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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacactcttaattcattattgtcagaattctattaaaacttgtttgcattcctggttataacatggatcatgcaaacaatgaatattggtaatggaacagGTTTCAAATTGGTTCATAAATGCTCGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACTTGGAGGAGATGAAAGATCATGAACTAAATGGTTCTG

Basic information

species Glycine max
transcript GLYMA02G35450.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G35450.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g06020.1 (Oryza sativa), 3'ss of exon 4
---------------------tacactcttaattcatt-attgtcagaattctattaaaacttgtttgcattcctggttataaca-----tggatcatgcaaacaatgaatattggtaatggaacagGTTTCAAATTGGTTCATAAATGCTCGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACTTGGAGGAGATGAAAGATCATGAACTAAATGGTTCTG
                      |   | ||| |   || ||||   |  || |  |   |||   |    ||| |||||  |        || ||  ||  ||   |  || |||||       |||||||| || |||||||| |||||  | ||  |||| |||||||| ||||||||||| |||||| |||||||||  || || || ||       ||    |
gtcagaattaagatggagtttaatttttttactgtgttgattgattggtttttgattttactgcgtgttcttcttggttgaattgggtgttgaattttgtgaatttt--attttggtttgatttcagGTTTCGAACTGGTTCATCAATGCCAGGGTGAGGCTGTGGAAGCCGATGGTGGAGGAGATGTACCTGGAGGAGACCAAGGACCAGGACGGCGGCGGCGGCG

upper sequence: GLYMA02G35450.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G458728_T07 (Zea mays), 3'ss of exon 4
-----tacactcttaattcattattg--tcagaattctattaa--aacttgtttgcattcctggtta--taacatggatcatgcaaacaatgaatattggtaatggaacagGTTTCAAATTGGTTCATAAATGCTCGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACTTGGAGGAGATGAAAGATCATGAACTAAATGGTTCTG
     || |    | | || || ||   |    || ||   ||  || |||  ||  || |||| |   |||  |   |   | ||| |||   |  |     |     |||| || ||||||||||| |||||  | || ||||| |||||||| ||||||||||| |||||| |||||||||  || || || ||       ||    |
gtcggtaaagctgtgaatctttctttctttcttatcctgcgaatcaatttgactgttttactggcttcttaaattaacttccgaaaaaaattgttcctttctgt----tagGTGTCCAATTGGTTCATCAATGCGAGGGTGCGGCTGTGGAAGCCTATGGTGGAGGAGATGTACCTGGAGGAGACAAAGGACCAGGACGCTGGAGGCGGCG

upper sequence: GLYMA02G35450.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G35940.2 (Arabidopsis thaliana), 3'ss of exon 4
tacactcttaattcattattgtcagaattctattaaaacttgtttgcattcctggttataacatggatcatgcaaacaatgaatattggtaatggaacagGTTTCAAATTGGTTCATAAATGCTCGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACTTGGAGGAGATGAAAGATCATG--AACTAAATGGTTCTG
           | | || |    |  ||||| |      || || |  || ||    | | | |   | | | |||   | | | |   ||||     |||| || || ||||| ||||| ||  |||||||| | ||||| |||||||||||||| |||||| ||||||| ||||| || || |  ||  | ||||     
----------gtacgtt-tcaaaatgattctttcttgtgttattag-gttacttaagaaagcgttt-ttaagtaaat--ttattttctttaattatttagGTGTCGAACTGGTTTATAAACGCGAGAGTTCGGTTATGGAAACCAATGGTGGAGGAGATGTACATGGAGGAAATGAAGGAGCAGGCAAAGAACATGGGAT--

upper sequence: GLYMA02G35450.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0105g00230.t01 (Vitis vinifera), 3'ss of exon 11
tacactcttaattcattattgtcagaattctattaaaacttgtttgcattcctggttataa--catggatcatgcaaacaatgaatattggtaatggaacagGTTTCAAATTGGTTCATAAATGCTCGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACTTGGAGGAGATGAAAGATCATGAACTAAATGGTTCTG
               |    |  |||||  |        || ||||  |   || ||  |    ||||    |   ||| |   |  || || ||    ||||| || || ||||||||||||||||| ||||| || ||||||||||||||||| ||||||||| |||||||  | || || || |||   ||||| || |
--------------gtgcgcgctagaatcttg-----ggttttttgtgtctttgtttgcagattatgggaactctcaacca--gagctttgtgataatgcagGTGTCTAACTGGTTCATAAATGCTCGGGTTCGTCTCTGGAAGCCAATGGTGGAAGAAATGTACATGGAGGAAGTCAAGGACCACGAAGAGAATGGATCAG

upper sequence: GLYMA02G35450.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S220_67V6.1 (Physcomitrella patens), 3'ss of exon 4
tacactcttaattcattattgtcagaattctattaaaacttgtttgca--ttcctggttataa---catggatcatgcaaacaatgaatattggtaatggaacagGTTTCAAATTGGTTCATAAATGCTCGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACTTGGAGGAGATGAAAGATCATGAACTAAATGGTTCTG
      ||  | ||   |  |   |||   |   || |   ||   ||  |  | |   || |     || |||    |     ||   | | | |   || |||||||| ||||||||||| || || ||||| ||||| |||||||||||||| ||||| |||||| | |||||    |||||  |      | ||  | |||
-----cctccactccagaacgcttgaacagtgagaagatcagtcatcaggtagcagaaaatgaatatctgaatctacgatgttttgttgacttgcatgcgagcagGTTTCTAATTGGTTCATCAACGCACGAGTACGGCTGTGGAAGCCAATGGTAGAGGAGATGTACGTAGAGGAACAAAAAGAGTACCCTGGAGATCATACTG

upper sequence: GLYMA02G35450.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S258_6V6.1 (Physcomitrella patens), 3'ss of exon 4
tacactcttaattcattattgtcagaattctattaaaacttgtttgcattc--ctggttataacatggatcatgcaaacaatgaatattggtaatggaacagGTTTCAAATTGGTTCATAAATGCTCGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACTTGGAGGAGATGAAAGATCATGAACTAAATGGTTCTG
         |   |  | |||| | |  || | |       |   | ||     |  ||  |  |||| |      |   | |   | |  |     | ||||| || || |||||||| || || ||||||||  | |||||||||||||| |||||||||||| |||||||   ||||||  |      | ||  |||| 
ccagtatccagaacgcttttgttaaacatccacttttgtcagaggggatagaattacttgcag-atggcttgacagagttacgtg-acttctgtgaaatcagGTCTCTAACTGGTTCATCAACGCACGAGTTCGATTATGGAAGCCAATGGTAGAGGAAATGTACGTGGAGGAACAGAAAGAGTACTCCGAAGATCATTCTA

upper sequence: GLYMA02G35450.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ24138 (Selaginella moellendorffii), 3'ss of exon 6
tacactcttaattcattattgtcagaattctattaaaacttgtttgcattcctggttataacatggatcatgcaaacaatgaatattggtaatggaacagGTTTCAAATTGGTTCATAAATGCTCGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACTTGGAGGAGATGAAAGATCATGAACTAAATGGTTCTG-
                    ||  |   | ||  ||||   | ||   | |  ||      | ||  |  ||     ||       ||| |      ||||| || || ||||| || ||||| ||||| ||||| |||||||| ||||| |||||||||||   ||||||||| ||||| || || ||    |||   | 
--------------------gtgcgtgctttaaaaaaa---gcttttgtcctcggaagcttcttg--ttgtg-gcttaacttgctgtggaatctctgcagGTCTCCAACTGGTTTATTAATGCCCGAGTCCGGCTCTGGAAGCCTATGGTCGAGGAAATGTATCAGGAGGAGATTAAAGAGCAGGAGCTCGG-GGTGGCGT

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|19270212|gb|BM886468.1|BM886468
EST:     ACTCGGACAAACACATGCTTGCAAAACAAACAGGGCTCACCAGAAGCCAG                         GTTTCAAATTGGTTCATAAATGCTCGAGTTCGGCTTTGGAAGCCAATGGTG
genomic: ACTCGGACAAACACATGCTTGCAAAACAAACAGGGCTCACCAGAAGCCAGgtaacaccac ... aatggaacagGTTTCAAATTGGTTCATAAATGCTCGAGTTCGGCTTTGGAAGCCAATGGTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcattcctggttataacatggatcatgcaaacaatgaatattggtaatggaacagGTTTCAAATTGGTTCATAAATGCTCGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACTTGGAGGAGATGAAAGATCATGAACTAAATGGTTCTG
          ttataac  putative branch site (score: 2)
                            aaacaatgaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacactcttaattcattattgtcagaattctattaaaacttgtttgcattcctggttataacatggatcatgcaaacaatgaatattggtaatggaacagGTTTCAAATTGGTTCATAAATGCTCGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACTTGGAGGAGATGAAAGATCATGAACTAAATGGTTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA