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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagattcccatgtttatataagtaatgagcaatgaattcctgctgctttatcaagtcatagtaactggctcatttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG

Basic information

species Glycine max
transcript GLYMA07G01440.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 10
-------------------gttagatt-cccatgtttatataagta--atgagcaatgaattcctgctgctttatcaagtcatagtaactggctcatttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG
                   | |  ||   ||||  || | | || |  |||| |||| || |  | |  ||  |  || ||  | | |     |  ||  |       ||||| ||||||||||||||||||||||| |||||||||||||||||||| |||| ||| || ||||||||||| ||  ||||||||||||||||
gtaattctgtacatgttaagatgaataatccatacttctttgaggatcatgaacaataaactatttc-actggagtaactctgattcatgtattgcttcctgaaactgcagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAG

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 10
gttagattcccatgtttatataagtaatgagcaatgaattcctgct--gctttatcaagtcatagtaactggctcatttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG
|| |  || |     | |  | | | |||   ||    |   || |  |   | |||     || |  |  | | ||||  | ||   ||||| |||||| ||||||||||||||||||| ||||| || ||||| |||||||| ||||| |||||| | |||||| ||||||| ||||||||
gtgaagtttcg----taacctgaatgatggcaaaaatgtcaatgttaagacatgtcacaatctaatgccgtgttaatttcatcttttgcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 10
gttagattcccatgtttatataagtaatgagcaatgaattcctgctgctttatcaagtcatagtaactggctcatttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG
|| ||| |           || | |||  || |   |  |  ||       |   |  |||| |  || |||  |  | |  |   ||| | |||||| | ||||| || || ||||| ||||| || |||||||||||||| ||||| |||||| | | |||| |||||||||| ||  |
gtgagactttgtcaaccgaatgactaaaaagaagccatatgatg-------actgatacataat--ctagct-gtactctaattttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 10
gttagat-tcccatgtt-----tatataagtaatga------gcaatgaattcctgctgctttatcaagtcatagt--aactggctcat-ttttttttggc----cagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG
|| |  | | |||||||     || |||| | ||||      |     ||| | |    | |  |   |    ||   |||||   ||| | ||  ||||     ||| | |||||||||||||||||||| ||||||||||| || ||||||||||||| |||||||||||||||  | ||  |||||||||| |||||
gtaatttcttccatgttaagagtaaataattgatgattctttgtggacaatgcataacacatatttttgctggagccaaactgatccatgtgttacttggaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 10
gttagat-tcccatgtttatataagtaat--------------gagcaatgaattcctgctgctttatcaagtcatagtaactggctcatttttttttggc-----cagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG
|| |  | | ||||||| | |||| ||||              |  ||||||||  |   |  |||  |  |  |    | |||   ||| | ||  |        ||| | |||||||||||||||||||| |||||||| || || ||||||||||||| |||||||||||||||  | ||  |||||||||| |||||
gtaatttcttccatgttaagataaataattgatggttctttgtgcacaatgaatagcacatatttttgctgg--aacaaacctgatccatgtgttactcaaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G165418_T01 (Zea mays), 3'ss of exon 10
gttagattcccatgtttatataagtaatgagcaatgaattcctgctgctttatcaagtcatagtaactggctcatttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG
|| | |||| |     |  |||| |||  || ||   |||     || |  |  ||   |  |||| |   | || |   |     ||||| |||||| | || || ||||| |||||||| || ||||||||||| ||||| ||||| |||||| | |||||| |||||||||||||  |
gtgaaattctctcaactgaataattaaaaaggaagctatt-----tgatgaacaaaagtaatgtaattttatgatatcactactttcagCTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGG

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 10
gttagattcccatgtttatataagtaatgagcaatgaattcctgctgc-tttatcaagtcatagtaactggctcatttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG
  |  |||  | | |  || | | | |  |  || ||       |    | |         |  || |  |   |   | |||||  ||||||||||||||||| || || |||||||||||||| || |||||||| || || || || |||||| | | |||| ||||||||||||| ||
-gtgaattttcttatc-atctgaatgagaatgaaagagccgtatcaatatctgctgtaatctgatagcgtgggtaacatcttttg--cagCTTTGTGATTTATACGAGAACGATTCAATTTTTGACAAATTTGAGTGCTGCCTCAGCGGCGATGGACTCCATGTTGCAACTGGTTCTTATAG

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 12
gttagattcccatgtttatataagtaatgagcaatgaattcctgctgctttatcaagtcatagtaactggctcatttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG
|| || |||| |   || |   ||  ||      ||      || ||||||    | |  || |  ||   |  |  ||||     ||||| ||||||||||||||||||||||| || ||||| ||||| ||||||||| |||||||  |||| ||||| |   | || |||||||||||
gtcagtttcctaatattttgagagagatacatt-tggcgagttggtgctttgctgaatggtattccctttgtggtcatttt-----cagCTCTGTGATTTATATGAAAATGATTCCATCTTTGACAAGTTCGAGTGTTGTATAAGTGGCAATGGCTTGCGAGCAGCTACAGGTTCTTACAG

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
gttagattcccatgtttatataagtaatgagcaatgaattcctgctgctttatcaagtcatagtaactggctcatttttttttggc--cagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG
             | || | |  ||    | |  | | ||  || | || | |  |    ||   ||  | |   ||||    ||   ||||| || ||| ||||||||||||| || || |||||||| |||||||||||||| ||||| ||||||||| | ||  |||| |||||||||||
-------gtgagagcttctttctgtggc-atcttttatttgttgattctgtgttgaaagctaaccac--gttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 10
gttagattcccatgtttatataagtaatgagcaatg-aattcctgc--tgctttat-caagtcatagtaactg---gctcatttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG
|| || || |  |  | | | ||||  |   ||    || | || |  | || | | || |  |   | ||     | |  |||  || |  |||| | |||||||||||||||||||||||||| |||||||| ||||| |||||||| |||||||||||| |||||||  | || |||||||||||
gtgagcttgctttcctcagaaaagtcttacacagaacaacttctacattactctctgcatgctaattttaccctctgtttctttccttctctccagTTGTGTGATTTATATGAAAATGATTCAATCTTTGATAAATTTGAATGTTGTCTGAGTGGTGATGGAATGCGTGTAGCTACAGGTTCTTACAG

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S10_312V6.1 (Physcomitrella patens), 3'ss of exon 10
-------gttagattcccatgtttatataagtaatgagcaatgaa-ttcctgctgctttatcaagtcatagtaact-ggctcatttttttttggc--cagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG
        | || | |   ||    | |  || |  | || | ||  | ||  |  | |   |     ||  || |  |   |  ||| | || |  ||||||||||||||||| || |  || ||||| ||||| ||||||||||| || || ||||| |||||  |||| ||| | ||||||||||| ||
ttctgttatcagctgcaattgggattgtcggtgagaaacagttaagctactaattttgttcaatacagtaacaattcagtggagctttctgtgtctgcagCTTTGTGATTTATACGAGAGCGACTCAATATTTGACAAGTTTGAGTGCTGCCTTAGTGGAGATGGTCTGCGCGTTGCCACTGGTTCTTATAG

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 10
------gttagattcccat-gtttatataagtaatg--agcaatgaattcctgctgctttatcaagtcatagtaactggctcattttttt---ttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG
      || | |||  | | |   ||  || |  |     || ||||   |||| | ||  | ||    |  | ||    |   |||| |   ||   |||||||||||| | || || || || || ||||| || ||||||||||||||||| ||||| |||||   ||||||| ||||||||||||||||
agaaaggtcacattgtcttagccaattcaaatggtatcgacattgaagatctgcag-ttggtgaacatttgcttaccaattttattttataccttttacagCTTTGTGATCTCTACGAGAACGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCACGCGTGTTGCAACTGGTTCTTACAG

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 10
-------gttagattcccatgtttatataa-gtaatgagcaatgaatt-cctg-----ctgctttatcaag-tcatagtaactggctcatttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG
        | |  |     |  |    |||    ||||  | | | || || |      | ||||||  |  |  ||| ||||   ||   | ||||    |||||||||||| | ||||| || || || || || || |||||||| |||||||| ||||| |||||  |||||||  |||||||||| |||||
gcttcaaataatgtatagctagtggcttaatacgatgattagtcagttacccgagtgttttctttattgaacttgtagaaacta-ttcgcgtcttttg---cagCTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAG

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S301_53V6.1 (Physcomitrella patens), 3'ss of exon 10
-----------gttagattcccatgtttatataagtaatgagcaatgaattcctgctgctttatcaagtcatagtaac-tggctcatttttttttggc--cagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG
           ||||  ||    || |  |||  |   |  | | | ||   | || | |   |       || |||  |   |  |||| | | |    |||||||  |||||||| |||||||| || ||||| || ||||||||||||||||| ||||| |||||  |||||||  | |||||||| |||||
atcttattcgtgttatttttatctggtattattggc--ttggtattcaagatccgcaggtgc-tgggaatgtactaatataagttgttttgtatcgtttgcagCTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAG

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
----------gttagattcccatgtttatataagtaatgagcaa--tgaattcctgctgctt-tatcaag-tcatagtaactggctcatttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG
            || |     | |   |     | ||| ||     |   ||  ||  | || |||  |  ||| || || |  || |  ||||||||  ||||| |||||| | ||||| || |||||||| || |||||||||||||||||| | ||||| |||||  |||||||  |||||||||| |||||
cttcaatcaaaatataactgaaggcagaacaggggaattagttggttatgtttgtgtcgtttgtattgaactcacagaaatta-cttacgtttttttg--cagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaattcctgctgctttatcaagtcatagtaactggctcatttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG
                          tagtaac  putative branch site (score: 1)
                                    ctcattttttttt  putative PPT
                                     tcattttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagattcccatgtttatataagtaatgagcaatgaattcctgctgctttatcaagtcatagtaactggctcatttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA