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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccatccttattctcaagtaaatgtattctgttttactttaactcttcaaataatttacagaaatgtcattttactttcactttgattctattttcaaacatacgtataagctctccgtacaagtctatgaaaacaagaaacaaagttctggcattgattaatctcccaaattgtacttatttgttgtctttgttagGTTGAAAATCAAGAGGGTGTTGCAAATTTTGATGAAATACTGGAAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG

Basic information

species Glycine max
transcript GLYMA16G26830.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G26830.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g20880.1 (Oryza sativa), 3'ss of exon 2
gtatccatccttattctcaagtaaatgtattctgttttactttaactcttcaaataatttacagaaatgtcattttactttcactttgattctattttcaaacatacgtataagctctccgtacaagtctatgaaaacaagaaacaaagttctggcattgattaatctcccaaattgtacttatttgttgtctttgttagGTTGAAAATCAAGAGGGTGTTGCAAATTTTGATGAAATACTGGAAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG
                                                                                                                             ||| | |    ||| |    | |  | ||  |||   |  |   |  |||  |  |    |||| | ||   ||||||||||||||||| |||||||| ||| ||||||| ||| | | |||||||||||| |||||||| |||||||| ||  |||||||||| || |||||||
--------------------------------------------------------------------------------------------------------------------------gttagtttctctttacatgctttacacatttgttattatatgttgatcttaatc-tgttatgatgtttttttgtgtagGTTGAAAATCAAGAAGGTGTTGCTAATGTTGATGAGATAATTGCAAATTCAGATGCTTTCATGGTTGCAAGAGGAGATTTGGGAATGGAGATCCCAATTG

upper sequence: GLYMA16G26830.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g16960.1 (Oryza sativa), 3'ss of exon 2
gtatccatccttattctcaagtaaatgtattctgttttactttaactcttcaaataatttacagaaatgtcattttactttcactttgattctattttcaaacatacgtataagctctccgtacaagtctatgaaaacaagaaacaaagttctggcattgattaatctcccaaattgtacttatttgttgtctttgttagGTTGAAAATCAAGAGGGTGTTGCAAATTTTGATGAAATACTGGAAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG
                                                                                                                        ||| ||   | |       || |    | ||||    |  | |  |  |  | ||| ||   || | |||  ||| | ||||||| ||||||||||| || || || |||||||| || |||| | | || ||||| || ||||| ||||| |||||  |||||||||||||||| || |
------------------------------------------------------------------------------------------------------------------------gtataacattctcttt-tgagtattgcacttctaagctgcact--ttgcaaagatttta---atctattgaattt-tcagGTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCTGATGCTTTTATGGTTGCAAGGGGTGATTTGGGAATGGAAATTCCGATAG

upper sequence: GLYMA16G26830.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G003883_T01 (Zea mays), 3'ss of exon 2
gtatccatccttattctcaagtaaatgtattctgttttactttaactcttcaaataatttacagaaatgtcattttactttcactttgattctattttcaaacatacgtataagctctccgtacaagtctatgaaaacaagaaacaaagttctggcattgattaatctcccaaattgtacttatttgttgtctttgttagGTTGAAAATCAAGAGGGTGTTGCAAATTTTGATGAAATACTGGAAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG
                                                                                                                        || | ||  | |        |   ||||   || | |    || |  | | |  || || || |||  ||    ||  ||||||| ||||||||||| || || || |||||||| || |||| ||| || ||||| || |||||||||||||||||  | |||||||||||||| || |
-------------------------------------------------------------------------------------------------------------------gtatggttctagcattttcttttgggtttcaaa---ctagtagattttcaaattcaaggttataattgttt--tgaacatgc-agGTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCTGATGCTTTTATGGTGGCAAGAGGTGATTTAGGAATGGAAATTCCTATAG

upper sequence: GLYMA16G26830.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G26390.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatccatccttattctcaagtaaatgtattctgttttactttaactcttcaaataatttacagaaatgtcattttactttcactttgattctattttcaaacatacgtataagctctccgtacaagtctatgaaaacaagaaacaaagttctggcattgattaatctcccaaattgtacttatttgttgtctttgttagGTTGAAAATCAAGAGGGTGTTGCAAATTTTGATGAAATACTGGAAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG
                                                                                                       | |  ||||    |  |   |||    ||  |||  | | |   |          |  | |   ||  |   | |  ||| || |||   |||| |||||||||| ||||| ||||| || ||||||||||| ||  ||  ||| || ||||| || ||| | |||||||||||||| |||||||| ||||||||||
-----------------------------------------------------------------------------------------------------gtacatatatacatacatcactcaaactaatataaatcacatatcca----------tactcagattcttatgatatg-ttactt-ttgatattgtcagGTTGAAAACCAAGAAGGTGTAGCGAATTTTGATGATATCTTGATAAACTCGGATGCGTTTATGATCGCAAGAGGTGACCTTGGAATGGAGATTCCAATTG

