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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaacaaatactaatcccttactttctctctttcctttcttggattgaacatttcttacatatgaattttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAACTCTGAGCCTCGTGGATTTG

Basic information

species Arabidopsis thaliana
transcript AT1G08110.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G08110.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os05g22970.1 (Oryza sativa), 3'ss of exon 5
--------------gtaagaaacaaatactaatccct-tactttctctctttcctttcttggattgaacatttcttacatatgaattttac-ttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAACTCTGAGCCTCGTGGATTTG
               |   || |   | ||  || || ||||    |  |||  || |   | | | || |  || | ||||     | |   || ||||||||||| ||||| | ||||||||| || |||||||| || ||||||||||| || |||||||| ||||
gtatgtgtttttattttgtaatcttgtccttctctctgtactaatacattttatttcccatgttagcacgtcactcatatatctccctaatactgtagCAACTGGGGCACAGAAAATGATCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG

upper sequence: AT1G08110.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G125310_T01 (Zea mays), 3'ss of exon 5
gtaagaaacaaatactaatcccttactttctctctttcctttcttggattgaacatttcttac-atatgaatt--------ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAACTCTGAGCCTCGTGGATTTG
|| ||         |   |  |||  |      |  | ||||  | | |||||   |  | |  | || ||||         ||| || ||||||||||| || || | ||| ||||| || |||||||| || ||||||||||| || |||||||| ||||
gtgagtcttgttaccccgtatctttgtgcgatgcacttctttaatagcttgaatggtcatcaggaaattaattaacactttgtacctgtagCAACTGGGGCACGGAAAATGACCCTGAATTCAAAGGTTACCATAATGGGAACTCAGACCCTCGTGGTTTTG

upper sequence: AT1G08110.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G08470.1 (Glycine max), 3'ss of exon 5
gtaagaaacaaatactaatcccttactttctctctttcctttcttggattgaacatttcttacatatgaattttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAACTCTGAGCCTCGTGGATTTG
    | |   ||||  ||| |  ||  ||   |  | |   |||         | ||||| ||| || |  |  |  | ||| || |||||||| || |||||||||||||| ||||| || |||||||| || ||||| |||||||| ||||
----gtatggaatataaatacgctatatttctttatccgagtct---------cttttctaaca-ataagata-atgtacagTAATTGGGGTACTGAAAGTGATCCTGAGTTCAAAGGCTACCACAATGGCAATTCTGAACCTCGTGGCTTTG

upper sequence: AT1G08110.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G08470.2 (Glycine max), 3'ss of exon 5
gtaagaaacaaatactaatcccttactttctctctttcctttcttggattgaacatttcttacatatgaattttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAACTCTGAGCCTCGTGGATTTG-----------------------------
    | |   ||||  ||| |  ||  ||   |  | |   |||         | ||||| ||| || |  |  |  | ||| || |||||||| || |||||||||||||| ||||| || |||||||| || ||||| |||||||| ||||                             
----gtatggaatataaatacgctatatttctttatccgagtct---------cttttctaaca-ataagata-atgtacagTAATTGGGGTACTGAAAGTGATCCTGAGTTCAAAGGCTACCACAATGGCAATTCTGAACCTCGTGGCTTTGGTATGTGATATTTCATTTCATTTAATTTG

upper sequence: AT1G08110.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv06s0061g00460.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------gtaagaaacaaatactaatcccttactttctctctttcctttcttggattg-aacatttcttacatatgaattttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAACTCTGAGCCTCGTGGATTTG
                                 |     | |  ||||  |     |  | | | |||   || | |   ||| | |  |       ||  ||  || ||||||||||||||| |||||||||||||| || |||||||| |||||||||||||| || |||||||||||||
gtaacaattatcatttattttgatgtcctctctatctgcaaaacaatctttctggcttacccatccctagttttgctgacaacgtgtaatgttccaaaaaattg-ttacagCAACTGGGGTACTGAGAGTGATCCTGACTTCAAAGGTTACCACAATGGGAACTCAGAACCTCGTGGATTTG

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|86058486|gb|DR354243.1|DR354243
EST:     GAGAGAACGGTTTAGACATTTGGTCAACCGGCAACAATTGAATTGACTCA                         CAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
genomic: GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
EST: gi|164071570|gb|ES210398.1|ES210398
EST:     AACCGGCAACAATTGAATTGACTCA                         CAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAAGGTTATCACAATGGGA
genomic: AACCGGCAACAATTGAATTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAA-GGTTATCACAATGGGA
EST: gi|163996677|gb|ES146529.1|ES146529
EST:     GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCA                         CAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGG
genomic: GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGG
EST: gi|86058484|gb|DR354241.1|DR354241
EST:     GAGAGAACGGTTTAGACATTTGGTCAACCGGCAACAATTGAATTGACTCA                         CAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
genomic: GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
EST: gi|86058487|gb|DR354244.1|DR354244
EST:     GAGAGAACGGTTTAGACATTTGGTCAACCGGCAACAATTGAATTGACTCA                         CAACTGGGGTACAGAGAGTGATCCTGAGTTTAA
genomic: GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAA
EST: gi|124905866|gb|EH979946.1|EH979946
EST:     CGGCAACAATTGAATTGACTCA                         CAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
genomic: CGGCAACAATTGAATTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
EST: gi|164008433|gb|ES056397.1|ES056397
EST:     CCGGCAACAATTAGAATTGACTCA                         CAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
genomic: CCGGCAACAATT-GAATTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
EST: gi|124832562|gb|EH917001.1|EH917001
EST:     GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCA                         CAACTGGGGTAACAAGAGAGTGAT
genomic: GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTA-CA-GAGAGTGAT
EST: gi|86042017|gb|DR337772.1|DR337772
EST:     GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCA                         CAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
genomic: GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
EST: gi|86058483|gb|DR354240.1|DR354240
EST:     GAGAGAACGGTTTAGACATTTGGTCAACCGGCAACAATTGAATTGACTCA                         CAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
genomic: GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
EST: gi|164201310|gb|ES050439.1|ES050439
EST:     CCGGCAACAATTGAATTGACTCA                         CAACTGGGGTACAGAGAGTGATCCTGAAGTTTAAAGGTTATCACAATGGGA
genomic: CCGGCAACAATTGAATTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGA-GTTTAAAGGTTATCACAATGGGA
EST: gi|164216707|gb|ES198873.1|ES198873
EST:     AACCGGCAACAATTGAATTGACTCA                         CAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
genomic: AACCGGCAACAATTGAATTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
EST: gi|125320038|gb|EL334123.1|EL334123
EST:     GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCA                         CAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAG
genomic: GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAG
EST: gi|86042021|gb|DR337776.1|DR337776
EST:     GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCA                         CAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
genomic: GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
EST: gi|86058480|gb|DR354237.1|DR354237
EST:     GAGAGAACGGTTTAGACATTTGGTCAACCGGCAACAATTGAATTGACTCA                         CAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
genomic: GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
EST: gi|86058481|gb|DR354238.1|DR354238
EST:     GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCA                         CAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
genomic: GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
EST: gi|164137702|gb|ES076473.1|ES076473
EST:     CCGGCAACAATTGAATTGACTCA                         CAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
genomic: CCGGCAACAATTGAATTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
EST: gi|86079248|gb|DR375005.1|DR375005
EST:     GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCA                         CAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
genomic: GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
EST: gi|86058489|gb|DR354246.1|DR354246
EST:     GAGAGAACGGTTTAGACATTTGGTCAACCGGCAACAATTGAATTGACTCA                         CAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
genomic: GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
EST: gi|86086149|gb|DR381908.1|DR381908
EST:     GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCA                         CAACTGTGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
genomic: GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
EST: gi|86058490|gb|DR354247.1|DR354247
EST:     AGAGAACGGTTTAGACATTTGGTCAACCGGCAACAATTGAAATTGACTCA                         CAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
genomic: AGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAA-TTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
EST: gi|301501106|gb|HO206646.1|HO206646
EST:     GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCA                         CAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
genomic: GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
EST: gi|164009687|gb|ES206363.1|ES206363
EST:     AACCGGCAACAATTGAATTCGACTCA                         CAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGA
genomic: AACCGGCAACAATTGAATT-GACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGA
EST: gi|164137104|gb|ES212519.1|ES212519
EST:     AACCGGTCAACAATTGAATTGACTCA                         CAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
genomic: AACCGG-CAACAATTGAATTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
EST: gi|125146475|gb|EL181184.1|EL181184
EST:     GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCA                         CAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCA
genomic: GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCA
EST: gi|86058479|gb|DR354236.1|DR354236
EST:     GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCA                         CAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
genomic: GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
EST: gi|125024517|gb|EL096786.1|EL096786
EST:     CGGCAACAATTGAATTGACTCA                         CAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAAGGTTATCACAATGGGA
genomic: CGGCAACAATTGAATTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAA-GGTTATCACAATGGGA
EST: gi|86058488|gb|DR354245.1|DR354245
EST:     GAGAGAACGGTTTAGACATTTGGTCAACCGGCAACAATTGAATTGACTCA                         CAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
genomic: GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
EST: gi|86058485|gb|DR354242.1|DR354242
EST:     GAGAGAACGGTTTAGACATTTGGTCAACCGGCAACAATTGAATTGACTCA                         CAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
genomic: GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA
EST: gi|86058491|gb|DR354248.1|DR354248
EST:     GAGAGAACGGTTTAGACATTTGGTCAACCGGCAACAATTGAATTGACTCA                         CAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTCATCACAATGGGAA
genomic: GAGAGAACGGTTTGGACATTTGGTCAACCGGCAACAATTGAATTGACTCAgtaagaaaca ... ttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctctctttcctttcttggattgaacatttcttacatatgaattttacttgcagCAACTGGGGTACAGAGAGTGATCCTGAGTTTAAAGGTTATCACAATGGGAACTCTGAGCCTCGTGGATTTG
                             ttcttac  putative branch site (score: 2)
                                           ttttactt  putative PPT
                           atttcttacatatgaa  TA-rich tract