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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttccttggaatgtggaaagttgtcaactatctactatcttaattttttagcagctccctaagtttcaacttatttttatttatttatctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA

Basic information

species Glycine max
transcript GLYMA11G34840.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G34840.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g51220.1 (Oryza sativa), 3'ss of exon 4
-gttttccttggaatgtggaaagttgtcaa-ctatctactatcttaatt--ttttagcagctccctaagtttca-acttatttttatttatttatctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA
 ||| |  |   |||       ||| | |  ||    |||| ||||| |  | ||         || |   | | | ||  ||||  || |||   |  | | |||| ||||| ||||| ||||||||||| |||||||| |||||||||||||| |||||||||||||| || || |||  
agttataat--aaatcacctgtgttattagtctgatcactaacttaagtgctcttgtttatatgctgatcctgatagttgctttttcttgttt---tgttttcagGTGGCTGACTCACTTGAGAAAGGAACAGAACATGAGGATGAATACATGATTAGTGAAAAGGAGCTTCTTGTTAACCG

upper sequence: GLYMA11G34840.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G439457_T02 (Zea mays), 3'ss of exon 5
gttttccttggaatgtggaaagttgtcaactatctactatcttaattttttagcagctccctaagtttcaacttatttttatttatttatctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA
 |  |    || |  ||  ||  ||  |  |   |  ||||       ||      |    |   ||   | || |  |  ||  |||||     |  |||| ||||| ||||| || || ||||| ||||| || ||||||||||||||||||||||||||||| || || |||  
atggttgacggtaaatgttaacctgcgatattctttttatcactgaacttcgttcacatgattgtttcttaattctggtagttgctttattatgaaccagGTGGCTGACTCACTTGAAAAGGGAACAGAACACGAGGATGAATACATGATCAGTGAAAAGGAGCTTCTTGTTAACCG

upper sequence: GLYMA11G34840.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G439457_T01 (Zea mays), 3'ss of exon 5
gttttccttggaatgtggaaagttgtcaactatctactatcttaattttttagcagctccctaagtttcaacttatttttatttatttatctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA-----------------------
 |  |    || |  ||  ||  ||  |  |   |  ||||       ||      |    |   ||   | || |  |  ||  |||||     |  |||| ||||| ||||| || || ||||| ||||| || ||||||||||||||||||||||||||||| || || |||                         
atggttgacggtaaatgttaacctgcgatattctttttatcactgaacttcgttcacatgattgtttcttaattctggtagttgctttattatgaaccagGTGGCTGACTCACTTGAAAAGGGAACAGAACACGAGGATGAATACATGATCAGTGAAAAGGAGCTTCTTGTTAACCGGTTTGTGAACTTGTGTACTTCAT

upper sequence: GLYMA11G34840.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G58030.1 (Arabidopsis thaliana), 3'ss of exon 4
gttttccttggaatgtggaaagttgtcaactatctactatcttaattttttagcagctccctaagtttcaacttatttttatttatttatctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA
   |   | |  || |  ||     | |  | |  | | | |  ||      ||   | |||   ||  |||| |     | |||   | |      ||||||||||||||||| || |||||||| |||||||||||||| ||||||||||||||||||||||| || || |||| 
--gtgagtggcgatttcaaattcaattagttgttgagtgtttctatcgacatgcctgttcctggattctaactcac----acttaacgaacatgccatagGTTGCTGATTCACTTGAAAAAGGAACAGAACATGAAGATGAGTACATGATCAGTGAAAAGGAGCTTCTTGTTAACAG

upper sequence: GLYMA11G34840.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0037g00110.t01 (Vitis vinifera), 3'ss of exon 4
gttttccttggaatgtggaaagttgtcaactatctactatcttaattttttagcagctccctaagtttcaac-----ttatttttatttattt-atctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA
   |  |      | |  |    ||| ||  |       |  | | |||||| ||   || | |  | || |     ||||  || | ||||| || | ||||||||| ||||| ||||| |||||||| ||||| || ||||||||||||||||||||||| || |||||||| || || | 
---tggccatacttcttcatttctgttaa--aagaggcctgatgaatttttatca-tgccatgaaatgcagccatctttatcattttctatttgatatcatattagGTAGCTGACTCACTTGAGAAAGGTACTGAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAG

upper sequence: GLYMA11G34840.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S266_44V6.1 (Physcomitrella patens), 3'ss of exon 2
------gttttccttgg-aatgtggaaagttgtcaactatctactatcttaattttttagcagctccctaagtttcaacttatttttatttatttatctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA
      |  || ||    ||  |   |   | ||     | |   |  ||  | | |||   ||||||  |   | |   | |||   ||| ||   ||      ||||||| |||||  | ||||| || || |||||||||||||||||||||||||| || ||||| || || ||||||||
aacgtggcctttctgatcaagatactattatatcgtaggtttttcaattttgtgtgttaagtgctccc--acactgagactgtttgggttttttccact-----cagGTTGCGGATTCTTTAGAGAAGGGTACGGAACATGAAGATGAATACATGATCAGCGAGAAGGAACTGCTTGTAAACAA

upper sequence: GLYMA11G34840.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S303_47V6.1 (Physcomitrella patens), 3'ss of exon 4
gttttc--cttggaatgtggaa---agttgtcaactatctactatcttaattttt--------tagcagctcccta--agtttcaacttatttttatttattt---atctaatatta------gGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA
|||||   |||||    |   |   ||      |   | |  | ||| || ||||        ||   |   |  |  | | |||  | |||||  || ||||   || |  |||||      ||| || |||||  | || || || || |||||||||||||| |||||||||||||| |||||||| || || |||| 
gtttttaacttggcccttacgatcgagcctctgatagtttggtgtctcaagttttctcacatgtaattgactcgcactaatgtcatttcattttgtttcattttatattttgtattacactcagGTGGCAGATTCTTTAGAAAAGGGCACGGAACATGAAGATGAGTACATGATCAGTGAGAAGGAGCTTCTTGTTAACAG

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|254320117|gb|GR831033.1|GR831033
EST:     GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAG                         GTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
genomic: GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAGgtgagcttct ... ctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
EST: gi|151411948|gb|EV281759.1|EV281759
EST:     GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAG                         GTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
genomic: GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAGgtgagcttct ... ctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
EST: gi|207751764|gb|GD723645.1|GD723645
EST:     GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAG                         GTAGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
genomic: GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAGgtgagcttct ... ctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
EST: gi|208278600|gb|GE077931.1|GE077931
EST:     GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAG                         GTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
genomic: GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAGgtgagcttct ... ctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
EST: gi|151396616|gb|EV266493.1|EV266493
EST:     GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGAAAAG                         GTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
genomic: GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAGgtgagcttct ... ctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
EST: gi|151410774|gb|EV280589.1|EV280589
EST:     GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAG                         GTTGCTGATTCTCTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
genomic: GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAGgtgagcttct ... ctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
EST: gi|192320522|gb|FK011932.1|FK011932
EST:     GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAG                         GTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
genomic: GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAGgtgagcttct ... ctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
EST: gi|208134278|gb|GD931371.1|GD931371
EST:     GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAG                         GTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
genomic: GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAGgtgagcttct ... ctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
EST: gi|207701893|gb|GD683445.1|GD683445
EST:     GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAG                         GTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
genomic: GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAGgtgagcttct ... ctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
EST: gi|298191865|gb|HO035947.1|HO035947
EST:     GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAG                         GTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
genomic: GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAGgtgagcttct ... ctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
EST: gi|208256579|gb|GE057408.1|GE057408
EST:     GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAG                         GTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
genomic: GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAGgtgagcttct ... ctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
EST: gi|13477866|gb|BG507568.1|BG507568
EST:     GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAG                         GTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
genomic: GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAGgtgagcttct ... ctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
EST: gi|151405191|gb|EV275005.1|EV275005
EST:     GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAG                         GTTGCTGATTCACTGGAGAAAGGAACTGAACATGAGGATGAATACATGATC
genomic: GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAGgtgagcttct ... ctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
EST: gi|208221539|gb|GE018619.1|GE018619
EST:     GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAG                         GTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
genomic: GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAGgtgagcttct ... ctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
EST: gi|208098926|gb|GD891497.1|GD891497
EST:     TACAGTATGGAAAGTATTATTTGGAAAG                         GTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
genomic: TACAGTATGGAAAGTATTATTTGGAAAGgtgagcttct ... ctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
EST: gi|8286428|gb|BE023996.1|BE023996
EST:     GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAG                         GTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
genomic: GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAGgtgagcttct ... ctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
EST: gi|192320523|gb|FK011933.1|FK011933
EST:     GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAG                         GTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
genomic: GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAGgtgagcttct ... ctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
EST: gi|151412057|gb|EV281869.1|EV281869
EST:     GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAG                         GTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
genomic: GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAGgtgagcttct ... ctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
EST: gi|42723157|gb|CK769056.1|CK769056
EST:     GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAG                         GTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
genomic: GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAGgtgagcttct ... ctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
EST: gi|193492237|gb|FK455263.1|FK455263
EST:     GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAG                         GTTGCTAATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
genomic: GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAGgtgagcttct ... ctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
EST: gi|9987096|gb|BE661204.1|BE661204
EST:     GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAG                         GTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
genomic: GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAGgtgagcttct ... ctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
EST: gi|208134214|gb|GD927919.1|GD927919
EST:     GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAG                         GTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC
genomic: GTATTCTTTCTTTTGTACACAGTACAGTATGGAAAGTATTATTTGGAAAGgtgagcttct ... ctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttagcagctccctaagtttcaacttatttttatttatttatctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA
                                           atctaat  putative branch site (score: 3)
                                        tttatct  CT-rich tract
                taagtttcaacttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttccttggaatgtggaaagttgtcaactatctactatcttaattttttagcagctccctaagtttcaacttatttttatttatttatctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- -ttccttg
- - - - - gaatgtg
- - - - - - - - - - - -tgtcaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gctccct