upper sequence: GLYMA16G26830.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0007g07600.t01 (Vitis vinifera), 3'ss of exon 2
gtatccatccttattctcaagtaaatgtattctgttttactttaactcttcaaataatttacagaaatgtcattttactttcactttgattctattttcaaacatacgtataagctctccgtacaagtctatgaaaacaagaaacaaagttctggcattgattaatctcccaaat-tgtacttatttgttgtctttgttagGTTGAAAATCAAGAGGGTGTTGCAAATTTTGATGAAATACTGGAAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG
                                                                                                                            | ||  | |    |||  |||   |||   | |||      | |   ||   | |   || || |    ||||  ||||||||||||||||||||||||| |||||||||||||| || | ||| ||||||||||| |||||||| || |||||||| ||||||||||| || ||||
--------------------------------------------------------------------------------------------------------------------------gtatgttga-ggttgcaaagaactctgttgaagtatttgcatttttgggaaggatatgactaattttgtgatttggcagGTTGAAAATCAAGAGGGTGTTGCTAATTTTGATGAAATTCTTGCAAACTCAGATGCATTTATGGTGGCCAGGGGTGACCTTGGAATGGAAATCCCCATTG

upper sequence: GLYMA16G26830.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S124_70V6.2 (Physcomitrella patens), 3'ss of exon 3
gtatccatccttattctcaagtaaatgtattctgttttactttaactcttcaaataatttacagaaatgtcattttactttcactttgattctattttcaaacatacgtataagctctccgtacaagtctatgaaaacaagaaacaaagttctggcattgattaatctcccaaattgtacttatttgttgtctttgttagGTTGAAAATCAAGAGGGTGTTGCAAATTTTGATGAAATACTGGAAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG
                                                                        |||||||  || | |||  |   ||| |||      | | |     ||       |||||  ||| ||  | |||| || || |     || |||   |            |||| | |||    |||||||| ||||| || ||| | |  || || ||||| ||| || || |  |||| | | |||||||||||||||| |||||||||||||| ||||| |  |
----------------------------------------------------------------------ggttttact--cagtatgagacaggtttaaaat---tatgtgattctgcc-------tctattcaaagaatca-caaaattgtgtc-----ttgatcctgc------------tttgatttctaccatagGTTGAGAATCAGGAAGGTCTGGTGAACTTCGATGACATATTGAAAGAGACAGACGGAGTCATGGTGGCAAGAGGGGACCTGGGAATGGAGATTCCTACGG

upper sequence: GLYMA16G26830.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S90_133V6.1 (Physcomitrella patens), 3'ss of exon 3
gtatccatccttattctcaagtaaatgtattctgttttactttaactcttcaaataatttacagaaatgtcattttactttcactttgattctattttcaaacatac-gtataagctctccgtacaagtctatgaaaacaagaaacaaagttctggcattgattaatctcccaaattgtacttatttgttgtctttgttagGTTGAAAATCAAGAGGGTGTTGCAAATTTTGATGAAATACTGGAAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG
                                                                                            ||||    || ||    |  ||||  |   | ||  ||     | ||   ||| |   |     |||   ||  |        ||||    ||  |   ||  ||  ||||||| || || || ||| | |  || || || || ||| ||  | | || |||| | |||||||||| |||||||||||||| ||||| |||||||  |
------------------------------------------------------------------------------------------cttattgcggaagatcttatcgaagccttagctgcatttc-----acactgaaaata---tcaacacatccgtttgttgtgggtgttgtttgaatcgg--atcaatgc-agGTTGAGAACCAGGAAGGTCTGGTCAACTTCGACGATATATTGAGAGAGTCGGATGGAGTCATGGTGGCTAGAGGTGACCTGGGTATGGAGATTCCAACAG

upper sequence: GLYMA16G26830.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S90_134V6.1 (Physcomitrella patens), 3'ss of exon 3
gtatccatccttattctcaagtaaatgtattctgttttactttaactcttcaaataatttacagaaatgtcattttactttcactttgattctattttcaaacatacgtataagctctccgtacaagtctatgaaaacaagaaacaaagttctggcattgattaatctcccaaattgtacttatttgttgtctttgttagGTTGAAAATCAAGAGGGTGTTGCAAATTTTGATGAAATACTGGAAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG
                                                                                     |||  |  |   ||||   | ||   || ||||       |   |    ||||   | | |||    |  || ||     | ||||||      |||| || |    ||||  |||| || || || || ||| | |  || || || || ||| || || |  | |||| | |||||||||| |||||||||||||| ||||| |||||||  |
-------------------------------------------------------------------------------------ttg--tgcaaaatcaacattccgaccaatctcttgtcgtgatatttctgaaaccgtagaaaaa---ttaacaatg-----tgtcccaaccctgccttaattat----tttga-agGTCGAGAACCAGGAAGGTCTGGTCAACTTCGACGATATATTGAAAGAGACGGATGGAGTCATGGTGGCCAGAGGTGACCTGGGTATGGAGATTCCAACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagttctggcattgattaatctcccaaattgtacttatttgttgtctttgttagGTTGAAAATCAAGAGGGTGTTGCAAATTTTGATGAAATACTGGAAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG
              gattaat  putative branch site (score: 3)
                                          ttgtcttt  putative PPT
                          aaattgtacttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccatccttattctcaagtaaatgtattctgttttactttaactcttcaaataatttacagaaatgtcattttactttcactttgattctattttcaaacatacgtataagctctccgtacaagtctatgaaaacaagaaacaaagttctggcattgattaatctcccaaattgtacttatttgttgtctttgttagGTTGAAAATCAAGAGGGTGTTGCAAATTTTGATGAAATACTGGAAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG