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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaccatatcatgatccatgctatatatagtgcacttcaactacataaagttatatcctgttacatatatgaatttagccatatgggctttcctatggtagGTTCCTATTGGAGGAGCTTACAGGCTCATTGATGTGCCAATGAGTAACTGCATCAACAGTGGTATCAACAAGGTGTATATCCTCACCCAGTTTAACTCTG

Basic information

species Glycine max
transcript GLYMA07G38820.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G38820.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g52460.1 (Oryza sativa), 3'ss of exon 2
-------aaccatatcatgatccatgctatatatagtgcacttcaactacataaagttatatcctgttacatatatgaatttagccatatgggctttc-ctatggtagGTTCCTATTGGAGGAGCTTACAGGCTCATTGATGTGCCAATGAGTAACTGCATCAACAGTGGTATCAACAAGGTGTATATCCTCACCCAGTTTAACTCTG
        | | ||  |  | |   |     |   |    ||||  |  || ||  ||             || ||    | |    | |    |||  | || | |||| || ||||| ||||| |||||||| || || ||||| ||||| |||||||| ||||| || |||||||||||||| || ||||||||||| ||||| |
gtgagtacagcgtacaaacaccttagtcccgtcgcggtttcttctgccgcaaaagattcagcaaatgcgagtaaattgtctcatggttgttaatttttgccattgcagGTGCCCATTGGCGGAGCGTACAGGCTGATCGACGTGCCGATGAGCAACTGCATAAACAGCGGCATCAACAAGGTGTACATTCTCACCCAGTTCAACTCCG

upper sequence: GLYMA07G38820.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G391936_T03 (Zea mays), 3'ss of exon 2
---------------------------------------------------aaccatatcatgatccatgctatatatagtgcacttcaactacataaagttatatcctgttacatatatgaatttagccatatgggctttcctatggtagGTTCCTATTGGAGGAGCTTACAGGCTCATTGATGTGCCAATGAGTAACTGCATCAACAGTGGTATCAACAAGGTGTATATCCTCACCCAGTTTAACTCTG
                                                   ||  | |  |  |||  || |  |    ||    |  ||  |  |||| |  |    ||  | | |  || |  |   |||  |  | |    ||   |||| || ||||| || || ||||||||||| || ||||| ||||| |||||||| ||||| || ||||||||||| || |||||||| ||||| |||||  
gtgagtgcgtgccagtatgccattagttcagtagttcttcatttttttttaaaaaaaactacaatc--tggtgcagtcggttgtgtctaaggatttaaattcgtggattgggagacacgtgtagct---catccgttcctctgcatttcagGTGCCAATTGGCGGCGCGTACAGGCTCATCGACGTGCCGATGAGCAACTGCATAAACAGCGGGATCAACAAGGTCTACATCCTCACGCAGTTCAACTCGC

upper sequence: GLYMA07G38820.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0020g02880.t01 (Vitis vinifera), 3'ss of exon 2
aaccatatcatga-tccatgctatatatagtgcacttcaactacataaagttatatcctgttacatatatgaatttagccatatgggctttcctatggtagGTTCCTATTGGAGGAGCTTACAGGCTCATTGATGTGCCAATGAGTAACTGCATCAACAGTGGTATCAACAAGGTGTATATCCTCACCCAGTTTAACTCTG
          | | ||||   |  |   | ||     ||  |   |  |   | || |   ||  | ||| |||||||  | |||||  |    || |||||| || ||||||||  | || ||||| ||||||||||||||||| ||||||||||||||||| ||||||||||| || || ||||| || || || || |
---------gtaagtccactttggaagcaatgtggggcatttttttttatacagattccaataggtttat-aatttaga-aaatgggtgt----attgtagGTCCCGATTGGAGGGTCATATAGGCTGATTGATGTGCCAATGAGCAACTGCATCAACAGTGGAATCAACAAGGTCTACATTCTCACTCAATTCAATTCAG

upper sequence: GLYMA07G38820.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S237_47V6.1 (Physcomitrella patens), 3'ss of exon 2
--aaccatatcatgatccatgctatatatagtgcacttcaactacataaagt-tatatcctgttacatatatgaatttagccatatgggctttcctatggtagGTTCCTATTGGAGGAGCTTACAGGCTCATTGATGTGCCAATGAGTAACTGCATCAACAGTGGTATCAACAAGGTGTATATCCTCACCCAGTTTAACTCTG
   ||| | |  ||     ||  || | ||||  |   |   | || ||  | | | |  ||  ||  |  |||  | |      |  |  |   ||   ||||| ||  | || || || ||| | || ||||||||||| ||||| |||||||||||||| || ||||||||| | ||  | || || ||||| || ||  
aacaccttttggtgcgaattgagatctgtagtagagggcttgttcacaatttctctgtgatgggacccaactga--tcaattgagtttgtatctgta-attagGTGCCGCTCGGCGGCGCCTACCGACTGATTGATGTGCCGATGAGCAACTGCATCAACAGCGGAATCAACAAGATCTACGTTCTTACGCAGTTCAATTCCA

upper sequence: GLYMA07G38820.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S2_204V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------------------------------------------------------------------aaccatatcatgatccatgctatatatagtgcacttcaactacataaagttatatcctgttacatatatgaatttagccatatgggctttcctatggtagGTTCCTATTGGAGGAGCTTACAGGCTCATTGATGTGCCAATGAGTAACTGCATCAACAGTGGTATCAACAAGGTGTATATCCTCACCCAGTTTAACTCTG
                                                                                                 |  ||||  ||| |  |  ||   |||| |     |  ||    | ||  |  | |||| |   |  |      |  |  ||      |   ||| | |||| || |||||||| |  ||| || | ||||||||||| ||||||||||| ||||| || || |||||||| || |  ||||||||||| || |||||  
gtaagccccttaacacatcctagaatttgtgtttgcaaactcttctctgaagctttgtcttcttcaatttgttgatgcttgtttgaaaacaaactagacgcatagaatgttaaaacctcattataat-tttattgacagtgtgaa--tgaaccctggttagtgaaaactcgtgactgtaattttgtatgtattgcagGTGCCAATTGGAGGTGGCTACCGGTTAATTGATGTGCCCATGAGTAACTGTATCAATAGCGGAATCAACAAAGTTTTCATCCTCACCCAATTCAACTCCA

upper sequence: GLYMA07G38820.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S175_26V6.1 (Physcomitrella patens), 3'ss of exon 2
---aaccatatcatgatccatgctatatatagtgcacttcaactacataaagttatatcctgttacatatatgaatttagccat-atgggctttcctatggtagGTTCCTATTGGAGGAGCTTACAGGCTCATTGATGTGCCAATGAGTAACTGCATCAACAGTGGTATCAACAAGGTGTATATCCTCACCCAGTTTAACTCTG
    |  | |  ||  |  |  |||| |||     |   ||  | ||| || || ||   | |  |  | ||    |||  ||| ||      |  |   | |||| || ||||||||||  ||  | || |||||||| || ||||||||||||||||||||||| ||||||||  | |  || || || || || || || |
tctgattaga--attttttactctatttattacttatagcagat-catgaatttgtaatttat-gcccacattttgttatacatcattcatacttttggtgcagGTGCCGATTGGAGGAGGATATCGACTGATTGATGTTCCTATGAGTAACTGCATCAACAGTGGCATCAACAAAATCTTCATTCTTACTCAATTCAATTCGG

upper sequence: GLYMA07G38820.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ28514 (Selaginella moellendorffii), 3'ss of exon 2
aaccatatcatgatccatgctatatatagtgcacttcaactacataaagttatatcctgttacatatatgaatttagccatatgggctttcctatggtagGTTCCTATTGGAGGAGCTTACAGGCTCATTGATGTGCCAATGAGTAACTGCATCAACAGTGGTATCAACAAGGTGTATATCCTCACCCAGTTTAACTCTG
                              | |    |||        ||| | | |   |    |||| |  ||   | |   ||| |    |    |||| || |||||||| |||||||| || ||||| ||||||||||| || ||||||||||| || || |||||  | |  |||||||| ||||||||||| |
------------------------------gtaagaaaacgcttcttcgttgtctgccaattttaatataatgttgctctt---ggcatgttcactacagGTACCAATTGGAGGCGCTTACAGACTTATTGACGTGCCAATGAGCAATTGCATCAACAGCGGAATAAACAAAATCTTCATCCTCACTCAGTTTAACTCGG

upper sequence: GLYMA07G38820.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ30406 (Selaginella moellendorffii), 3'ss of exon 2
-----------------------------------------------------aaccatatcatgatccatgctatatatagtgcacttcaactacataaagttatatcctgttacatatatgaatttagccatatgggctttcctatggtagGTTC-----------CTATTGGAGGAGCTTACAGGCTCATTGATGTGCCAATGAGTAACTGCATCAACAGTGGTATCAACAAGGTGTATATCCTCACCCAGTTTAACTCTG
                                                                                                                                               |   ||| | ||||           | |||||||| |||||||| || ||||| ||||||||||| || ||||||||||| || || |||||  | |  |||||||| ||||||||||| |
gtaagaaaacgcttcttcgttgtctgccaattttaatataatgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnctcttggcatgttcactacagGTACCAATTGGAGGCGCTTACAGACTTATTGACGTGCCAATGAGCAATTGCATCAACAGCGGAATAAACAAAATCTTCATCCTCACTCAGTTTAACTCGG

upper sequence: GLYMA07G38820.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ04435 (Selaginella moellendorffii), 3'ss of exon 1
aaccatatcatgatccatgctatatatagtgcacttcaactacataaagttatatcctgttacatatatgaatttagccatatgggctttcctatggtagGTTCCTATTGGAGGAGCTTACAGGCTCATTGATGTGCCAATGAGTAACTGCATCAACAGTGGTATCAACAAGGTGTATATCCTCACCCAGTTTAACTCTG
                              | |    |||        ||| | | |   |    |||| |   | |   | | | | |    |    |||| || |||||||| |||||||| || ||||| ||||||||||| || ||||||||||| || || |||||  | |  |||||||| ||||||||||| |
------------------------------gtaagaaaacgcttcttcgttgtctgccaattttaatataa---tggtgctcttgacatgttcactacagGTACCAATTGGAGGCGCTTACAGACTTATTGACGTGCCAATGAGCAATTGCATCAACAGCGGAATAAACAAAATCTTCATCCTCACTCAGTTTAACTCGG

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|151404121|gb|EV273931.1|EV273931
EST:     GAGCTGGAACCCGTCTCTTCCCTCTTACTAAGCGACGAGCCAAACCTGCT                         GTTCCTATTGGAGGAGCTTACAGGCTCATTGATGTGCCAATGAGTAACTGC
genomic: GAGCTGGAACCCGTCTCTTCCCTCTTACTAAGCGACGAGCCAAACCTGCTgtaagtttct ... cctatggtagGTTCCTATTGGAGGAGCTTACAGGCTCATTGATGTGCCAATGAGTAACTGC
EST: gi|7283824|gb|AW596426.1|AW596426
EST:     GAGCTGGAACCCGTCTCTTCCCTCTTACTAAGCGACGAGCCAAACCTGCT                         GTTCCTATTGGAGGAGCTTACAGGCTCATTGATGTGCCAATGAGTAACTGC
genomic: GAGCTGGAACCCGTCTCTTCCCTCTTACTAAGCGACGAGCCAAACCTGCTgtaagtttct ... cctatggtagGTTCCTATTGGAGGAGCTTACAGGCTCATTGATGTGCCAATGAGTAACTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagttatatcctgttacatatatgaatttagccatatgggctttcctatggtagGTTCCTATTGGAGGAGCTTACAGGCTCATTGATGTGCCAATGAGTAACTGCATCAACAGTGGTATCAACAAGGTGTATATCCTCACCCAGTTTAACTCTG
                                         ctttcctat  CT-rich tract
              ttacatatatgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaccatatcatgatccatgctatatatagtgcacttcaactacataaagttatatcctgttacatatatgaatttagccatatgggctttcctatggtagGTTCCTATTGGAGGAGCTTACAGGCTCATTGATGTGCCAATGAGTAACTGCATCAACAGTGGTATCAACAAGGTGTATATCCTCACCCAGTTTAACTCTG

- -catatca
- - - - - - - ccatgct
- - - - - - - - - - - - - - -tgcactt
- - - - - - - - - - - - - - - - - - caactac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatatg