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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttaagtgtgccatatgtgtcatttggttgttcagctaagtttttttgttttattaaccatctattctctgtgtgcagTGGGTTCAATGTGATAAATGTGAAGCATGGCAACATCAAATTTGTGCTTTATTTAATGGCAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA

Basic information

species Glycine max
transcript GLYMA07G00230.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os06g49130.2 (Oryza sativa), 3'ss of exon 6
----------gtatgttaagtgtgccatatgt---gtcatttggttgttcagctaagtt--tttttgttttattaaccat--ctattctctg--tgtgcagTGGGTTCAATGTGATAAATGTGAAGCATGGCAACATCAAATTTGTGCTTTATTTAATGGCAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA
          ||| |  |  |   || | |||   |   |   ||  || | |||   |  || |||  |  | |    |  |||||   ||  | | ||||||||||| ||||| |||||||||   ||||||||||| || |||||  | || |||| |||||||||||||| || | |||| ||||| ||||||   |
agaggaaggggtaagc-actttctccttctgttaggctgtagagtattttatctatactgattcttgcatactgatttgttcctattgattggatctacagTGGGTTCAGTGTGACAAATGTGAATGCTGGCAACATCAGATCTGTGCACTTTTCAATGCCAGAAGAAATGATGTTGAAGAAGCAGAATACACTTGCTTCA

upper sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 7
-------------gtatgttaagtg-tgccatatgtgtcatttggttgttcagctaagtttttttgttttattaa--ccatctattctctgtg---tgcagTGGGTTCAATGTGATAAATGTGAAGCATGGCAACATCAAATTTGTGCTTTATTTAATGGCAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA
               || ||  ||| |    | | |||    |     ||  | ||  ||  |||  | ||||||  |  | ||     |||    ||||||||||||| ||||| || ||||||   ||||| || || || |||||| |||||||||| ||||| |||||||| || ||||| || || || ||||| |
gtaagttcctttttcatttttggtgattttgtgtctgtatcatcaaaatttgggtatcttccttttgtatattaaatctttttaaatgatgtattctgcagTGGGTTCAGTGTGACAAGTGTGAATGCTGGCAGCACCAGATATGTGCTCTATTTAATGGTAGAAGGAATGATGGAGGGCAAGCAGAGTACACCTGCCCAA

upper sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G139977_T01 (Zea mays), 3'ss of exon 6
gtatgttaagt-gtgccat--atgtgtcatttggtt---gttcag------ctaa-gtttttttgttttattaaccatctat-----tctctgtgtgcagTGGGTTCAATGTGATAAATGTGAAGCATGGCAACATCAAATTTGTGCTTTATTTAATGGCAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA
||| ||   |  || ||||  || |||  |||  |    | |||       || |  ||||| | || |  ||| ||| |        | |  | ||||||||||||||||||| |||||||||   |||||||||||||||||||||||||||||||| ||||| || ||||| ||||||||||||||||||||||| |
gtaagtactgcagttccattgatatgtggtttcataaaagctcaagagtttctgatatttttcttttgtgctaaacattttcaaaccacacattctgcagTGGGTTCAATGTGACAAATGTGAATGTTGGCAACATCAAATTTGTGCTTTATTTAATGGAAGAAGGAACGATGGAGGACAAGCTGAATATACTTGCCCCA

upper sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 6
gtatgttaagt-gtgccatatgtgtcatttggttgttcag------ctaa-gtttttttgttttattaaccatctattctctgtg-----tgcagTGGGTTCAATGTGATAAATGTGAAGCATGGCAACATCAAATTTGTGCTTTATTTAATGGCAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA
|||||||  |  || ||||   |  ||  |    | |||       ||||  ||||| | |  |  ||| ||| |        ||     ||||||||||||||||||| |||||| ||   ||||||||||||||||||||| |||||||||| ||||| || | ||| |||||||||||||||||||||||  
gtatgttttgcagttccattgata-cacataaaagctcaaaagtttctaatatttttctttggtgctaaacattttcaaatcatgcattctgcagTGGGTTCAATGTGACAAATGTCAATGCTGGCAACATCAAATTTGTGCTCTATTTAATGGAAGAAGGAACGGTGGAGGACAAGCTGAATATACTTGCCCCC

upper sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G55970.1 (Arabidopsis thaliana), 3'ss of exon 5
----------------gtatgttaagtgtg---ccatatgtgtcatttggttgttcagctaagtttttttgttt---tattaaccat-ctattctctgtgtgcagTGGGTTCAATGTGATAAATGTGAAGCATGGCAACATCAAATTTGTGCTTTATTTAATGGCAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA
                 | |   || | ||   |    | |||  |||  ||  |  | |   ||||||||| |   | | |||||  | | |   | | |||||||||| ||||||||||| |||||||||||||| |||  |||||||||||| || ||  || |||||||| |||| | |    |  | || ||||||||||
gtatgtatgcctcatgatttcggaaatttgtttcttcctttgtttttttttttctttgttttctttttttgtgtgtgtctgaaccaaaccaatggttttctgcagTGGGTGCAATGTGATAAGTGTGAAGCATGGCAGCATATAATTTGTGCTTTGTTCAACAGCCGAAGAAATCATGGAGAATCCACCAAGTACACTTGCCCTA

upper sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 8
------gtatgttaagtgtgc---catatgtgtcatttggtt---gttcagctaagtttttttgttttattaaccatctattctctgtgt---------gcagTGGGTTCAATGTGATAAATGTGAAGCATGGCAACATCAAATTTGTGCTTTATTTAATGGCAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA
      |  | |  | | ||    | ||| |    ||||  |   ||     || ||||||||  || ||     || |  | ||| |||         ||||||||| ||||||||||||||||| || ||||| ||||| || ||||||||||||||||| ||||| ||||| || || || ||||| ||||| |||||  
gtaaaagcctatccactctgtagacttattttgtgtttgtctcccgtctttgtatgtttttttagttcatgctatattttgtttctatgtatgatttttgcagTGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTATTTAATGGGAGAAGGAATGACGGAGGGCAGGCTGAGTATACCTGCCCAT

upper sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 7
---------gtatgttaagtgtgccatatgtgtcatttgg---ttgttcagctaagtttttttgttttattaac--catctattctctgtgtgcagTGGGTTCAATGTGATAAATGTGAAGCATGGCAACATCAAATTTGTGCTTTATTTAATGGCAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA
            | | |   | |   ||| |||||||||    | |||  | |   |||| |   ||| |  |   | | |  | | | | || ||||||| ||||||||||||||| | || ||||| |||||||| |||||| ||||||||||  | || |||||||| || |||||||| ||||| |||||  
gtaagactatcctatcagtagagttgtat-tgtcatttgcatctcgttttgttggtttttctgagtttgtctatttcgtttgatgttttt-tgtagTGGGTCCAATGTGATAAATGTCAGGCCTGGCAGCATCAAATATGTGCTCTATTTAATGGGCGGAGGAATGATGGGGGGCAAGCTGAGTATACCTGCCCAT

upper sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G12980.1 (Arabidopsis thaliana), 3'ss of exon 7
------------gtatgttaagtgtgccatatgtgtcatttggttg--ttcagctaagtttttttgttttattaaccatctattctctgtgtgcagTGGGTTCAATGTGATAAATGTGAAGCATGGCAACATCAAATTTGTGCTTTATTTAATGGCAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA---
               |  | |||    ||  ||| | ||  || |   || |  | || |  |||  | | ||    | | |||   | |||||||||||| ||||||||||||||| |||||||||| ||||||||||||||||| || || ||| | || ||| ||||    ||||| || || ||||||||||   
gtatgcctcttcagttactgagttctgcaattgttttatagggattattttatattagctgctttactctttttctgaaccattaattctgtgcagTGGGTGCAATGTGATAAATGTCAAGCATGGCAGCATCAAATTTGTGCTTTGTTCAACGGCCGTAGGAATCATGG---GCAAGCCGAGTACACTTGCCCTAATT

upper sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 6
---------------gtatgttaa-gtgtgccatatgtgtcatttggttgttcagctaagtttttttgttttattaaccatctattctctgtgtgcagTGGGTTCAATGTGATAAATGTGAAGCATGGCAACATCAAATTTGTGCTTTATTTAATGGCAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA
                | | |||   | || ||| | |||    |  ||||      ||    | || | ||  | | ||| |  |     | ||||||||||||||||||| ||||||||||| |||||||||||||||||||| || || |||||  | || ||||||||||| || |||||||||||||||||||
gtatgttttattcatttcttttagtatctgtcat-tatgttggattattgtctgagcaatcgctcttatgtt--tgaacatttgcttctattttgcagTGGGTTCAATGTGACAAATGTGAAGCTTGGCAACATCAAATTTGTGCCTTGTTCAATGGTCGGAGGAATGATGGTGGGCAGGCTGAATATACTTGCCCTA

upper sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ09423 (Selaginella moellendorffii), 3'ss of exon 2
gtatgttaagtgtgccatatgtgtcatttggttgttcagctaagtttttttgttttattaaccatctattctctgtgtgcagTGGGTTCAATGTGATAAATGTGAAGCATGGCAACATCAAATTTGTGCTTTATTTAATGGCAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA
                 ||||||    |   || ||   ||    ||  |||     |    | | |||  | | ||  ||||||||||||||||| || ||  | | |||||| |||||||| ||||| ||||||||||| ||||||||||| |||||  |  | |||| || ||||||  
----------------gtatgtgcttctatattttttctct----ttccttgaaacgtctgacttgtatggtttatg--cagTGGGTTCAATGTGACAAGTGCAATGTATGGCAGCATCAAATCTGTGCCTTATTTAATGGTAGAAGAAATGAAGGTGGTGACACGGAATTTATTTGCCCCT

upper sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ34595 (Selaginella moellendorffii), 3'ss of exon 5
gtatgttaagtgtgccatatgtgtcatttggttgttcagctaagtttttttgttttattaacc-atctattctctgtgtgcagTGGGTTCAATGTGATAAATGTGAAGCATGGCAACATCAAATTTGTGCTTTATTTAATGGCAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA
         || ||   | | | |  |||  || |  |  |    | |||  ||  |    || |  | |    | | ||||||||||||||||||| || ||  | | |||||| |||||||| ||||| ||||||||||| ||||||||||| |||||  |  | |||| || ||||||  
---------gtatgtgtttttttttttttacttctatattttttctctttccttgaaacgtccgacttgtatggtttatgcagTGGGTTCAATGTGACAAGTGCAATGTATGGCAGCATCAAATCTGTGCCTTATTTAATGGTAGAAGAAATGAAGGTGGTGACACGGAATTTATTTGCCCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggttgttcagctaagtttttttgttttattaaccatctattctctgtgtgcagTGGGTTCAATGTGATAAATGTGAAGCATGGCAACATCAAATTTGTGCTTTATTTAATGGCAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA
                            tattaac  putative branch site (score: 1)
                                     tctattctct  putative PPT
             taagtttttttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttaagtgtgccatatgtgtcatttggttgttcagctaagtttttttgttttattaaccatctattctctgtgtgcagTGGGTTCAATGTGATAAATGTGAAGCATGGCAACATCAAATTTGTGCTTTATTTAATGGCAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA