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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAGgtgatgatttgatccaattaagggtttgttgttttctatgatggcttcctttccttagttggtgttgcatgttctgtgtgttgttctttatgttttacac...

Basic information

species Glycine max
transcript GLYMA05G30150.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G30150.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os02g34680.1 (Oryza sativa), 5'ss of exon 4
AAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAGgtgat-gatttgatccaattaagggtttgttgttttctatgatggcttcctttccttagttg-gtgttgcatgttctgtgtgttgttctt-tatgttttacac--
|||||| | || ||||| ||| |||| || |||||||| ||||||||||| |||| | | ||||| || ||||||||||||||||| ||||| ||  || |||||     |     ||||    ||      |   |||  ||||||   ||  | || | |    ||  |    |||   ||  | ||| |   
AAATTTTTAGACAGCTCTAAGCTGAAGAGGCATTTTCTTATTCATACAGGAGAGAAGAACTTTGTCTGCCCTCATGAAGGCTGTGGAAAGgtaattaatatgatctctcca-----ttgtaaactttgtcattcatttctattccttgactgcattttccgtacgatgcataaatttcaaatacatgttaaatag

upper sequence: GLYMA05G30150.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os05g01550.1 (Oryza sativa), 5'ss of exon 4
AAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAGgtgatgatttgatccaattaagggtttgttgttttctatgatggcttcctttccttagttggtgttgcatgttctgtgtgttgttctttatgttttacac-
|||||  | |||||||| |||||||| |||||    || |||||||||||  ||| ||||||| | ||||| |||  |||||||||||||||||| |  | ||||   ||         | | | |    ||| || |  ||      ||  |  | ||  | ||   |||| || |   | ||||   | 
AAATTCGTAGATAGCTCCAAGTTGAAGAGACACCACCTTATTCATACAGGACAGAAGGATTTTATCTGTCCCCATCCAGGCTGTGGTAAGgtgattaccttatccctctactcaaagaatctctaccg-aatgactgcacttttgcctttacttctccacatactacttgttcttttactttttttttcca

upper sequence: GLYMA05G30150.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM5G885700_T01 (Zea mays), 5'ss of exon 4
AAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAGgtgatgatttgatccaattaa--gggtttgttgt---tttctatgatggcttcctttccttagttggtgttgcatgttctgtgtgttgttctttatgttttacac
|||||  | ||||| || |||||||| ||||||||||| ||||||||||| || | | |||||||||| || |||||||| ||||| ||||| || |     |||  |  |  | ||||| | |   ||| ||  || | ||| | |  | |  ||||| |   |  |       |  ||| |    | ||||  
AAATTCTTAGATAGTTCTAAGTTGAAGAGACATTTTCTTATTCATACAGGAGAAAAGAATTTTGTGTGCCCACATGAAGGTTGTGGGAAGgtaatcacactgtcctctccattgtgtttgctattcatttttactatagtttcttctaatcatgtggtgatttgtagttc-----tctttcatagcatgttactg

upper sequence: GLYMA05G30150.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G140016_T01 (Zea mays), 5'ss of exon 4
AAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAGgtgatgatttgatccaattaa--gggtttgttgtt--ttctatgatggcttcctttccttagttggtgttgcatgttctgtgtgttgttctttatgttttacac
|||||  | |||||||| |||||||| ||||||||||| || ||||| || |||| | |||||||||| || |||||||| ||||| | ||| ||       ||   |  |  | ||||| | ||  ||   ||| |  ||  | |  | |  ||||| |   |  | |   | |  ||| |    | ||||  
AAATTCTTAGATAGCTCTAAGTTGAAGAGACATTTTCTTATCCATACTGGAGAGAAGAATTTTGTGTGCCCACATGAAGGTTGTGGGAGGgtaatctcactgtctgctccattgtgtttgctattcatttcctgacg-tttgttatgatcatgtggtgatttgtacttt---tctcattcgtagcatgttacta

upper sequence: GLYMA05G30150.1 (Glycine max), 5'ss of exon 4
lower sequence: AT4G06634.1 (Arabidopsis thaliana), 5'ss of exon 4
AAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAGgtgatga--tttgatc-caattaagggtttg--ttgttt--tctatgatggcttcctttcctta---gttggtgttgcatgttctgtgtgttgttctttatgttttacac----
|||||||||||||| ||||||||||| ||||||| ||| |||||||| || |||||  ||| | | ||| || ||||||| ||||| ||||||||    ||||||| |  | |   | ||   || |||  | ||| ||       ||     |   | | ||||||| |||| |  ||    |||| || ||| |  |     
AAATTTCTGGATAGTTCAAAGTTGAAGAGACATTATCTTATTCATACTGGAGAGAGAAATTATATATGTACTTATGAAGGATGTGGAAAGgtgattgattttgatcactctcactagcttagtttatttggtgtataattaggcaattaggcaaagggattgtgttgcgtgtttta-gtaactttctgta-gttgtggatgcag

upper sequence: GLYMA05G30150.1 (Glycine max), 5'ss of exon 4
lower sequence: AT4G06634.3 (Arabidopsis thaliana), 5'ss of exon 4
AAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAGgtgatga--tttgatc-caattaagggtttgttgttttctatgatggcttcctttccttagttggtgttgcatgttctgtgtgttgttctttatgttttacac
|||||||||||||| ||||||||||| ||||||| ||| |||||||| || |||||  ||| | | ||| || ||||||| ||||| ||||||||    ||||||| |  | |   | ||  | | ||   ||     ||       |  |     |     ||||  |||| ||  |   | | | |     
AAATTTCTGGATAGTTCAAAGTTGAAGAGACATTATCTTATTCATACTGGAGAGAGAAATTATATATGTACTTATGAAGGATGTGGAAAGgtgattgattttgatcactctcactagcttagtttatttggtgtataattaggcaattaggcaaagggattgtgttgcgtgttttagtaactttctgtag---

upper sequence: GLYMA05G30150.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv12s0035g00660.t01 (Vitis vinifera), 5'ss of exon 4
AAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAGgtgatgatttgatccaattaagggtttg--ttgttttctatgatggcttcctttccttagttggtgttgcatgttctgtgtgttgttctttatgttttacac
|||||| ||||||| |||||| |||||||||| || || ||||||||||| ||||| ||||||||||||||||||||||||||||| |||||||| |||  ||||  | ||   | ||   ||| |   || | || || |  |||  |     |  |    || |    ||   ||  || | |||  |  
AAATTTTTGGATAGTTCAAAGCTGAAAAGACACTTCCTGATTCATACAGGAGAGAGAGATTTTGTGTGTCCTCATGAAGGCTGTGGGAAGgtgatcattctatcccctcaatattctggtctgtgtgaaataagggttttccctccaaatccatttcttagcgtacaagatgagattggttgtctttctc--

upper sequence: GLYMA05G30150.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S42_134V6.1 (Physcomitrella patens), 5'ss of exon 4
AAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAGgtgatgatttgatccaattaagggtttgttgttttctatgatggct----tcctttccttagttggtgttgcatgttctgtgtgttgttctttatgttttacac
   ||  | || ||||||||| |||||||||||||||| |||||||| ||||||| | ||||||| |||||   |||||||||||| ||||||      | ||    || |   | || | || |  |   || ||    ||  |||  |||||  ||| |  | |||  | | | |      |||  |    |
CGTTTCGTCGACAGCTCAAAGCTGAAAAGACATTTTCTGATTCATACGGGGGAGAAGCATTTTGTTTGTCCATTTGAAGGCTGTGGCAAGgtg----cgtcatggggttcaccatctgctattattgaaattgcctcacgtctattctctagtttttgtgggttattccttttatcgcgaaagatgggtccagc

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|193694541|gb|FK628593.1|FK628593
EST:     TTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG                         GCCTTCTCCCTGGATTTCAACTTAAGGTCTCACATGAAAACACATTCCCAA
genomic: TTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAGgtgatgattt ... tctgctgcagGCCTTCTCCCTGGATTTCAACTTAAGGTCTCACATGAAAACACATTCCCAA
EST: gi|193372458|gb|FK337411.1|FK337411
EST:     TTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG                         GCCTTCTCCCTGGATTTCAACTTAAGGTCTCACATGAAAACACATTCCCAA
genomic: TTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAGgtgatgattt ... tctgctgcagGCCTTCTCCCTGGATTTCAACTTAAGGTCTCACATGAAAACACATTCCCAA
EST: gi|6094874|gb|AW119541.1|AW119541
EST:     TTTGTGTGTCCTCATGAAGGCTGTGGTAAG                         GCCTTCTCCCTGGATTTCAACTTAAGGTCTCACATGAAAACACATTCCCAA
genomic: TTTGTGTGTCCTCATGAAGGCTGTGGTAAGgtgatgattt ... tctgctgcagGCCTTCTCCCTGGATTTCAACTTAAGGTCTCACATGAAAACACATTCCCAA
EST: gi|193548503|gb|FK504936.1|FK504936
EST:     TCATACGAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG                         GCCTTCTCCCTGGATTTCAACTTAAGGTCTCACATGAAAACACATTCCCAA
genomic: TCATAC-AGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAGgtgatgattt ... tctgctgcagGCCTTCTCCCTGGATTTCAACTTAAGGTCTCACATGAAAACACATTCCCAA
EST: gi|192333661|gb|FK025772.1|FK025772
EST:     TTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG                         GCCTTCTCCCTGGATTTCAACTTAAGGTCTCACATGAAAACACATTCCCAA
genomic: TTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAGgtgatgattt ... tctgctgcagGCCTTCTCCCTGGATTTCAACTTAAGGTCTCACATGAAAACACATTCCCAA
EST: gi|193646854|gb|FK588833.1|FK588833
EST:     TTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG                         GCCTTCTCCCTGGATTTCAACTTAAGGTCTCACATGAAAACACATTCCCAA
genomic: TTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAGgtgatgattt ... tctgctgcagGCCTTCTCCCTGGATTTCAACTTAAGGTCTCACATGAAAACACATTCCCAA
EST: gi|5126756|gb|AI748492.1|AI748492
EST:     TTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG                         GCCTTCTCCCTGGATTTCAACTTAAGGTCTCACATGAAAACACATTCCCAA
genomic: TTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAGgtgatgattt ... tctgctgcagGCCTTCTCCCTGGATTTCAACTTAAGGTCTCACATGAAAACACATTCCCAA
EST: gi|193701743|gb|FK640435.1|FK640435
EST:     TTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG                         GCCTTCTCCCTGGATTTCAACTTAAGGTCTCACATGAAAACACATTCCCAA
genomic: TTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAGgtgatgattt ... tctgctgcagGCCTTCTCCCTGGATTTCAACTTAAGGTCTCACATGAAAACACATTCCCAA
EST: gi|207811734|gb|GD785979.1|GD785979
EST:     TTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG                         GCCTTCTCCCTGGATTTCAACTTAAGGTCTCACATGAAAACACATTCCCAA
genomic: TTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAGgtgatgattt ... tctgctgcagGCCTTCTCCCTGGATTTCAACTTAAGGTCTCACATGAAAACACATTCCCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAGgtgatgatttgatccaattaagggtttgttgttttctatgatggcttcctttccttagttggtgttgcatgttctgtgtgttgttctttatgttttacac

- - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctttcc