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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcctccaataagtaatttgatgctagaatgtataaccatagaaagaagaggaactctatggccttgttgtatgcttgtttgtttgaccttcattttatcattgcagGGTTGATAGAAATAAATATCAGATTCAGATTCCTTTGCCTCCAAAAATTGATCCAAGTGTGACCATGATGACTGTTGAAGAGAAGCCAGATGTAACATAT

Basic information

species Glycine max
transcript GLYMA07G05220.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 5
----gtatgcctccaataagtaatttgatgctagaatgtataaccatagaaagaagaggaactctatggccttgttgtatgcttgtttgtttgaccttcattttatcattgcagGGTTGATAGAAATAAATATCAGATTCAGATTCCTTTGCCTCCAAAAATTGATCCAAGTGTGACCATGATGACTGTTGAAGAGAAGCCAGATGTAACATAT
     ||||||| | |||  | || |   | | | ||||   |   |   | |       |  |  ||  ||   |||||     ||  | | || || | |        |||| |||||| | || || || |||||||| ||||||||||| || |||||||| |||||||| ||||||||||| ||||| || || || ||||| ||||||
agtcatatgccttctata--tcatatatagtttgtatgtc--attgttctaggtctgttgaaccactgtactcactgtataa--attcatctcacgtttaat--------gcagTGTTGATCGGAACAAGTACCAGATTCAAATTCCTTTGCCACCCAAAATTGACCCAAGTGTTACCATGATGACAGTTGAGGAAAAACCTGATGTGACATAT

upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g09290.2 (Oryza sativa), 3'ss of exon 5
gtatgcctcca-ataagtaatttgatgctagaatgtataaccatagaaagaagaggaactctatggccttgttgtatgcttgtttgtttgaccttcattttatcattgcagGGTTGATAGAAATAAATATCAGATTCAGATTCCTTTGCCTCCAAAAATTGATCCAAGTGTGACCATGATGACTGTTGAAGAGAAGCCAGATGTAACATAT
       |||| ||| ||  ||||         ||| | |   |       | || || | |||   |   ||| ||  |   ||||||  | | |  | ||||||  ||| |||||| |||| || || || ||||| ||||||||||| ||||| |||||||| || || |||||||||||||| ||||| || |||||||| || || 
------ttccacatatgttgtttgcattgcacttgtgtgatgctgttcttga-agtaattatattatca-attggattgta--ttgtttctcatcctgtgtatcat-acagAGTTGATCGAAACAAGTACCAAATTCAAATTCCTTTGCCACCAAAGATTGATCCCAGCGTTACCATGATGACTGTGGAAGAAAAACCAGATGTGACTTAC

upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 5
gtatgcctccaataagtaatttgatgctagaatgtataaccatag--aaagaagaggaactctatggc-cttgttgtatgcttgtttgtttgaccttcattttatcattgcagGGTTGATAGAAATAAATATCAGATTCAGATTCCTTTGCCTCCAAAAATTGATCCAAGTGTGACCATGATGACTGTTGAAGAGAAGCCAGATGTAACATAT
            |  || ||||     |    |||   |  ||     ||  ||  ||||| | |  | | |  || |       || | | ||       || |  |||||| |||||| | || || || |||||||| || ||| | || ||||||||||| |||||||| |||||||||||||| || || ||||||||||| || || 
----------ttttggttatttctccatgtgttgtgctattattcccgaatgagttgaactgtttctcacctagtgaaaaaactattatctcact---ggattcttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGACCCAAGTGTTACCATGATGACTGTGGAGGAAAAGCCAGATGTGACGTAC

upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 5
gtatgcctccaataagtaatttg-atgctagaatgtataaccatagaaagaagaggaactctatggccttgttgtatgcttgtttgtttgaccttcattttatcattgcagGGTTGATAGAAATAAATATCAGATTCAGATTCCTTTGCCTCCAAAAATTGATCCAAGTGTGACCATGATGACTGTTGAAGAGAAGCCAGATGTAACATAT
       | |  | | |  | ||   |||    | | |    |  |||  |   | | || |     | |  || |  |||  |  | | ||    ||  |    |||||| |||||| | || || || |||||||| || ||| | || ||||||||||| |||||||| ||||||||||| || || || ||||||||||| || || 
-------ttcggttatttctctgcgcgctgtgctattt--ttaccgaataagttgaaccttttcccacctagtgaaaactttgtgatctcacacgtatgct--tgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGACCCAAGTGTTACCATGATGACCGTGGAGGAAAAGCCAGATGTGACGTAC

upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 5
gtatgcctccaataagtaatttgatgctagaatgtataaccatagaaagaagaggaactctatggccttgttgtatgcttgtttgtttgaccttcattttatcattgcagGGTTGATAGAAATAAATATCAGATTCAGATTCCTTTGCCTCCAAAAATTGATCCAAGTGTGACCATGATGACTGTTGAAGAGAAGCCAGATGTAACATAT
  ||||||  |  |||  || |  | |        ||||   | |   |  ||  || | |||    ||  ||| | ||||||||| | |||  |||  |  ||||||||||||||| ||||||||||||||||||| ||||| ||||| ||||| |||||||||||||| ||||||||||| || |||||||| || ||||| ||||||
-gatgccttta--aaggcatgtacttc-----ctcataatttttgt--ggtgaaaaaatttatttgtttaatgtgttcttgtttgtctcaccaacatgctgccattgcagGGTTGATCGAAATAAATATCAGATTCAAATTCCCTTGCCCCCAAAGATTGATCCAAGTGTAACCATGATGACAGTAGAAGAGAAACCGGATGTGACATAT

upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------------------------------------------gtatgcctccaataagtaatttgatgctagaatgtataaccatagaaagaagaggaactctatggccttgttgtatgcttgtttgtttgacctt------cattttat-cat-tgcagGGTTGATAGAAATAAATATCAGATTCAGATTCCTTTGCCTCCAAAAATTGATCCAAGTGTGACCATGATGACTGTTGAAGAGAAGCCAGATGTAACATAT
                                                                                  |  |||||   |   |        | |  | || |  | |  || ||| ||| ||    ||    || ||  | || | |     || || ||      |||  ||| ||| |||||||| |||||||| || ||||| || |||||||| |||||||| || ||||| || || || || |||||||| || || || ||||||||||| || || 
gtacgttttcttaacttctcgttctactttatactcggttcctgagtgagctgtattgatcatgtgaagataggtctctagttgggcctcacttgtctggacgttcgttttactgcagtatcgaaggaaggagatgatgattaaaagctggtattttgttcgagatgttaactttttcggtcataatatacatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGACCCCAGCGTTACAATGATGACAGTGGAGGAAAAGCCAGATGTCACCTAC

upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ29161 (Selaginella moellendorffii), 3'ss of exon 5
gtatgcctccaataagtaatttgatgctagaatgtataaccatagaaagaagaggaactctatggccttgttgtatgcttgtttgtttgaccttcattttatcattgcagGGTTGATAGAAATAAATATCAGATTCAGATTCCTTTGCCTCCAAAAATTGATCCAAGTGTGACCATGATGACTGTTGAAGAGAAGCCAGATGTAACATAT
                                                   |      | | |     |||| |     |   ||      ||   | ||   ||| ||| |||||||| || ||||||||||| || || |||||||| || || |||||||| || || || |||||||| || || |||||||| |||||||| || 
---------------------------------------------------gtatggtttttttcttatgttctcgatgtaaatgacatttctgtgtgtt-ctattacagTGTTGATAGGAACAAATATCAGATCCAAATACCTTTGCCCCCTAAGATTGATCCGAGCGTCACTATGATGACGGTGGAGGAGAAGCCCGATGTAACTTAC

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|207733086|gb|GD710938.1|GD710938
EST:     CTAGGAGACAAGGTTTCCCCCACTGACATAGAGGAAGGGATGCGTGTTGG                         GGTTGATAGAAATAAATATCAGATTCAGATTCCTTTGCCTCCAAAAATTGA
genomic: CTAGGAGACAAGGTTTCCCCCACTGACATAGAGGAAGGGATGCGTGTTGGgtatgcctcc ... atcattgcagGGTTGATAGAAATAAATATCAGATTCAGATTCCTTTGCCTCCAAAAATTGA
EST: gi|298168532|gb|HO009462.1|HO009462
EST:     CTAGGAGACAAGGTTTCCCCCACTGACATAGAGGAAGGGATGCGTGTTGG                         GGTTGATAGAAATAAATATCAGATTCAGATTCCTT
genomic: CTAGGAGACAAGGTTTCCCCCACTGACATAGAGGAAGGGATGCGTGTTGGgtatgcctcc ... atcattgcagGGTTGATAGAAATAAATATCAGATTCAGATTCCTT
EST: gi|192302201|gb|FG997281.1|FG997281
EST:     CTAGGAGACAAGGTTTCCCCCACTGACATAGAGGAAGGGATGCGTGTTGG                         GGTTGATAGAAATAAATATCAGATTCAGATTCCTTTGCCTTCAAAAATTGA
genomic: CTAGGAGACAAGGTTTCCCCCACTGACATAGAGGAAGGGATGCGTGTTGGgtatgcctcc ... atcattgcagGGTTGATAGAAATAAATATCAGATTCAGATTCCTTTGCCTCCAAAAATTGA
EST: gi|208236095|gb|GE030659.1|GE030659
EST:     C-AGGAGACAAGGTTTCCCCCACTGACATAGAGGAAGGGATGCGTGTTGG                         GGTTGATAGAAATAAATATCAGATTCAGATTCCTTTGCTTCCAAAAATTGA
genomic: CTAGGAGACAAGGTTTCCCCCACTGACATAGAGGAAGGGATGCGTGTTGGgtatgcctcc ... atcattgcagGGTTGATAGAAATAAATATCAGATTCAGATTCCTTTGCCTCCAAAAATTGA
EST: gi|193512879|gb|FK468649.1|FK468649
EST:     CTAGGAGACAAGGTTTCCCCCACTGACATAGAGGAAGGGATGCGTGTTAG                         GGTTGATAGAAGTAAATATCAGATTCAGATTCCTTTGCCTCCAAAAATTGA
genomic: CTAGGAGACAAGGTTTCCCCCACTGACATAGAGGAAGGGATGCGTGTTGGgtatgcctcc ... atcattgcagGGTTGATAGAAATAAATATCAGATTCAGATTCCTTTGCCTCCAAAAATTGA
EST: gi|16346898|gb|BI972493.1|BI972493
EST:     CTAGGAGACAAGGTTTCCCCCACTGACATAGAGGAAGGGATGCGTGTTGG                         GGTTGATAGAAATAAATATCAGATTCAGATTCCTTTGCCTCCAAAAATTGA
genomic: CTAGGAGACAAGGTTTCCCCCACTGACATAGAGGAAGGGATGCGTGTTGGgtatgcctcc ... atcattgcagGGTTGATAGAAATAAATATCAGATTCAGATTCCTTTGCCTCCAAAAATTGA
EST: gi|209711453|gb|BW665205.1|BW665205
EST:     CTAGGAGACAAGGTTTCCCCCACTGACATAGAGGAAGGGATGCGTGTTGG                         GGTTGATAGAAATAAATATCAGATTCAGATTCCTTTGCCTCCAAAAATTGA
genomic: CTAGGAGACAAGGTTTCCCCCACTGACATAGAGGAAGGGATGCGTGTTGGgtatgcctcc ... atcattgcagGGTTGATAGAAATAAATATCAGATTCAGATTCCTTTGCCTCCAAAAATTGA
EST: gi|193407658|gb|FK374476.1|FK374476
EST:     GGATGCGTGTTGG                         GGTTTGATAGAAATAAATATCAGATTCAGATTCCTTTGCCTCCAAAAATTG
genomic: GGATGCGTGTTGGgtatgcctcc ... atcattgcagGG-TTGATAGAAATAAATATCAGATTCAGATTCCTTTGCCTCCAAAAATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactctatggccttgttgtatgcttgtttgtttgaccttcattttatcattgcagGGTTGATAGAAATAAATATCAGATTCAGATTCCTTTGCCTCCAAAAATTGATCCAAGTGTGACCATGATGACTGTTGAAGAGAAGCCAGATGTAACATAT
                             gtttgac  putative branch site (score: 4)
                                         ttttatc  putative PPT
                                     ttcattttatcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcctccaataagtaatttgatgctagaatgtataaccatagaaagaagaggaactctatggccttgttgtatgcttgtttgtttgaccttcattttatcattgcagGGTTGATAGAAATAAATATCAGATTCAGATTCCTTTGCCTCCAAAAATTGATCCAAGTGTGACCATGATGACTGTTGAAGAGAAGCCAGATGTAACATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG