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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatagcgcatagtgttctatttaaagcataaggcacttgttatgttgtcatgataatgtgatgctgtacagctcaaagttctattgttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGCCACACTTTGGAGTCTCTTCGAGGAATTAAA

Basic information

species Glycine max
transcript GLYMA07G18160.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G19230.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 11
--tatagcgcatagtg-ttctatttaaagcataaggcacttgttatgttgtcatgataatgtgatgctgtacagctcaaagttctattgttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGCCACACTTTGGAGTCTCTTCGAGGAATTAAA
  | | |     |       |  ||    |||||   |    | |  |  | || ||    | ||  | | || || | ||  |   |    | | ||| ||||||||| ||||||||  ||||||| ||||| || ||||| |||||||||||||| ||||| || |||||||||||  || | ||||| || |||||||| 
tttgttggtttcatcaaccttgcttcctccataacatatgcat-acctgctgattatctgttaattttctcca-ctaagaggccatctaaaat-cttttgcagTGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGCAGCTCAGGAGATCTTTGGCCACACACTGCAATCTCTCCGTGGAATTAAG

upper sequence: GLYMA16G19230.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 9
tatagcgcatagtgttctatttaaagcataaggcacttgttatg-ttgtcatgataatgtgatgctgtacagctcaaagttctattgttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGCCACACTTTGGAGTCTCTTCGAGGAATTAAA
 ||      |      ||||||    |  |   ||| | | ||| | ||| |       |  |  | ||    ||| | || | |  | ||   | | ||||||||| ||||||||  |||| || ||||||||||| || |||||||||||||| || || |||||||||||||||||| | || ||||| |||||||| 
catgagtattgactgcctatttttgtcg-acttcacatttcatgatagtcctctatccctcttaatctaattatcatatttttctgctattctatgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAG

upper sequence: GLYMA16G19230.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM5G871262_T02 (Zea mays), 3'ss of exon 11
tatagcgcatagtgttctatttaaagcataaggcacttgttatgttgtcatgataatgtgatgctgtacagctcaaagttctattgttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGCCACACTTTGGAGTCTCTTCGAGGAATTAAA
| |      |    ||   |    ||| |      | | ||  ||  ||   | |   |  |  | ||     || | || |  ||   ||  | | ||||||||| ||||||||  |||| || |||||||| ||||| ||||||||||| || || || || ||||||||||| ||| | || ||||| |||||||| 
tttgattggtttatttggctgctgagctttgtcttcgtatttcgtgatcgaaaaatcatcttaatctaactaccatacttttcctgccatatgtgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTATTATGCACAAGCAACTGCTGCTCAAGAGATCTTTGGCCACACATTGCAATCCCTTCGTGGAATTAAG

upper sequence: GLYMA16G19230.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 11
-tatagcgcatagtgttc-tatttaaagcataaggcacttgttatgttgtcatgataatgtgatgctgtacagctcaaagttctattgttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGCCACACTTTGGAGTCTCTTCGAGGAATTAAA
 ||     | ||||  || |||||   |      |      | |        |  |||  |       ||||    |   || |       |    || ||||||||| || |||||| |||| |||||||  || ||||||||||| || || || ||||| |||||||||||||||||| |||| ||||| || ||||| 
gtaggcttcttagttctcatatttcccgtcagctgatagcatcaaaagtatgtattaacttttattcttacaatcgactattgtggctcactgaaattccagTGTGATTCAATTCTGCGCCACTGCATTTGGATATTATGCTCAAGCCACCGCCGCTCAGGAGATATTTGGCCACACTTTGCAGTCCCTTCGCGGTATTAAG

upper sequence: GLYMA16G19230.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 11
tatagcgcatagtgttctatttaaagcat--aaggcacttgttatgttgtcatgataatgtgatgctgtaca-gctcaaagttctattgtt--ttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGCCACACTTTGGAGTCTCTTCGAGGAATTAAA
     |   |||   || |   ||  | |  ||   ||   |  |    |||  || |  || |  |   ||   ||  |||  | | |||  ||     | ||| ||||| || || ||  |||| |||||||  || || |||||||| ||||| |||||||| |||||||||||||| ||| |||| ||| |||||||||| 
-----ctattagatgtcaaaccaagacttttaatatacagctgctaccctcacaattacatgttaatcctcacagtctgagtaatgtggttcatttaaaatgcagCGTGATTCAATTTTGTGCCACTGCATTTGGATATTACGCTCAAGCCACTGCTGCCCAGGAGATATTTGGCCACACATTGCAGTCCCTTAGAGGAATTAAG

upper sequence: GLYMA16G19230.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 11
----------------------------------------------------------tata-gcgcatagtgttctatttaaagcataaggcacttgttatgttgtcatgataatgtgatgctgtacagctcaaagttctattgttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGCCACACTTTGGAGTCTCTTCGAGGAATTAAA
                                                           | | | |   | | ||    |||    ||   | |  | ||       | || ||   || |  | || |  |||  ||| |    |  | |  |||||||||||| || |||||| ||||||||||||  |||||||||||||||||||| || ||||||||||||||||||||  |||| |||||   ||||||||||
gtttgcatgtttagtcctctaaattcattaacagatataattgggttgggaccagcaccacaaggggggactcttactgttattttatgtagaatatatttccagaccttggtag-atgtttatctataa-tcattgttgttggctcctccaatttcagTGTGATTCAATTCTGCGCCACAGCATTTGGTTACTATGCTCAAGCAACTGCTGCACAGGAAATATTTGGCCACACACTGGAATCTCTCAAAGGAATTAAA

upper sequence: GLYMA16G19230.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ37798 (Selaginella moellendorffii), 3'ss of exon 11
tatagcgcatagtgttctatttaaagcataaggcacttgttatgttgtcatgataatgtgatgctgtacagctcaaagttctattgttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGCCACACTTTGGAGTCTCTTCGAGGAATTAAA
                                        ||||   |    | | | | |   |  | | ||| || ||  ||      | || | ||||||||||||||||||||| | ||||||||| |  ||||| |  |||||  |||| || ||||||||||| |  ||  | ||||| ||||| ||||| || 
---------------------------------------gtatgcactatcaagattcttagctttcaaaactccaacttggat---acaaactctccagTGTGATCCAGTTCTGCTCTAAAGCATTTGCATTGTATGCGCGTGCAACCACAGCTCAAGAAATATTTGGTCTTACACTTGAGTCCCTTCGTGGAATCAAG

upper sequence: GLYMA16G19230.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ32053 (Selaginella moellendorffii), 3'ss of exon 11
tatagcgcatagtgttctatttaaagcataaggcacttgttatgttgtcatgataatgtgatgctgtacagctcaaagttctattgttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGCCACACTTTGGAGTCTCTTCGAGGAATTAAA
                                        ||||   |    | | | | |   |  | | ||| || ||  ||      | || | ||||||||||||||||||||| | ||||||||| |  ||||| |  |||||  |||| || ||||||||||| |  ||  | || || ||||| ||||| || 
---------------------------------------gtatgcactatcaagattcttagctttcaaaactccaacttggat---acaaactctccagTGTGATCCAGTTCTGCTCTAAAGCATTTGCATTGTATGCGCGTGCAACCACAGCTCAAGAAATATTTGGTCTTACACTTGAATCCCTTCGTGGAATCAAG

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|51337760|gb|CO981626.1|CO981626
EST:     ATGAACTCTTTTCTGTTTAATGTGGGCCTTATTCTTCTTTGTTCCATTAG                         TGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGC
genomic: ATGAACTCTTTTCTGTTTAATGTGGGCCTTATTCTTCTTTGTTCCATTAGgtcagtatag ... accttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGC
EST: gi|15814514|gb|BI786789.1|BI786789
EST:     ATGAACTCTTTTCTGTTTAATGTGGGCCTTATTCTTCTTTGTTCCATTAG                         TGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGC
genomic: ATGAACTCTTTTCTGTTTAATGTGGGCCTTATTCTTCTTTGTTCCATTAGgtcagtatag ... accttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGC
EST: gi|254348009|gb|GR854258.1|GR854258
EST:     ATGAACTCTTTTCTGTTTAATGTGGGCCTTATTCTTCTTTGTTCCATTAG                         TGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGC
genomic: ATGAACTCTTTTCTGTTTAATGTGGGCCTTATTCTTCTTTGTTCCATTAGgtcagtatag ... accttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGC
EST: gi|51335080|gb|CO978946.1|CO978946
EST:     ATGAACTCTTTTCTGTTTAATGTGGGCCTTATTCTTCTTTGTTCCATTAG                         TGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGC
genomic: ATGAACTCTTTTCTGTTTAATGTGGGCCTTATTCTTCTTTGTTCCATTAGgtcagtatag ... accttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcatgataatgtgatgctgtacagctcaaagttctattgttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGCCACACTTTGGAGTCTCTTCGAGGAATTAAA
                                      ttgttttaccttttc  CT-rich tract
                                    tattgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatagcgcatagtgttctatttaaagcataaggcacttgttatgttgtcatgataatgtgatgctgtacagctcaaagttctattgttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGCCACACTTTGGAGTCTCTTCGAGGAATTAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - agtgttc
- - - - - - - - - - - - - - - - -cacttgt
- - - - - - - - - - - - - - - - - - - - - tgttgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgct