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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttccctttgcttattgcatcccttattctagattgtttgagaaacatttaacttcatagatatgtggttgtgtccttacaattgctcatggaatggacagAATGGTGATGCTGAAGATGGTAAGTCAAAGAAGCTTCAATATGAAGGTCCTGATCCTGAATTGGCTGCAATGCTTGAAAGGGACGTGTTAGAAACCTCTC

Basic information

species Glycine max
transcript GLYMA08G22210.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G22210.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g49000.1 (Oryza sativa), 3'ss of exon 2
ttccctttgcttattgcatcccttattctagattgtttgagaaacatttaacttcatagatatgtggttgtgt-----ccttacaattgctcatggaatgg--acagAATGGTGATGCTGAAGATGGTAAGTCAAAGAAGCTTCAATATGAAGGTCCTGATCCTGAATTGGCTGCAATGCTTGAAAGGGACGTGTTAGAAACCTCTC
     ||  ||| |  ||||| |     ||| ||   |     |  ||   ||  || |   |   |||   |     || |  | || || ||    |    ||||| | | ||||||||||| || ||||| ||||||   ||||||||||| || |||   || |||||||| |||||||||||||| ||  | ||  |  | |
-----ttatcttgtctcatccttctggataggtt--ctacagtatgttcttctatatggtggtcaagtttcttgaaaaccatgtattttcttattattttcttacagAGTAGCGATGCTGAAGAAGGCAAGTCCAAGAAGGGGCAATATGAAGGACCAGATATGGACTTGGCTGCCATGCTTGAAAGGGATGTCCTGGATTCTACCC

upper sequence: GLYMA08G22210.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G054715_T01 (Zea mays), 3'ss of exon 2
ttccctttgcttattgcatcccttattc--tagattgtttgagaaacatttaacttcatagatat-gtggttgtgt--ccttacaattgctcatggaatggacagAATGGTGATGCTGAAGATGGTAAGTCAAAGAAGCTTCAATATGAAGGTCCTGATCCTGAATTGGCTGCAATGCTTGAAAGGGACGTGTTAGAAACCTCTC
      ||||   ||  ||   ||       | ||||   |  |   | |    |  |  ||||  ||  |||      ||| |  || |   |    |    ||| | |||||||||| || |||||||| ||||||  |||||||||||| || |||   || || |||||||||||||||||||| ||  | ||  |  |||
-----attgccacttatatttttttgcgggcaaattgccagctactgactggcttctaatgataaagtttttgaaaaatcttccttttccaattcttttttctagAGTAGTGATGCTGAGGAAGGTAAGTCCAAGAAGGGTCAATATGAAGGGCCAGATATGGACTTAGCTGCAATGCTTGAAAGGGATGTTCTGGATTCTACTC

upper sequence: GLYMA08G22210.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G054715_T02 (Zea mays), 3'ss of exon 1
ttccctttgcttattgcatcccttattctagattgtttgagaaacatttaacttcatagatatgtggttgtgtccttacaattgctcatggaatggacagAATGGTGATGCTGAAGATGGTAAGTCAAAGAAGCTTCAATATGAAGGTCCTGATCCTGAATTGGCTGCAATGCTTGAAAGGGACGTGTTAGAAACCTCTC-----
  |   |   || ||||   |    | | || |    |||    | | |||    | || | |       | | | |        || |    |    ||| | |||||||||| || |||||||| ||||||  |||||||||||| || |||   || || |||||||||||||||||||| ||  | ||  |  |||     
cacttatatttttttgcgggcaaattgccagcta--ctgactggcttctaatgataaagtttttgaaaaatcttccttttccaattcttt---tttctagagtagTGATGCTGAGGAAGGTAAGTCCAAGAAGGGTCAATATGAAGGGCCAGATATGGACTTAGCTGCAATGCTTGAAAGGGATGTTCTGGATTCTACTCCAGGA

upper sequence: GLYMA08G22210.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G017305_T01 (Zea mays), 3'ss of exon 2
ttccctttgcttattgcatcccttattctagattgtttgagaaacatttaacttcatagatatgtggttgtgt----ccttacaattgctcatggaatggacagAATGGTGATGCTGAAGATGGTAAGTCAAAGAAGCTTCAATATGAAGGTCCTGATCCTGAATTGGCTGCAATGCTTGAAAGGGACGTGTTAGAAACCTCTC
      ||||   ||   |   |      | ||||   |  |   | ||   |  |  ||||| |  || ||      |||    || |   |    |   |||| | |||||||||| || |||||||| ||||||  ||| |||||||| || |||   || || |||||||||||||||||||| ||  | ||  |  |||
----aattgccagttatttttttgtgagcaaattgccagttactgaattgcttctaatgatatttttttttgaaaaatcttctttttccaactctgttttccagAGTAGTGATGCTGAGGAAGGTAAGTCCAAGAAGGGTCAGTATGAAGGGCCAGATATGGACTTAGCTGCAATGCTTGAAAGGGATGTTCTGGATTCTACTC

upper sequence: GLYMA08G22210.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G80350.1 (Arabidopsis thaliana), 3'ss of exon 2
-ttccctttgcttattgcatcccttatt-ctagattgtttgagaaacatttaacttcatagatatgtggttgtgtccttacaattgctcatggaatggacagAATGGTGATGCTGAAGATGGTAAGTCAAAGAAGCTTCAATATGAAGGTCCTGATCCTGAATTGGCTGCAATGCTTGAAAGGGACGTGTTAGAAACCTCTC
 ||     |  |       |  | | |   ||  |||  |  | |   |  | ||   |  |        |    | ||    || ||| | ||     ||||||||||||||||||||||| |||||||| | |      ||||| || ||||||   ||  ||||||| |||||||||||||| ||||| ||  |  |||
ctttagagtcatggccatgtttcctgtggttatgttgagtcggtagtttccacctattttcaacaactaataaaactttcggcttcctcgttgat--atcagAATGGTGATGCTGAAGATGGGAAGTCAAAAAGGGGATTGTATGAGGGACCTGATGAGGACCTGGCTGCTATGCTTGAAAGGGATGTGTTGGACTCAACTC

upper sequence: GLYMA08G22210.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0002g05260.t01 (Vitis vinifera), 3'ss of exon 2
---ttccctttgcttattgcatcccttattctagattgtttgagaaacatttaac-ttcatagatatgtggttgtgtccttacaattgctcatggaatggacagAATGGTGATGCTGAAGATGGTAAGTCAAAGAAGCTTCAATATGAAGGTCCTGATCCTGAATTGGCTGCAATGCTTGAAAGGGACGTGTTAGAAACCTCTC
   ||| |||||        |    | ||  ||  |||| ||     ||||| || ||||   |       || ||       | ||| |  || ||| |  |||||||||||||||||||||| || ||||||| |   || ||||| || |||||||| || ||||||||||||||||||||||| || || || ||    |
accttcactttgtaagaaataatagtgatg-taacttgtgtgt---tcatttgaccttcagttagtcaatattctgcttcctaatttgtttgtgtaattgctagAATGGTGATGCTGAAGATGGAAAATCAAAGAGGGCACAGTATGAGGGACCTGATCCAGACTTGGCTGCAATGCTTGAAAGGGATGTTTTGGAGACTAGCC

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|17024043|gb|BM095077.1|BM095077
EST:     CTTCTTCTGGAAAGGCTAGCAAGACAGATACTGCTGCTGCAGCTGTAACT                         AATGGTGATGCTGAAGATGGTAAGTCAAAGAAGCTTCAATATGAAGGTCCT
genomic: CTTCTTCTGGAAAGGCTAGCAAGACAGATACTGCTGCTGCAGCTGTAACTgtaagtttca ... gaatggacagAATGGTGATGCTGAAGATGGTAAGTCAAAGAAGCTTCAATATGAAGGTCCT
EST: gi|209717031|gb|BW654394.1|BW654394
EST:     CTTCTTCTGGAAAGGCTAGCAAGACAGATACTGCTGCTGCAGCTGTAACT                         AATGGTGATGCTGAAGATGGTAAGTCAAAGAAGCTTCAATATGAAGGTCCT
genomic: CTTCTTCTGGAAAGGCTAGCAAGACAGATACTGCTGCTGCAGCTGTAACTgtaagtttca ... gaatggacagAATGGTGATGCTGAAGATGGTAAGTCAAAGAAGCTTCAATATGAAGGTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttaacttcatagatatgtggttgtgtccttacaattgctcatggaatggacagAATGGTGATGCTGAAGATGGTAAGTCAAAGAAGCTTCAATATGAAGGTCCTGATCCTGAATTGGCTGCAATGCTTGAAAGGGACGTGTTAGAAACCTCTC
                           tccttac  putative branch site (score: 2)
          atagatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttccctttgcttattgcatcccttattctagattgtttgagaaacatttaacttcatagatatgtggttgtgtccttacaattgctcatggaatggacagAATGGTGATGCTGAAGATGGTAAGTCAAAGAAGCTTCAATATGAAGGTCCTGATCCTGAATTGGCTGCAATGCTTGAAAGGGACGTGTTAGAAACCTCTC

- -cctttgc
- - - - - - - -gcatccc
- - - - - - - - - - - - - - - - ttgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtggttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caattgc