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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTTTGTGTTAGCAGTGGAAAAGATGCCATCTCTTCCTTGAAGCCACCCCATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGGgtatgtatgcacctggaatactttctttcagaatctgatatttttaatatctggagtaatatttgaaatttctacaaacatagaaaagagtttttaattc...

Basic information

species Glycine max
transcript GLYMA08G11060.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G11060.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os01g69920.2 (Oryza sativa), 5'ss of exon 8
TGGTTTGTGTTAGCAGTGGAAAAGATGCCATCTCTTCCTTGAAGCCACCCCATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGGgtatgtatgcacctggaatactttctttcagaatctgatatttttaatatctggagtaatatttgaaatttctacaaacatagaaaagagtttttaattc-------
|   |||||    ||| || ||| | || ||| | |   | || || || ||  | |||||||| ||||||||||| || || |||||||||||||||||||| || |   |    | | |||   ||  | |     |||| || ||| ||    |   ||||    | |  ||  |  ||  |   | |  |||  |        
TTACTTGTGCAGACAGCGGGAAAAAAGCAATCACATTGCTAAAACCCCCGCACAATTTTGATGCTTGTTTCATGGACATACAGATGCCAGAAATGGATGGgtaagtcttttctgacactgcttgtgttttgca----gtattgtttata-ctaatttggcatttctcttgtgcacgtatgtatcatctaatggttaccttttttcag

upper sequence: GLYMA08G11060.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G471529_T01 (Zea mays), 5'ss of exon 9
TGGTTTGTGTTAGCAGTGGAAAAGATGCCATCTCTTCCTTGAAGCCACCCCATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGGgtatgtatgcacctggaatactttctttcagaatctgatatttt-taatatctggagtaatatttgaaatttctacaaacatagaaaagagtttttaattc----------------------------------------------------------
|   ||||| |  |||||| || || || ||| |     |||| || || ||  | |||||||| ||||||||||| || || ||||| |||||||||||||  |  |  | |     |  | |||||    |      || |    |||  |     | ||| || ||||  ||   |  |   | | |||  ||  |                                                            
TAACTTGTGCTGACAGTGGGAAGGAAGCAATCACACTGCTGAAACCTCCTCACAATTTTGATGCTTGTTTCATGGACATACAGATGCCTGAAATGGATGGgtgagattttatccc---ttttatctttggatactcatcatctcaccatactttagacattatctgtaatta-tattcagttgatacacagtacttgctcttgtcatcgatttatatttgtcttgttctcttttgtcatgcatttggcacattttgcag

upper sequence: GLYMA08G11060.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G423456_T01 (Zea mays), 5'ss of exon 8
TGGTTTGTGTTAGCAGTGGAAAAGATGCCATCTCTTCCTTGAAGCCACCCCATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGGgtatgtatgcacctggaatactttctttcagaatctgatatttttaatatctggagtaatat----ttga-aatttctacaaacatagaaaagagtttttaattc-------------------------------------
|   ||||| |   || || ||  | || ||| |     |||| || || ||    |||||||| ||||||||||| || || ||||| |||||||||||||  || |   | | | ||| |     ||  | | |  | |    | |||||| |   ||||    |||| ||    |||   |       |  | |||  |||                                      
TAACTTGTGCTGATAGCGGGAAGAAAGCAATCACGCAACTGAAACCTCCTCACAGTTTTGATGCTTGTTTCATGGACATACAGATGCCTGAAATGGATGGgtgagttttatctttgtatattcatcatctcactatactttagacactatctgtacctatatccagttgataaacaatacttgctcttgtcaccgatttacattttcttgttctcttgtgtcatgcatttggtaccttgcag

upper sequence: GLYMA08G11060.1 (Glycine max), 5'ss of exon 10
lower sequence: AT1G27320.1 (Arabidopsis thaliana), 5'ss of exon 9
TGGTTTGTGTTAGCAGTGGAAAAGATGCCATCTCTTCCTTGAAGCCACCCCATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGGgtatgtatgcacctggaatactttctttcagaatctgatatttttaatatctggagtaatatttgaaatttctacaaacatagaaaagagtttttaattc
|||| || | |   ||||| | | | || ||||| |   | |||||||| ||  |||||||||| || |||||||| ||||| ||||||||||||||||||||||  ||    ||| |||||   |||    |    |  ||   ||||| |      | | ||||||| | |     |   |       | |  |    
TGGTCTGCGCTGAGAGTGGGATAAAGGCAATCTCATTGCTTAAGCCACCTCACGAGTTTGATGCTTGCTTCATGGACATTCAGATGCCAGAAATGGATGGgtatgcctga--ttggtatactagtttttttga---aaagttcgaaatatgtaataagaaaattgaaatgtttttctgccctgtctt---tctgcag---

upper sequence: GLYMA08G11060.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv01s0010g03780.t01 (Vitis vinifera), 5'ss of exon 9
TGGTTTGTGTTAGCAGTGGAAAAGATGCCATCTCTTCCTTGAAGCCACCCCATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGGgtatgtatgcacctggaatactttctttcagaatctgatatt---tttaatatctggagtaatatttgaaatttctacaaaca---tagaaaagagtttttaattc-----------------------
| || ||||    |||||| |||  ||| ||| |     | || || |||||  | ||||||||||||||||||||||| || |||||||||||||| |||||||||||   |     || ||  |   |    || | ||    |||  ||||   | |  | | |      ||||   |     |      ||| || |  ||                        
TCGTCTGTGCAGACAGTGGGAAAAGTGCAATCCCACTGCTTAAACCTCCCCACGACTTTGATGCCTGTTTCATGGATATCCAGATGCCAGAAATGGACGGgtatgtatgtcgccatggtatttgatgcgatttgcttacatcaaattttctatc-aaactcctctctactgcatctatctatgattttcgtttgagcttgtctttataaatgtgaatctcctcccacag

upper sequence: GLYMA08G11060.1 (Glycine max), 5'ss of exon 10
lower sequence: PP1S252_49V6.1 (Physcomitrella patens), 5'ss of exon 13
TGGTTTGTGTTAGCAGTGGAAAAGATGCCATCTCTTCCTTGAAGCCACCCCATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGGgtatgtatgcacctggaatactttctttcagaatctgatattt--ttaatatctggagtaatatttgaaatttc-tacaaacatagaaaagagtttttaattc
| |  ||||||  ||| |||| ||  || |||      || || || || ||  | |||||||| |||||||||||| | |||||||||||||||||||||||||  | |  |   | ||| |   ||||   | | ||||||  | ||          |  || | |    |  | ||   ||    | ||   |  | |  
TTGAGTGTGTTCACAGCGGAAGAGCAGCAATCCAGAAGTTAAAACCTCCTCACAACTTTGATGCGTGTTTCATGGATGTGCAAATGCCAGAAATGGATGGgtatggtttcttccttactacatatattcatgct-taatatttagtgaaggctcttgagagcatcttactcctgatgcactgattttcatgaagctc-agtc-

upper sequence: GLYMA08G11060.1 (Glycine max), 5'ss of exon 10
lower sequence: PP1S194_72V6.1 (Physcomitrella patens), 5'ss of exon 15
TGGTTTGTGTTAGCAGTGGAAAAGATGCCATCTCTTCCTTGAAGCCACCCCATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGGgtatgtatgcacctggaatactttctttcagaatctgata---tttttaatat-ctggagtaatatttgaaatttctacaaacatagaaaagagtttttaattc
| |  ||||||| |||||| | || ||| |||      |||||||| || ||  | |  ||||||||||| |||||| | ||||||||||||||||||||||| |  |     |   |  |    ||||   || || ||   ||| | | || || |  | | |||    ||        |     |||      | ||    
TTGACTGTGTTAACAGTGGGAGAGCTGCGATCCAAAGTTTGAAGCCTCCGCACAATTACGATGCCTGTTTTATGGATGTGCAAATGCCAGAAATGGATGGgta-gggtttctttcccactcgagttttcgtcatttggtaaattttctgagatgcttgcatcaaattcatgatgcaggttcattcgaaaactcaaatatac---

upper sequence: GLYMA08G11060.1 (Glycine max), 5'ss of exon 10
lower sequence: PP1S50_141V6.1 (Physcomitrella patens), 5'ss of exon 13
TGGTTTGTGTTAGCAGTGGAAAAGATGCCATCTCTTCCTTGAAGCCACCCCATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGGgtatgtatgcacctggaatactttctttcagaatctgatatttttaatatctggagtaatatttgaaatttctacaaacatagaaaagagtttttaattc---------
| |  ||||||  |||||||| || ||| |||      |||||||| |||||  | || ||||||||||| |||||  | || |||||||||||||||||||| |  | |  |      ||| |   |||   ||   |  ||  |||| ||| | ||  |      |||   |||||     |  | ||   | || |          
TTGAGTGTGTTTACAGTGGAAGAGCTGCTATCCAGAAGTTGAAGCCTCCCCACAATTTCGATGCCTGTTTTATGGACGTGCAGATGCCAGAAATGGATGGgtagggttccttc-----cactcttagtca---tccactcgttgcaatagctgca-tataagcctgcattaaaacaaatggtaactaaagagctcaagtttgctgaaat

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|6482286|gb|AW201557.1|AW201557
EST:     CATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGG                         ATTTGAAGCTACAAAGCGAATTAGGGAGATGGAAGATAGTGTGAACAGAGA
genomic: CATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGGgtatgtatgc ... ttcccaacagATTTGAAGCTACAAAGCGAATTAGGGAGATGGAAGATAGTGTGAACAGAGA
EST: gi|5126405|gb|AI748141.1|AI748141
EST:     CATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGG                         ATTTGAAGCTACAAAGCGAATTAGGGAGATGGAAGATAGTGTGAACAGAGA
genomic: CATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGGgtatgtatgc ... ttcccaacagATTTGAAGCTACAAAGCGAATTAGGGAGATGGAAGATAGTGTGAACAGAGA
EST: gi|151394584|gb|EV264455.1|EV264455
EST:     CATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGG                         ATTTGAAGCTACAAAGCGAATTAGGGAGATGGAAGATAGTGTGAACAGAGA
genomic: CATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGGgtatgtatgc ... ttcccaacagATTTGAAGCTACAAAGCGAATTAGGGAGATGGAAGATAGTGTGAACAGAGA
EST: gi|18038767|gb|BM307061.1|BM307061
EST:     CATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGG                         ATTTGAAGCTACAAAGCGAATTAGGGAGATGGAAGATAGTGTGAACAGAGA
genomic: CATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGGgtatgtatgc ... ttcccaacagATTTGAAGCTACAAAGCGAATTAGGGAGATGGAAGATAGTGTGAACAGAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTTTGTGTTAGCAGTGGAAAAGATGCCATCTCTTCCTTGAAGCCACCCCATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGGgtatgtatgcacctggaatactttctttcagaatctgatatttttaatatctggagtaatatttgaaatttctacaaacatagaaaagagtttttaattc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA