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'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttaccttcaactgttattagtttggaagaagcaacaaaaagataggggacttgaaaccttttataggctttaatgatgatttaaaattgacattcttttatgcctttggtttattcttggagtatgagaaataactgaaaatatttctataacaatttgcatgacacttgatcccgtagGTATCTGCTGCCCGAGAAGAAGTGCCAGGAAGACGTGGTTATCCTGGATATATGTATACAGATCTTGCAACAATTTATGAACGAGCTGGGAGAATTGAGG

Basic information

species Glycine max
transcript GLYMA10G42940.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 9
gtaatttaccttcaactgttattagtttggaagaagcaacaaaaagataggggacttgaaaccttttataggctttaatgatgatttaaaattgacattcttttatgcctt-tggtttattcttggagtatgagaaataactgaaaatatttctataacaatttgcatgacacttgatcccgtagGTATCTGCTGCCCGAGAAGAAGTGCCAGGAAGACGTGGTTATCCTGGATATATGTATACAGATCTTGCAACAATTTATGAACGAGCTGGGAGAATTGAGG
                                                                                     |     || |  |||   |        || |  |||  || | | | |   ||          | |  || ||||   |  ||    |||      ||||||||| || |||||||||||||||||||| || ||||| |||||||||||||||||||| ||||| ||||| || ||||| ||||||||| | ||||| |
----------------------------------------------------------------------------------acatctccttttatgttcgactgcaataaatgataaattgctgaaattttatttattgtgattggcactaatacaacacggta-attgtgctta--tatgtagGTATCAGCAGCCCGAGAAGAAGTGCCAGGTAGGCGTGGGTATCCTGGATATATGTATACTGATCTGGCAACCATATATGAGCGAGCTGGGCGTATTGAAG

upper sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 9
gtaatttaccttcaactgttattagtttggaagaagcaacaaaaagataggggacttgaaaccttttataggctttaatgatgatttaaaattgacattcttttatgcctttggtttattcttggagtatgagaaataactgaaaatatttctataacaat-ttgcatgacacttga---tcccgtagGTATCTGCTGCCCGAGAAGAAGTGCCAGGAAGACGTGGTTATCCTGGATATATGTATACAGATCTTGCAACAATTTATGAACGAGCTGGGAGAATTGAGG
                                                                                |  |||||| ||  || ||      ||  ||| | | ||     |   |   ||  | |      || ||||||  | |||  | ||||    |||    |   |||||| ||||| ||||||||||| |||||||| || |||||||||||||||||||||||||| ||||| |||||||| ||||| || |||||| | ||||| |
--------------------------------------------------------------------------------agtatttaagatcaacctt------tgtatttaggtaatcaaatggtaaattgatttcatgtttgatgtttcta--ataatgctacatgggcattgtgctttttgtagGTTTCTGCAGCCCGAGAAGAGGTGCCAGGTAGGCGTGGTTATCCTGGATATATGTATACTGATCTGGCAACAATATATGAGCGTGCTGGGCGTATTGAAG

upper sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 9
gtaatttaccttcaactgttattagtttggaagaagcaacaaaaagataggggacttgaaaccttttataggctttaatgatgatttaaaattgacattcttttatgcctttggtttattcttggagtatgagaaataactgaaaatatttctataacaatttgcatgacacttgatcccgtagGTATCTGCTGCCCGAGAAGAAGTGCCAGGAAGACGTGGTTATCCTGGATATATGTATACAGATCTTGCAACAATTTATGAACGAGCTGGGAGAATTGAGG
                                                                         ||| ||    |||||| ||| || || | |       || | | |||    ||  |   ||  |   ||    || |  |   ||| |  ||||    |||  |   |||||| ||||| ||||||||||| |||||||| || |||||||||||||||||||||||||| ||| | |||||||| ||||| || |||||| | ||||| |
-------------------------------------------------------------------------ttttatat--atttaagattaaccttttcta------ttagctaattaaatgacaaattgatgtcgttgtttctaataatgctaca-tgggcattgtgctt--ttttgtagGTTTCTGCAGCCCGAGAAGAGGTGCCAGGTAGGCGTGGTTATCCTGGATATATGTATACTGATTTGGCAACAATATATGAGCGTGCTGGGCGTATTGAAG

upper sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 9
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 10
gtaatttaccttcaactgttattagtttggaagaagcaacaaaaagataggggacttgaaaccttttataggctttaatgatgatttaaaattgacattcttttatgcctttggtttattcttggagtatgagaaataactgaaaatatttctataacaatttgcatgacacttgatcccgtagGTATCTGCTGCCCGAGAAGAAGTGCCAGGAAGACGTGGTTATCCTGGATATATGTATACAGATCTTGCAACAATTTATGAACGAGCTGGGAGAATTGAGG
                                                                                     | | ||  || |||    |   |  ||     ||||||| | | ||||  || |  | ||    |   |||    ||  | |   |||    ||| ||||| ||||||||||| ||||||||||| ||||| |||||||| || || || ||||| || ||  | || || || || ||  |||| ||| ||||||| |
------------------------------------------------------------------------------------gtgataaccgatatttgcatgctctgttcaca-attcttgaactttgag--atgataggaagc-ctgaaatagtgtttaacgttg-actaatacccttagGTCTCTGCTGCCCGTGAAGAAGTGCCTGGAAGGCGTGGTTACCCAGGTTACATGTACACCGACTTGGCTACCATATACGAGAGAGCAGGGCGAATTGAAG

upper sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 9
gtaatttaccttcaactgttattagtttggaagaagcaacaaaaagataggggacttgaaaccttttataggctttaatgatgatttaaaattgacattcttttatgcctttggtttattcttggagtatgagaaataactgaaaatatttctataacaatttgcatgacacttgatcccgtagGTATCTGCTGCCCGAGAAGAAGTGCCAGGAAGACGTGGTTATCCTGGATATATGTATACAGATCTTGCAACAATTTATGAACGAGCTGGGAGAATTGAGG
                                                                              |  | ||||     |    |  |||||    |   ||      ||| | | |   || | |      ||  || |    |||  | | |     |||   | | ||||||||||||||||||||||||| || || || ||||| |||||||| ||||||||||| ||||| || || ||||||||||| |||||  | ||||| |
-----------------------------------------------------------------------------cttctaattttgttcttgagtatttttaa---tcaagtaccccattgaattcttcaaactcatcactgatgcttgtgatgcaaactactta----ttgcaactgcagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTATATGTATACTGATCTGGCGACGATTTATGAACGTGCTGGACGTATTGAAG

upper sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 9
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 9
gtaatttaccttcaactgttattagtttggaagaagcaacaaaaagataggggacttgaaaccttttataggctttaat-gatgatttaaaattgacattcttttatgcctttggtttattcttggagtatgagaaataactgaaaatatttctataacaatttgcatgacacttgatcccgtagGTATCTGCTGCCCGAGAAGAAGTGCCAGGAAGACGTGGTTATCCTGGATATATGTATACAGATCTTGCAACAATTTATGAACGAGCTGGGAGAATTGAGG
                                                                       |||  | | | | | |||        | | ||||    | | | | |       | || |  | ||| ||   | |||||| | |  |  |||  ||   |||| | |    |||| |||||||| || |||||||| || ||  | ||||| || ||||| |||||||| || |||||||| || ||||||||||| |||||  | |||||||
-----------------------------------------------------------------------gctgcactcggttacttagttaatcaagtattttgaaacctcgatat----cgagggtctatgtaatgac--gatatatttttgt--cgttttcaat--tacttaaac----agGTGTCTGCTGCTCGTGAAGAAGTACCCGGTCGTCGTGGGTACCCTGGTTATATGTACACCGATCTTGCCACCATTTATGAACGTGCTGGACGTATTGAGG

upper sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 9
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 8
----gtaatttaccttcaactgttattagtttggaagaagcaacaaaaagataggggacttgaaaccttttatag-gctttaatgatgat-ttaaaattgacattcttttatgcctttggtttattc--ttggagtatgagaaataactgaaaatatttctataacaatttgca-tgacacttgatcccgtagGTATCTGCTGCCCGAGAAGAAGTGCCAGGAAGACGTGGTTATCCTGGATATATGTATACAGATCTTGCAACAATTTATGAACGAGCTGGGAGAATTGAGG
         || |  | ||    | || | |||||          | ||| |||      |||||   |  ||    ||     | || | |   || |    ||     |    | |  | |||||  ||||  | | |  || | ||  |  | |      ||   ||| || |  || ||  ||   ||||| |||||||| || ||||||||||| ||  | ||||| |||||||| || |||||||| ||||| || || ||||||||||| |||||  |||| || |
gtacaagtgtttctcttaaagacttttcgcttggactcctttttcagaagttagctcctgtgaaattctacatgctactccgcagttggtatctgaaatagtttttaagcaaatttgtaatctattcagttggtttttaattaagaccttcag-tgtgctacaaattttttccactctcaattcttcaaatagGTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTACATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAG

upper sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 9
lower sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 8
gtaatttaccttcaactgttattagtttggaagaagcaacaaaaagataggggacttgaaaccttttataggctttaatgatgatttaaaattgacattcttttatgcctttggtttattcttggagtatgagaaataactgaaaatatttctataacaatttgcatgacacttgatcc-cgtagGTATCTGCTGCCCGAGAAGAAGTGCCAGGAAGACGTGGTTATCCTGGATATATGTATACAGATCTTGCAACAATTTATGAACGAGCTGGGAGAATTGAGG
                                                                                                                              |||||  |  |  |    ||  ||   || | |  |   || ||    | |    |||||| ||||| || || || || ||||| ||  | ||||| |||||||| ||||||||||||||| | ||||||||||| || || |||||  ||||||| |
------------------------------------------------------------------------------------------------------------------------------gtatggtatgtttc----aagtttgtcatgagagctatgataaccagggctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG

upper sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 9
lower sequence: EFJ13375 (Selaginella moellendorffii), 3'ss of exon 8
gtaatttaccttcaactgttattagtttggaagaagcaacaaaaagataggggacttgaaaccttttataggctttaatgatgatttaaaattgacattcttttatgcctttggtttattcttggagtatgagaaataactgaaaatatttctataacaatttgcatgacacttgatcc-cgtagGTATCTGCTGCCCGAGAAGAAGTGCCAGGAAGACGTGGTTATCCTGGATATATGTATACAGATCTTGCAACAATTTATGAACGAGCTGGGAGAATTGAGG
                                                                                                                              ||||||        |  || | |||  || | | ||   || ||  | | |    |||||| ||||| || || || || ||||| ||  | ||||| |||||||| ||||||||||||||| | ||||||||||| || || |||||  ||||||| |
------------------------------------------------------------------------------------------------------------------------------gtatgatcgtatgtttcaagt-ttttcatgagagttatgataaccatggctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG

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|19452473|gb|BM953883.1|BM953883
EST:     TTCTTGTGATACTCACAGATATGAGTTCTTATGCTGATGCTCTTCGTGAG                         GTATCTGCTGCCCGAGAAGAAGTGCCAGGAAGACGTGGTTATCCTGGATAT
genomic: TTCTTGTGATACTCACAGATATGAGTTCTTATGCTGATGCTCTTCGTGAGgtaatttacc ... gatcccgtagGTATCTGCTGCCCGAGAAGAAGTGCCAGGAAGACGTGGTTATCCTGGATAT
EST: gi|16278890|gb|BI943147.1|BI943147
EST:     TTCTTGTGATACTCACAGATATGAGTTCTTATGCTGATGCTCTTCGTGAG                         GTATCTGCTGCCCGAGAAGAAGTGCCAGGAAGACGTGGTTATGCTGGATAT
genomic: TTCTTGTGATACTCACAGATATGAGTTCTTATGCTGATGCTCTTCGTGAGgtaatttacc ... gatcccgtagGTATCTGCTGCCCGAGAAGAAGTGCCAGGAAGACGTGGTTATCCTGGATAT
EST: gi|16283207|gb|BI945427.1|BI945427
EST:     TTCTTGTGATACTCACAGATATGAGTTCTTATGCTGATGCTCTTCGTGAG                         GTATCTGCTGCCCGAGAAGAAGTGCCAGGAAGACGTGGTTATCCTGGATAT
genomic: TTCTTGTGATACTCACAGATATGAGTTCTTATGCTGATGCTCTTCGTGAGgtaatttacc ... gatcccgtagGTATCTGCTGCCCGAGAAGAAGTGCCAGGAAGACGTGGTTATCCTGGATAT
EST: gi|16278507|gb|BI942940.1|BI942940
EST:     TTCTTGTGATACTCACAGATATGAGTTCTTATGCTGATGCTCTTCGTGAG                         GTATCTGCTGCCCGAGAAGAAGTGCCAGGAAGACGTGGTTATCCTGGATAT
genomic: TTCTTGTGATACTCACAGATATGAGTTCTTATGCTGATGCTCTTCGTGAGgtaatttacc ... gatcccgtagGTATCTGCTGCCCGAGAAGAAGTGCCAGGAAGACGTGGTTATCCTGGATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagaaataactgaaaatatttctataacaatttgcatgacacttgatcccgtagGTATCTGCTGCCCGAGAAGAAGTGCCAGGAAGACGTGGTTATCCTGGATATATGTATACAGATCTTGCAACAATTTATGAACGAGCTGGGAGAATTGAGG
     aataactgaaaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttaccttcaactgttattagtttggaagaagcaacaaaaagataggggacttgaaaccttttataggctttaatgatgatttaaaattgacattcttttatgcctttggtttattcttggagtatgagaaataactgaaaatatttctataacaatttgcatgacacttgatcccgtagGTATCTGCTGCCCGAGAAGAAGTGCCAGGAAGACGTGGTTATCCTGGATATATGTATACAGATCTTGCAACAATTTATGAACGAGCTGGGAGAATTGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA