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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcttgtatttcaaaaattaattgtgattaattatccttgtggcactgaaaaatccatctgatttatgtattctctccaaacttaatgccagGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGCATTCATCGAAGGTGGGATAGTGGTTATCGCATCACCTCAACTGCTGCAACATGGGACCAAGCTG

Basic information

species Glycine max
transcript GLYMA04G09080.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 14
----------------------------------gtcttgtatttcaaaaattaattgtgattaattatccttgtggcactgaaaaatccatctgatttatgtattctctccaaacttaatgccagGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGCATTCATCGAAGGTGGGATAGTGGTTATCGCATCACCTCAACTGCTGCAACATGGGACCAAGCTG
                                  |  ||  |||| |  |   |  |   | | | ||||  |     |   |||| ||  |  ||||| | |  |||| |  | ||   |   |||| || |||||||||||||| ||||| |||||||| || |||| | | |||||||||||||||||||| ||  |||| || || ||||| ||||| |  |
gtacgtttggagtgtccaagagccttgtaaaattgaatt-cattttagcagcaagctac-actgactatcaattgaatatgtaaaagtct-tgagattt-tattatctcgcatatctcttttgtagGTAGTAGAACTTGATTTCTTATATCCGAGTGAAGGAATCCATCAACGCTGGGATAGTGGTTATCGCATAACTGCAACAGCAGCCACATGTGACCAGGTGG

upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os01g10150.2 (Oryza sativa), 3'ss of exon 14
----------------------------------gtcttgtatttcaaaaattaattgtgattaattatccttgtggcactgaaaaatccatctgatttatgtattctctccaaacttaatgccagGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGCATTCATCGAAGGTGGGATAGTGGTTATCGCATCACCTCAACTGCTGCAACATGGGACCAAGCTG----
                                  |  ||  |||| |  |   |  |   | | | ||||  |     |   |||| ||  |  ||||| | |  |||| |  | ||   |   |||| || |||||||||||||| ||||| |||||||| || |||| | | |||||||||||||||||||| ||  |||| || || ||||| ||||| |  |    
gtacgtttggagtgtccaagagccttgtaaaattgaatt-cattttagcagcaagctac-actgactatcaattgaatatgtaaaagtct-tgagattt-tattatctcgcatatctcttttgtaggtagTAGAACTTGATTTCTTATATCCGAGTGAAGGAATCCATCAACGCTGGGATAGTGGTTATCGCATAACTGCAACAGCAGCCACATGTGACCAGGTGGCTTT

upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 14
---------------------------------------------------------------------------------gtcttgtatttcaaaaattaattgtgattaattatccttgtggca--ctgaaaaatccatctgatttatgtattctctccaaacttaatgccagGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGCATTCATCGAAGGTGGGATAGTGGTTATCGCATCACCTCAACTGCTGCAACATGGGACCAAGCTG
                                                                                  |  ||  | |||| ||   |   | |  ||  |    ||  | |  | | |   |  | ||   || | |||| |        ||  |   |||||||||| ||||| ||||||||||| ||||| || || |||||| | ||||||| ||| | |||||||||  | ||||| || |||||||| || || |
gtacgttgacgtgctcagaaggctggcctttgctttgaatcgtctactatccaggaaaaaacatatcgacatgccttgatattgctgactctcaagaacatagcttcaagaaaaacatatgctgaaaacagcattgttaaacttggttct-tatttttaatgtttttggttttagGTTGTGGAGCTTGACTTCTTGTATCCAAGTGAGGGTATCCATCGACGATGGGATAATGGATTTCGCATCACGGCTACTGCAGCTACATGGGATCAGGCAG

upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G095634_T01 (Zea mays), 3'ss of exon 7
--gtcttgtatttcaaaaattaattgtg-attaattatcc---ttgtggc---actgaaaaatccatctgatttatgtattctctccaaacttaatgccagGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGCATTCATCGAAGGTGGGATAGTGGTTATCGCATCACCTCAACTGCTGCAACATGGGACCAAGCTG
  ||| |  |  || |  || |  | || |   | |   |   | || ||   |||  |||| |    |  ||  || | | |   ||   |   | |||||| || ||||| ||||||||||||||||| || || ||||||  ||||||||| || |||||  | || ||| || || |||| || || || || ||||
gagtcgttcagatcgactatcacctctgcaccgacttctcgactagtcgcccgactttaaaacctcgtttcttattgaactattggcat-ttactttccagGTGGTTGAACTGGATTTCTTGTATCCCAGCGAGGGAATTCATAAAAGGTGGGACAGGGGTTACTGGATAACCGCAGCTCCTGCTACTTGTGATCAGGCTG

upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 14
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 14
-------------------------------------------------------------------------gtcttgtatttcaaaa-attaattg--tgattaattatccttgtggcactgaaaaatccatctgatttatgtattctctccaaacttaat-gcc------agGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGCATTCATCGAAGGTGGGATAGTGGTTATCGCATCACCTCAACTGCTGCAACATGGGACCAAGCTG
                                                                          |   |||  | |||| |||   ||    ||| |  || | |||        |  | |    |   ||      |||  || ||  || | |||      |||| || || |||||||||||||||||||||||||| |||||| || | ||||| ||||| || ||||| ||||| |||||||| || ||||| || || |
gtaattagcgctctaagcctacttgatttacgaaaaccgcatactatttttgcttcttcgactcggagcagatatgaagtaaatgaaaatatttgctgaccaatttagaattcctgtcatcggacatcacctgattacattcctctctcttaccgaatgtatttgccctctgcagGTCGTTGAGCTTGATTTCTTGTATCCCAGTGAAGGTATTCATAGACGATGGGACAGTGGATACCGCATAACCTCTACTGCTGCGACTTGGGATCAGGCAG

upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 14
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 14
--------------------------------------------------------------------------------------------gtcttgtatttcaaaaattaattgtgattaattatcct--------tgtggcactgaaaaatccatctgatttatgtattctctccaaacttaatgcc---agGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGCATTCATCGAAGGTGGGATAGTGGTTATCGCATCACCTCAACTGCTGCAACATGGGACCAAGCTG
                                                                                            |      || || |  | |  ||||||   |  | | |         |||    |||  |  | || || ||     | |    |     ||     |   |||| || || ||||| ||||||||||| || ||||| |||||  |  | ||||| ||||| ||||||||||| || |||||||| |||||||| ||||| |
gtgattaaaaccgtcgatcggtttttttattaaactttcatttatttttatcagctttatgattttagcatgatccaaagtgtacatcaattgagagacatatcgaggact--ttgtgacctaacaccttagaagtgacgtgtttttgattatgctatttgtttctcacaatgctgctttcttttgcctctgcagGTGGTTGAGCTTGACTTCTTGTATCCTAGCGAAGGTATTCACAGGCGATGGGACAGTGGATATCGCATCACATCTACTGCTGCCACATGGGATCAAGCAG

upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 14
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 12
gtcttgtatttcaaaaattaattgtgattaattatccttgtggcactgaaaaatccatctgatttatgtattctctccaaacttaatgccagGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGCATTCATCGAAGGTGGGATAGTGGTTATCGCATCACCTCAACTGCTGCAACATGGGACCAAGCTG
                         |  |  | |||| |  ||   |   | |    | |||      |||   |   | ||        |||| ||||| || |||||| | |||||||| |||||||| || ||  |||||||| |||| |||||||||||| | ||||| ||||| ||||| ||||| |
-------------------------gtctgttaatccattcgggcttcgcacacttgtttgacagcgctatatgcattacac--------agGTAGTGGAGCTGGATTTCCTCTATCCCAGCGAAGGCATCCACCGGCGGTGGGATTGTGGATATCGCATCACCGCCACTGCGGCAACTTGGGATCAAGCAG

upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 14
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 12
gtcttgtatttcaaaaattaattgtgattaattatccttgtggcactgaaaaatccatctgatttatgtattctctccaaacttaatgccagGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGCATTCATCGAAGGTGGGATAGTGGTTATCGCATCACCTCAACTGCTGCAACATGGGACCAAGCTG
                         |  |  | |||| |  ||   |   | |    | |||            | | |  | | |  | |||| ||||| || |||||| | |||||||| |||||||| || ||  |||||||| |||| |||||||||||| | ||||| ||||| ||||| ||||| |
-------------------------gtctgttaatccattcgggcttcgcacacttgtttgac---------agcgctatgcatgacac-agGTAGTGGAGCTGGATTTCCTCTATCCCAGCGAAGGCATCCACCGGCGGTGGGATTGTGGATATCGCATCACCGCCACTGCGGCAACTTGGGATCAAGCAG

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|193511053|gb|FK468952.1|FK468952
EST:     TCTAGATGGGCAATTGGTTATGTCCCGTGGGGCTGGTTTTTCAGACCAAG                         GTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGCATTCATCGAAGGTG
genomic: TCTAGATGGGCAATTG-TTATGTCCCGTGGGGCTGGTTTTTCAGACCA-Ggtcttgtatt ... ttaatgccagGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGCATTCATCGAAGGTG
EST: gi|207734224|gb|GD711068.1|GD711068
EST:     ATGGGCAATTGTTATGTCCCGTGGGGCTGGTTTTTCGGACCAG                         GTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGTATCCATCGAAGGTGG
genomic: ATGGGCAATTGTTATGTCCCGTGGGGCTGGTTTTTCAGACCAGgtcttgtatt ... ttaatgccagGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGCATTCATCGAAGGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtggcactgaaaaatccatctgatttatgtattctctccaaacttaatgccagGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGCATTCATCGAAGGTGGGATAGTGGTTATCGCATCACCTCAACTGCTGCAACATGGGACCAAGCTG
                                           acttaat  putative branch site (score: 4)
                        atttatgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcttgtatttcaaaaattaattgtgattaattatccttgtggcactgaaaaatccatctgatttatgtattctctccaaacttaatgccagGTTGTGGAACTTGATTTCTTGTATCCCAGTGAAGGCATTCATCGAAGGTGGGATAGTGGTTATCGCATCACCTCAACTGCTGCAACATGGGACCAAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG