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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTTGTCTGGGTATGATGAATATATTCCAATGGTAGACATACCTGTTGATGCTGGTTGGAAGAAGCAAGCATCTCTACAGAGGTCTTACACCTCTAAAGgttagtgacttatggcctagtatttattggtgtactcttcttattaatcctctcattattttcttattcactgaaaattaatccagttgtacaaatgctt...

Basic information

species Glycine max
transcript GLYMA06G01260.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G01260.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv03s0038g04470.t01 (Vitis vinifera), 5'ss of exon 12
AACTTGTCTGGGTATGATGAATATATTCCAATGGTAGACATACCTGTTGATGCTGGTTGGAAGAAGCAAGCATCTCTACAGAGGTCTTACACCTCTAAAGgttagtgacttatggcctagtatttat----tggtgtactcttcttattaatcct-ctcattattttcttattcactgaaa-attaatccagttgtacaaatgctt
| |||    ||||||||||||||| |||| ||||| |||| | |||||||||| |||||||||||||||||  |||| || ||| ||| | | || |||||||||| |  | |       |  | |     |||| |    ||   | || |  |  |||  |||| |  ||| |||      || ||    || | ||       
AGCTTCGGGGGGTATGATGAATATGTTCCCATGGTCGACAAAGCTGTTGATGCAGGTTGGAAGAAGCAAGCTGCTCTTCAAAGGCCTTCCTCATCCAAAGgttagtaagatctacttagatggtaaaaaaatggtttctgttttccaatatttatgttcaacatttaccaatttactccttcgttcatgtgattattcat------
















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|298198144|gb|HO039683.1|HO039683
EST:     TGCTGGTTGGAAGAAGCAAGCATCTCTACAGAGGTCTTACACCTCTAAAG                         GAGCACCTCCTCCTCTTGACACTCAGAAAACTCCTGATGGGCTTCAAGCTC
genomic: TGCTGGTTGGAAGAAGCAAGCATCTCTACAGAGGTCTTACACCTCTAAAGgttagtgact ... ttcaatacagGAGCACCTCCTCCTCTTGACACTCAGAAAACTCCTGATGGGCTTCAAGCTC
EST: gi|57575650|gb|CX548625.1|CX548625
EST:     TGCTGGTTGGAAGAAGCAAGCATCTCTACAGAGGTCTTACACCTCTAAAG                         GAGCACCTCCTCCTCTTGACACTCAGAAAACTCNTGATGGGCTTCAAGCTC
genomic: TGCTGGTTGGAAGAAGCAAGCATCTCTACAGAGGTCTTACACCTCTAAAGgttagtgact ... ttcaatacagGAGCACCTCCTCCTCTTGACACTCAGAAAACTCCTGATGGGCTTCAAGCTC
EST: gi|254335758|gb|GR847286.1|GR847286
EST:     TTGGAAGAAGCAAGCATCTCTACAGAGGTCTTACACCTCTAAAG                         GAGCACCTCCTCCTCTTGACACTCAGAAAACT-CTGATGGGCTTCAAGCTC
genomic: TTGGAAGAAGCAAGCATCTCTACAGAGGTCTTACACCTCTAAAGgttagtgact ... ttcaatacagGAGCACCTCCTCCTCTTGACACTCAGAAAACTCCTGATGGGCTTCAAGCTC
EST: gi|12490007|gb|BG043528.1|BG043528
EST:     TGCTGGTTGGAAGAAGCAAGCATCTCTACAGAGGTCTTACACCTCTAAAG                         GAGCACCTCCTCCTCTTGACACTCAGAAAACTCCTGATGGGCTTCAAGCTC
genomic: TGCTGGTTGGAAGAAGCAAGCATCTCTACAGAGGTCTTACACCTCTAAAGgttagtgact ... ttcaatacagGAGCACCTCCTCCTCTTGACACTCAGAAAACTCCTGATGGGCTTCAAGCTC
EST: gi|254335757|gb|GR847285.1|GR847285
EST:     TGCTGGTTGGAAGAAGCAAGCATCTCTACAGAGGTCTTACACCTCTAAAG                         GAGCACCTCCTCCTCTTGACACTCAGAAAACTCCTGATGGGCTTCAAGCTC
genomic: TGCTGGTTGGAAGAAGCAAGCATCTCTACAGAGGTCTTACACCTCTAAAGgttagtgact ... ttcaatacagGAGCACCTCCTCCTCTTGACACTCAGAAAACTCCTGATGGGCTTCAAGCTC
EST: gi|208240567|gb|GE035995.1|GE035995
EST:     TCTCTACAGAGGTCTTACACCTCTAAAG                         GAGCACCTCCTCCTCTTGACACTCAGAAAACTCCTGATGGGCTTCAAGCTC
genomic: TCTCTACAGAGGTCTTACACCTCTAAAGgttagtgact ... ttcaatacagGAGCACCTCCTCCTCTTGACACTCAGAAAACTCCTGATGGGCTTCAAGCTC
EST: gi|209697051|gb|BW667041.1|BW667041
EST:     TACACCTCTAAAG                         GAGCACCTCCTCCTCTTGACACTCAGAAAACTCCTGATGGGCTTCAAGCTC
genomic: TACACCTCTAAAGgttagtgact ... ttcaatacagGAGCACCTCCTCCTCTTGACACTCAGAAAACTCCTGATGGGCTTCAAGCTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACTTGTCTGGGTATGATGAATATATTCCAATGGTAGACATACCTGTTGATGCTGGTTGGAAGAAGCAAGCATCTCTACAGAGGTCTTACACCTCTAAAGgttagtgacttatggcctagtatttattggtgtactcttcttattaatcctctcattattttcttattcactgaaaattaatccagttgtacaaatgctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG