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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtggtaactcatgtaattttcccaaaaattttagtttttgctgcaatatcatttgatgaaaaaattgtctaacagTGGTTGAACAAGTCACTGGAAGAGATCTCGTGCTCAATCATTTAAGCATCCCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACAGA

Basic information

species Glycine max
transcript GLYMA07G37050.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G37050.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 10
gtaagtggtaactc-------atgtaattttc--ccaaaaattttagttt--ttgctgcaatatcatttgatgaaaaaattgtctaacagTG-----GTTGAACAAGTCACTGGAAGAGATCTCGTGCTCAATCATTTAAGCATCCCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACAGA
|||  | | || ||       || | || |||  | |    |  ||  ||  ||   | |   |    |||| |  || |  | | | | ||     || |||||| || |||| || || | | | || ||||||||||||||||| |||||||| ||||||||||| || || || ||||||||  | |||||
gtacattgcaaatctgtttagatttcatcttcttctatcgctcctatgttgcttatcgtatagttgcctgataagtaattcctatgaaaatgtagTTGTCGAACAAATCTCTGGGAGGGACCACATCCTAAATCATTTAAGCATCCCCGCTGCTTGCTTCACTCATCCAGAGATTAGTATGGTTGGGCTTACAGA

upper sequence: GLYMA07G37050.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 10
----------------gtaagtggtaactcatgtaattttcccaaaaattttagtttttgctgcaat--------atcatttgatgaaaaaat---tgtctaa---cagTGGTTGAACAAGTCACTGGAAGAGATCTCGTGCTCAATCATTTAAGCATCCCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACAGA
                 |      |   | ||   | ||   |  | ||||  | |||||||   |          |  |||||| |  || |   ||||| |    ||| ||||| | | || |||| | |||   | | || |||||| |||||||||| ||||| |||||||||||||| || || || ||||||||  | |||||
gtagatacagaataatttgttcactgttttattgtacttcagcgcatatttcgggttttgctttgaactagtgtagttctttgataactaatttcttgtctgaatatagTTGTTGAGCGAATCTCTGGGAAAGACAACATCCTAAATCATCTAAGCATCCCGGCTGCCTGTTTCACTCATCCGGAGATTAGTATGGTTGGGCTAACAGA

upper sequence: GLYMA07G37050.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 10
gtaagtggta-actcatgtaattttcccaaaaattttagtttttgct-gcaata----tcatttgatgaaaaaattgtctaa---cagTGGTTGAACAAGTCACTGGAAGAGATCTCGTGCTCAATCATTTAAGCATCCCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACAGA
|||| || |   ||||  |  || |   |   ||  | | |  || |  | |||    | ||  ||  |||   | |||| |    ||| || || ||| ||| ||| || ||   | |  | |||||  |||||||||||||||||||||||||||| ||||| ||||| |||||||| ||||||||
gtaaatgttgtgctcacctgtttcttttatccatgctcgatgctgatcactatagttcttatacgagcaaatgttggtctgaatatagTTGTGGAGCAAATCAGTGGGAGGGACAACATTTTAAATCACCTAAGCATCCCAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGA

upper sequence: GLYMA07G37050.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G152958_T02 (Zea mays), 3'ss of exon 10
gtaagtggtaactcatgtaattt----tcccaaaaattttagtttttgctgcaatatcatttgatgaaaaaat--tgtctaa---cagTGGTTGAACAAGTCACTGGAAGAGATCTCGTGCTCAATCATTTAAGCATCCCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACAGA
|||  ||  |  || | |   ||    |  |    |   |  || ||| || | |    | |||||   |  |  | |  ||    ||| ||||||||| || ||||||  |||| | | || |||||||||||||||||||| || |||||||| ||||| || || || |||||||||||||||||
gtacttgagagttcctttttcttgtggtttcttggagcatgcttattggtgtact--tgtctgatgttgacttcctattcaaatgtagTTGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCCCAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGA

upper sequence: GLYMA07G37050.1 (Glycine max), 3'ss of exon 10
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 10
--------------------------gtaagtg-gtaactcatgtaattttccc----------aaaaattttagtttttgctgcaatatcatttgatgaaaaaattgtctaa--cagTGGTTGAACAAGTCACTGGAAGAGATCTCGTGCTCAATCATTTAAGCATCCCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACAGA
                            || ||  |   || | |  ||||||            || |  |||| ||   ||  | ||   | |    |   | |||| |     |||||| || |||||||| || |||||||  ||||| |||||| | |||||||||||||||||||| |||||||||||||| || ||||| |||||||||||
gtaaatggttttatcaatatttcactccaaatgcatctttcttttgtttttccttttctacactgaatacgttagattgacctttattaaactctatgcatctacttgtgttggctagTGGTGGAGCAAGTCACAGGTAGAGATCATGTGCTTAATCATCTTAGCATCCCAGCTGCTTGTTTTACTCATCCTGAAATAAGTATGGTGGGATTGACAGA

upper sequence: GLYMA07G37050.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 10
----------------------gtaagtggtaactca-tgtaattttcccaaaaattttagtttttgctgcaatatcatttgatgaaaaaattgtctaacagTGGTTGAACAAGTCACTGGAAGAGATCTCGTGCTCAATCATTTAAGCATCCCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACAGA
                      |  | |   ||  || |   ||||||||     | ||  |      || | ||   | |||      | |        |||||| || |||||||  || |||||||  ||||| |||||| | ||||||||||||||||| || ||||||||||||||||||||||| ||||| |||||
gtaaatggcttatcagtaggaggctactaacaatgcaataatattttcccttttttcttcttgagccttgtattaaactctgagctcttactctgtggctagTGGTCGAGCAAGTCAGCGGCAGAGATCATGTGCTTAATCATCTTAGCATCCCAGCTGCTTGCTTTACTCATCCTGAAATCAGCATGGTGGGATTAACAGA

upper sequence: GLYMA07G37050.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S352_68V6.1 (Physcomitrella patens), 3'ss of exon 10
---------------------------------------------------------------------------------------gtaagtggtaactc-atgtaatt------ttcccaaaaattttagtttttgctgcaatatcatttgatgaaaaaattgtctaacagTGGTTGAACAAGTCACTGGAAGAGATCTCGTGCTCAATCATTTAAGCATCCCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACAGA
                                                                                        ||   | |   || | | ||||      ||     | ||||||||||    | |      | || ||||     || | | |||||  |||| ||  |  ||||  |||||   || || ||||||   ||| | ||||| ||||||||||| || ||||||||||||||||||||| | || ||
gtatgtcaattggctctaagacaaataaatgaagtatttatttatatatttattgatttttatcctcaatgctccaatgcttcaaagctattcgatggttccacgcaattgataaattttatgatattttagtttgaagtccttaccgagttaatga---ctttcttttacagTCATTGAGCAGATTGCTGGGCGAGATAATGTTCTGAATCATAACAGCGTTCCAGCAGCTTGTTTCACACACCCTGAAATCAGCATGGTTGGACTTACTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccaaaaattttagtttttgctgcaatatcatttgatgaaaaaattgtctaacagTGGTTGAACAAGTCACTGGAAGAGATCTCGTGCTCAATCATTTAAGCATCCCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACAGA
                              atttgat  putative branch site (score: 5)
                        aatatcatttgatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtggtaactcatgtaattttcccaaaaattttagtttttgctgcaatatcatttgatgaaaaaattgtctaacagTGGTTGAACAAGTCACTGGAAGAGATCTCGTGCTCAATCATTTAAGCATCCCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT