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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgccgtgcataccctgatcttggacttgtcaactgtatttttaacacaaatttctgattcaagaatggtttcctactttcctttgttttgaattgcatagGCTGATGTTGATGGGAATGGAGTACTTGACTATGGAGAGTTTGTAGCTGTTACAATTCACTTGCAAAAAATGGAGAATGATGAGCATTTCCACAAAGCAT

Basic information

species Glycine max
transcript GLYMA06G20170.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G20170.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G18890.1 (Arabidopsis thaliana), 3'ss of exon 5
tgccgtgcataccctgatcttggacttgtcaactgtatttttaacacaaatttctgattcaagaatggtttcctactttcctttgttttgaattgcatagGCTGATGTTGATGGGAATGGAGTACTTGACTATGGAGAGTTTGTAGCTGTTACAATTCACTTGCAAAAAATGGAGAATGATGAGCATTTCCACAAAGCAT
 |   |  |  |  ||  |||   ||  | ||       || |       | ||||||  ||  || | |    | | |   | | |||||   ||  |||| ||||| ||||| |||||  | || || |||||||||||||||||||| | |||||||||||| || || ||||||||||| | |||| |   ||| |
-gtaatttaagcattgcccttat-ctgattaaagaccaattcagtgttcttctctgat--aaacatagctg--aaatctgtatggctttga--cgcgcagGCGGATGTCGATGGAAATGGGTTTCTGGATTATGGAGAGTTTGTAGCTGTGATAATTCACTTGCAGAAGATAGAGAATGATGAACTTTTCAAACTAGCTT

upper sequence: GLYMA06G20170.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G74740.1 (Arabidopsis thaliana), 3'ss of exon 5
tgccgtgcataccctgatcttggacttgtcaactgtatttttaacacaaatttc--tgattcaagaatggtttcctacttt----cctttgttttgaatt---gcatagGCTGATGTTGATGGGAATGGAGTACTTGACTATGGAGAGTTTGTAGCTGTTACAATTCACTTGCAAAAAATGGAGAATGATGAGCATTTCCACAAAGCAT
                || ||  ||     | |  | |  |||  |  | |||   ||||  ||  ||| ||  || || |    | |   ||    |||       |||| |||||| |||| ||||||    | |||||||||||||||||||| || | |||||||||||| || |||||||||||||||||||||    |||| |
------------gtaaatgttttaccaaata-ccatttccttatgaggatttttcttgatcaaacgatgtttatcttctctggtacttacattcatgattttgatgcagGCGGATGTTAATGGAAATGGATGCTTGGACTATGGAGAGTTTGTAGCAGTGATAATTCACTTGCAGAAGATGGAGAATGATGAGCATTTCAGACAAGCTT

upper sequence: GLYMA06G20170.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv17s0000g05520.t01 (Vitis vinifera), 3'ss of exon 5
--tgccgtgcataccctgatcttgg-acttgtcaactgtatttttaacacaaatttctga--ttcaagaatggtttcctactttcctttgttttgaattgcatagGCTGATGTTGATGGGAATGGAGTACTTGACTATGGAGAGTTTGTAGCTGTTACAATTCACTTGCAAAAAATGGAGAATGATGAGCATTTCCACAAAGCAT
  ||   |  ||    |||  || | |  |      |||   || |      | | | ||  || |   |  |  |  || |  | | ||   |    ||  ||||||||||| |||||||||||||| || || ||||||||||||||||| || |||||||||||||| |  ||||||||||||||||||||||| | ||| |
cctgttatttattttatgacattagcagatagtccttgtgaattgag---ggactcccgacttttattcacagaataataataccttgtgaacttg--tggttagGCTGATGTGGATGGGAATGGAGTCCTGGATTATGGAGAGTTTGTAGCAGTGACAATTCACTTGCAGAGGATGGAGAATGATGAGCATTTCCAAAGAGCTT

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|58025159|gb|CX711900.1|CX711900
EST:     GTTCACAATTGGCTGAGCCAGAGATAAAGATGCTGATGGAAGTG                         GCTGATG-TGATGGGGAATGGAGTACTTGACTATGGAGAGTTNGTAGCTGT
genomic: GTTCACAATTGGCTGAGCCAGAGATAAAGATGCTGATGGAAGTGgtaaatttct ... aattgcatagGCTGATGTTGAT-GGGAATGGAGTACTTGACTATGGAGAGTTTGTAGCTGT
EST: gi|151396725|gb|EV266598.1|EV266598
EST:     AGGTTGGTTCACAATTGGCTGAGCCAGAGATAAAGATGCTGATGGAAGTG                         GCTGATGTTGATGGGAATGGAGTACTTGACTATGGAGAGTTTGTAGCTGTT
genomic: AGGTTGGTTCACAATTGGCTGAGCCAGAGATAAAGATGCTGATGGAAGTGgtaaatttct ... aattgcatagGCTGATGTTGATGGGAATGGAGTACTTGACTATGGAGAGTTTGTAGCTGTT
EST: gi|14258897|gb|BG881805.1|BG881805
EST:     AGGTTGGTTCACAATTGGCTGAGCCAGAGATAAAGATGCTGATGGAAGTG                         GCTGATGTTGATGGGAATGGAGTACTTGACTATGGAGAGTTTGTAGCTGTT
genomic: AGGTTGGTTCACAATTGGCTGAGCCAGAGATAAAGATGCTGATGGAAGTGgtaaatttct ... aattgcatagGCTGATGTTGATGGGAATGGAGTACTTGACTATGGAGAGTTTGTAGCTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaatttctgattcaagaatggtttcctactttcctttgttttgaattgcatagGCTGATGTTGATGGGAATGGAGTACTTGACTATGGAGAGTTTGTAGCTGTTACAATTCACTTGCAAAAAATGGAGAATGATGAGCATTTCCACAAAGCAT
      ttctgat  putative branch site (score: 3)
                                        ttttgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgccgtgcataccctgatcttggacttgtcaactgtatttttaacacaaatttctgattcaagaatggtttcctactttcctttgttttgaattgcatagGCTGATGTTGATGGGAATGGAGTACTTGACTATGGAGAGTTTGTAGCTGTTACAATTCACTTGCAAAAAATGGAGAATGATGAGCATTTCCACAAAGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
tgccgtg
- - - -cataccc
- - - - - - - - - cttggac
- - - - - - - - - - - - - - -caactgt
- - - - - - - - - - - - - - - - - - - - - -acacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -ctgattc