGTTTCATCGTGACTTGAAGCCAAAAAATATTCTAGCTAATGCTGATTGCAAGCTAAAATTATGTGATTTTGGACTTGCTCGAGTTTCATTTAA
                  |||  | |  | |     |  |||  | | ||     | ||   |  ||  |||||   ||  |||||| ||||||||||||||||||| || |||||||||||||||||||| |||||||| || |||||| | ||  | ||||||||||| |||||||| || ||||| ||
gttggtgcttttcagagatattatagcctcaccgtttgtttgcttttatgtcctgaatggccactaataaaaattttatggtttcttccagCAAATGTGTTTCATCGAGATTTGAAGCCAAAAAATATTCTTGCTAATGCCGACTGCAAGTTGAAGATTTGTGATTTTGGGCTTGCTCGGGTGTCATTCAA

upper sequence: GLYMA07G11470.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 2
---------------------------gtatcc--ttgtaattaagtccttgactgttgctgatag-tgataataaactaaaataacattttttcttgcagCAAATGTGTTTCATCGTGACTTGAAGCCAAAAAATATTCTAGCTAATGCTGATTGCAAGCTAAAATTATGTGATTTTGGACTTGCTCGAGTTTCATTTAA
                            ||     || | ||  | |   ||  |||  |   | | || | |    ||   ||     |  | |||  ||| ||||| |||||||| ||  | |||||||| ||| |  | || || |||||||||||||| ||| | |||||||||||||||||||| ||  | || | 
tgaaaatgtaactatatttcaagaagaatagtggattatgatctaatgaatgtgtgtctcgtttggatgttgacgtgcttctatttgggtgatgctt-tagCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTGATTGCAAGCTGAAAATTTGTGATTTTGGACTTGCTCGGGTGGCTTTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtccttgactgttgctgatagtgataataaactaaaataacattttttcttgcagCAAATGTGTTTCATCGTGACTTGAAGCCAAAAAATATTCTAGCTAATGCTGATTGCAAGCTAAAATTATGTGATTTTGGACTTGCTCGAGTTTCATTTAA
                                  aaataac  putative branch site (score: 2)
                                        cattttttctt  CT-rich tract
                 atagtgataataaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccttgtaattaagtccttgactgttgctgatagtgataataaactaaaataacattttttcttgcagCAAATGTGTTTCATCGTGACTTGAAGCCAAAAAATATTCTAGCTAATGCTGATTGCAAGCTAAAATTATGTGATTTTGGACTTGCTCGAGTTTCATTTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT