Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTTTGTGTTAGTAGTGGTAAAGATGCCATCTCTTCCTTGAAGCCACCCCATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGGgtatgtatgcacctggagtactttctttcagaatctgataatttatcattttggagtaatatttggaatttctacaaacatagaaaagagtttttagttc...

Basic information

species Glycine max
transcript GLYMA05G28070.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G28070.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os01g69920.2 (Oryza sativa), 5'ss of exon 8
TGGTTTGTGTTAGTAGTGGTAAAGATGCCATCTCTTCCTTGAAGCCACCCCATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGGgtatgtatgcacctggagtactt-tctttcagaatctgataatttatcattttggagtaatatttggaatttctacaaacatagaaaagagtttttagttc--
|   |||||     || || ||| | || ||| | |   | || || || ||  | |||||||| ||||||||||| || || |||||||||||||||||||| || |   |    | | ||| | |||   | | |  |   |  | |||| | | |  | ||  | |  | |  |  |||  ||  |     ||  |||  
TTACTTGTGCAGACAGCGGGAAAAAAGCAATCACATTGCTAAAACCCCCGCACAATTTTGATGCTTGTTTCATGGACATACAGATGCCAGAAATGGATGGgtaagtcttttctgacactgcttgtgttttgcagtattgtttatactaatttggcatttctcttgtgcacgtatgtat-catctaatggttaccttttttcag

upper sequence: GLYMA05G28070.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G471529_T01 (Zea mays), 5'ss of exon 9
TGGTTTGTGTTAGTAGTGGTAAAGATGCCATCTCTTCCTTGAAGCCACCCCATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGGgtatgtatgcacctggagtactttctttcagaatctgataatttatcat-tttggagtaatatttggaatttctacaaacatagaaaagagtttttagttc----------------------------------------------------------
|   ||||| |   ||||| || || || ||| |     |||| || || ||  | |||||||| ||||||||||| || || ||||| |||||||||||||  |  |  | |     |  | |||||    |      |  | | |||  ||     | ||| || ||||  ||   |  |   | | |||  ||  |                                                            
TAACTTGTGCTGACAGTGGGAAGGAAGCAATCACACTGCTGAAACCTCCTCACAATTTTGATGCTTGTTTCATGGACATACAGATGCCTGAAATGGATGGgtgagattttatccc---ttttatctttggatactcatcatctcaccatactttagacattatctgtaatta-tattcagttgatacacagtacttgctcttgtcatcgatttatatttgtcttgttctcttttgtcatgcatttggcacattttgcag

upper sequence: GLYMA05G28070.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G423456_T01 (Zea mays), 5'ss of exon 8
TGGTTTGTGTTAGTAGTGGTAAAGATGCCATCTCTTCCTTGAAGCCACCCCATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGGgtatgtatgcacctggagtactt----tctttcagaatctgataatttatc-------attttggagtaatatttggaattt-ctacaaacatagaaa-agagtttttagttc-----------------------------
|   ||||| |  ||| || ||  | || ||| |     |||| || || ||    |||||||| ||||||||||| || || ||||| |||||||||||||  || |   | | |  || |     |||  |   |  | | |   ||||       || |     | |||      | || ||     ||  ||   | | ||| | ||||                             
TAACTTGTGCTGATAGCGGGAAGAAAGCAATCACGCAACTGAAACCTCCTCACAGTTTTGATGCTTGTTTCATGGACATACAGATGCCTGAAATGGATGGgtgagttttatctttgtatattcatcatctcactatactttagacactatctgtacctatatccagttgataaacaatacttgctcttgtcaccgatttacattttcttgttctcttgtgtcatgcatttggtaccttgcag

upper sequence: GLYMA05G28070.1 (Glycine max), 5'ss of exon 9
lower sequence: AT1G27320.1 (Arabidopsis thaliana), 5'ss of exon 9
TGGTTTGTGTTAGTAGTGGTAAAGATGCCATCTCTTCCTTGAAGCCACCCCATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGGgtatgtatgcacc-tggagtactttctttcagaatctgataatttatcattttggagtaatatttggaatttctacaaacatagaaaagagtttttagttc
|||| || | |   ||||| | | | || ||||| |   | |||||||| ||  |||||||||| || |||||||| ||||| ||||||||||||||||||||||  ||     |  | || ||| ||| | ||  |   ||| | | ||     | |   | |     | |   |   | |     ||            
TGGTCTGCGCTGAGAGTGGGATAAAGGCAATCTCATTGCTTAAGCCACCTCACGAGTTTGATGCTTGCTTCATGGACATTCAGATGCCAGAAATGGATGGgtatgcctgattggtatactagtttttttgaaaagttcgaaatatgtaataagaaaattgaaatgtttttctgccctgtctttctgcag------------

upper sequence: GLYMA05G28070.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv01s0010g03780.t01 (Vitis vinifera), 5'ss of exon 9
TGGTTTGTGTTAGTAGTGGTAAAGATGCCATCTCTTCCTTGAAGCCACCCCATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGGgtatgtatgcacctggagtactttctttcagaatctgataatttatcattttggagtaatatttggaatttctacaaacatagaaaagagt--ttttagttc------------------------------
| || ||||     ||||| |||  ||| ||| |     | || || |||||  | ||||||||||||||||||||||| || |||||||||||||| |||||||||||   |    ||| ||  |      || || | |  |   |||||  |  || | |      | || ||   ||  |  |   |  ||| || |                               
TCGTCTGTGCAGACAGTGGGAAAAGTGCAATCCCACTGCTTAAACCTCCCCACGACTTTGATGCCTGTTTCATGGATATCCAGATGCCAGAAATGGACGGgtatgtatgtcgccatggtatttgatgc---gatttgcttacatcaaattttctatcaa-actcctctctactgcatctatctatgattttcgtttgagcttgtctttataaatgtgaatctcctcccacag

upper sequence: GLYMA05G28070.1 (Glycine max), 5'ss of exon 9
lower sequence: PP1S252_49V6.1 (Physcomitrella patens), 5'ss of exon 13
TGGTTTGTGTTAGTAGTGGTAAAGATGCCATCTCTTCCTTGAAGCCACCCCATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGGgtatgtatgcacctggagtactttctttcagaatctgataatttatca---ttttggagtaatatttggaatttctacaaacatagaaaagagtttttagttc
| |  ||||||   || || | ||  || |||      || || || || ||  | |||||||| |||||||||||| | |||||||||||||||||||||||||  | |  |   | ||| |   ||||   | | ||| ||  | |    | | |||      ||     |  | ||   ||    | ||   |  |||  
TTGAGTGTGTTCACAGCGGAAGAGCAGCAATCCAGAAGTTAAAACCTCCTCACAACTTTGATGCGTGTTTCATGGATGTGCAAATGCCAGAAATGGATGGgtatggtttcttccttactacatatattcatgct-taatatttagtgaaggctcttgagagcatcttactcctgatgcactgattttcatgaagctc-agtc-

upper sequence: GLYMA05G28070.1 (Glycine max), 5'ss of exon 9
lower sequence: PP1S194_72V6.1 (Physcomitrella patens), 5'ss of exon 15
TGGTTTGTGTTAGTAGTGGTAAAGATGCCATCTCTTCCTTGAAGCCACCCCATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGGgtatgtatgcacctggagtactttctttcagaatctgataatttatc----attttggagtaatatttggaatttctacaaacatagaaaagagtttttagttc
| |  |||||||  ||||| | || ||| |||      |||||||| || ||  | |  ||||||||||| |||||| | ||||||||||||||||||||||| |  | |      | | |    ||||   || || ||| || ||    ||  | |  | | |||    ||        |     |||      | ||    
TTGACTGTGTTAACAGTGGGAGAGCTGCGATCCAAAGTTTGAAGCCTCCGCACAATTACGATGCCTGTTTTATGGATGTGCAAATGCCAGAAATGGATGGgtagggtttctttcccact-cgagttttcgtcatttggtaaattttctgagatgcttgcatcaaattcatgatgcaggttcattcgaaaactcaaatatac---

upper sequence: GLYMA05G28070.1 (Glycine max), 5'ss of exon 9
lower sequence: PP1S50_141V6.1 (Physcomitrella patens), 5'ss of exon 13
TGGTTTGTGTTAGTAGTGGTAAAGATGCCATCTCTTCCTTGAAGCCACCCCATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGGgtatg----tatgcacctggagtactttctttcagaatctgataatttatcattttggagtaatatttggaatttctacaaacatagaaaagagtttttagttc
| |  ||||||   ||||| | || ||| |||      |||||||| |||||  | || ||||||||||| |||||  | || |||||||||||||||||||| |      | |||    |||  |    |        |       ||| |   || | ||| |     |||    || ||       |||  |  | |  | 
TTGAGTGTGTTTACAGTGGAAGAGCTGCTATCCAGAAGTTGAAGCCTCCCCACAATTTCGATGCCTGTTTTATGGACGTGCAGATGCCAGAAATGGATGGgtagggttccttccactcttagtcatccactcgttgcaatagctgcatataagcctgcattaaaac---aaatggtaactaaagagctcaagtttgctgaaat-

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|254339480|gb|GR848238.1|GR848238
EST:     CATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGG                         ATTTGAAGCTACAAAGCGAGTTAGGGAGATGGAAGATAGTGTGAACAGAGA
genomic: CATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGGgtatgtatgc ... tttccaacagATTTGAAGCTACAAAGCGAGTTAGGGAGATGGAAGATAGTGTGAACAGAGA
EST: gi|151402718|gb|EV272531.1|EV272531
EST:     CATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGG                         ATTTGAAGCTACAAAGCGAGTTAGGGAGATGGAAGATAGTGTGAACAGAGA
genomic: CATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGGgtatgtatgc ... tttccaacagATTTGAAGCTACAAAGCGAGTTAGGGAGATGGAAGATAGTGTGAACAGAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTTTGTGTTAGTAGTGGTAAAGATGCCATCTCTTCCTTGAAGCCACCCCATCAGTTTGATGCCTGTTTCATGGATATTCAAATGCCAGAAATGGATGGgtatgtatgcacctggagtactttctttcagaatctgataatttatcattttggagtaatatttggaatttctacaaacatagaaaagagtttttagttc

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