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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtactccaccatttccactaaaatctgttttccatctgtgatcataatagcctttggtaaactagtatgtgcttagaatgagatgagttaacttattggcgcagGTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACG

Basic information

species Arabidopsis thaliana
transcript AT1G12000.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 12
---------------------------gtttgtactccaccatttccact--aaaatctgttttccatctgtgatcataatagcct-----ttggtaaactagt--------atgtgcttagaatgagatga------------gttaacttattggcgcagGTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACG
                             ||| |  ||   |||   ||   | ||   | |||      |||||  |   ||| |     ||    ||| ||         |||  |||  ||||| ||||            |||    | ||  | |||||||| ||| | ||||||||||||||||||||||| || ||||| |||||  | ||| | ||||||||||| |||||||| ||||
gtatgcacactatagttccctgtcacttgttggatacccagattggaacctaagaacgggctttgtggaagtgatgtttgcagcatgtttgtttacgaaccagcgcaggcagatgaacttctaatgatatgatcatgctcttatgtttgtatttttactcagGTTGGCAACCTCGCTGCTCCTGTGGAAGAATGGACCGTTGGTGGAACTGCATTGACATCGTTGATGGATGTTGAGAGGAGGCACG

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 10
---------------------------------gtttgtactccaccatttccactaaaatctgttttccatctgtgatcataat----agcctttggtaa-actag---tatgtgcttagaatg-agatgagttaacttattggcg-cagGTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACG
                                    |  | |  |  |||||  ||| |   || |||  ||   |||   |  |    |   ||| |||| ||| |    ||   || |   |   |||  | ||   ||||     |||||||| || |||  ||||||||| |||||||||||||| ||||| ||||| |||||  | |||||||| || ||||||||||| |
gtttgtgccaatgcttctcattatcttctctaatcatcaaattaaatatttcttctaga--ttggttttaatgattgactgtggttgaaaatgtttcgtaatactggggccatcaactcaatttttggatctgctatgatatttttatcagGTTGGTAATTTGTGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 12
---------------------------------gtttgtactccaccatttccactaaaatctgttttccatctgtgatcataat----agcctttggtaa-actag---tatgtgcttagaatga-gatgagttaacttattg-gcgcagGTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACG
                                    |  | |     |||||  ||| |   || |||  ||   ||||  |  |    |   |||||||| ||| |    ||   || |   |   |||  | ||   ||||  |  |||||||| || ||   ||||||||| |||||||||||||| ||||| ||||| |||||  | |||||||| || ||||||||||| |
gtttgtgcctatgctcttcacattatcttctaatcatcaaattagatatttcttctaga--ttggttttaatgattgattgtggttcaaaatgtttggtaatactgggtccatcaactcaattttttgatttgctatgatattttgatcagGTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 12
------------------gtttgtactccaccatttccactaaaatctgttttccatctgtgatcataatagcctttgg--taaactagtatgtgcttag----------------aatgagatgagttaacttatt---------ggcgcagGTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACG
                  |  |  |       || ||  || |||| | |  |  ||  ||| | ||||| |  | |    | || | ||   || || |                ||     | | |||| || ||         ||  |||||||  || ||   |||||| || |||||||||||||| ||||| ||||| |||||  |  |||||||||| |||||||| || |
gtttgtgcttctctacatgccttaatcttttgatatcttcttaaatatctcctagattggtgttgataattgattgtactttgaaattgtgcttgttttgcaatattgaagtcaccaacctagttatttaatttgttttgatatttggatcagGTTGCCAATTTATGTGCTCCGGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACCTCACTGATGGATGTGGAGAGGAGGCATG

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 12
---------------------------------------------------------------------gtttgtactccaccatttccactaaaatctgttttccatctgt-gatcataatagcctttggtaaactagtatgtgcttagaatgagatgagttaacttattggcgcagGTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACG
                                                                      | | |  | |  | | |  | |  || || || |   ||| | ||   | ||||   ||  |||   |  |     || |    |  ||  |    | ||     |||||||||||  || ||||||| || |||||||||||||| ||||| |||||  | ||  | || |||||||| ||||||||||| |
gttggttcttcattccgcttaatcatttttgtactttttgatcagtcttccttttttttcatttttccaatatctcattctgcttatagagttcaaactcttgttattctatcgaaggttatagtagttaataactgaacaaactttttgt---aattgtttctcatcatgtcttcagGTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATG

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|116438104|gb|EG480696.1|EG480696
EST:     ATGGCGCTGGAGTACTCCTCAACAGTGGGAAGACCGGACTAATTTCTTCG                         GTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGC
genomic: ATGGCGCTGGAGTACTCCTCAACAGTGGGAAGACCGGACTAATTTCTTCGgtttgtactc ... attggcgcagGTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGC
EST: gi|164171411|gb|EL978750.1|EL978750
EST:     CTGGAGTACTCCTCAACAGTGGGAAGACCGGACTAATTTCTTCG                         GTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGTT
genomic: CTGGAGTACTCCTCAACAGTGGGAAGACCGGACTAATTTCTTCGgtttgtactc ... attggcgcagGTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCT
EST: gi|86088437|gb|DR384196.1|DR384196
EST:     ATGGCGCTGGAGTACTCCTCAACAGTGGGAAGACCGGACTAATTTCTTCG                         GTTGGGAACTTGGCTGCTCCTGTGGGAAGAATGGACTGTAGGTGGGACTGC
genomic: ATGGCGCTGGAGTACTCCTCAACAGTGGGAAGACCGGACTAATTTCTTCGgtttgtactc ... attggcgcagGTTGGGAACTTGGCTGCTCCTGT-GGAAGAATGGACTGTAGGTGGGACTGC
EST: gi|86060419|gb|DR356176.1|DR356176
EST:     ATGGCGCTGGAGTACTCCTCAACAGTGGGAAGACCGGACTAATTTCTTCG                         GTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCT
genomic: ATGGCGCTGGAGTACTCCTCAACAGTGGGAAGACCGGACTAATTTCTTCGgtttgtactc ... attggcgcagGTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCT
EST: gi|86060418|gb|DR356175.1|DR356175
EST:     ATGGCGCTGGAGTACTCCTCAACAGTGGGAAGACCGGACTAATTTCTTCG                         GTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCT
genomic: ATGGCGCTGGAGTACTCCTCAACAGTGGGAAGACCGGACTAATTTCTTCGgtttgtactc ... attggcgcagGTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCT
EST: gi|163973150|gb|ES211802.1|ES211802
EST:     GGCGCTGGTAGTTACTCCTCAACAGTGGGAAGACCGGACTAATTTCTTCG                         GTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGAC
genomic: GGCGCTGG-AG-TACTCCTCAACAGTGGGAAGACCGGACTAATTTCTTCGgtttgtactc ... attggcgcagGTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGAC
EST: gi|164064828|gb|ES107014.1|ES107014
EST:     ATGGCGCTGGAGTACTCCTCAACAGTGGGAAGACCGGACTAATTTCTTCG                         GTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCT
genomic: ATGGCGCTGGAGTACTCCTCAACAGTGGGAAGACCGGACTAATTTCTTCGgtttgtactc ... attggcgcagGTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCT
EST: gi|125026332|gb|EL098601.1|EL098601
EST:     CCTCAACAGTGGGAAGACCGGACTAATTTCTTCG                         GTTGGGAACTTGGCTGCTCCTGTGGAA
genomic: CCTCAACAGTGGGAAGACCGGACTAATTTCTTCGgtttgtactc ... attggcgcagGTTGGGAACTTGGCTGCTCCTGTGGAA
EST: gi|116438054|gb|EG480646.1|EG480646
EST:     ATGGCGCTGGAGTACTCCTCAACAGTGGGAAGACCGGACTAATTTCTTCG                         GTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGC
genomic: ATGGCGCTGGAGTACTCCTCAACAGTGGGAAGACCGGACTAATTTCTTCGgtttgtactc ... attggcgcagGTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGC
EST: gi|124737342|gb|EH828744.1|EH828744
EST:     CCTCAACAGTGGGAAGACCGGACTAATTTCTTCG                         GTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCT
genomic: CCTCAACAGTGGGAAGACCGGACTAATTTCTTCGgtttgtactc ... attggcgcagGTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctttggtaaactagtatgtgcttagaatgagatgagttaacttattggcgcagGTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACG
                                    agttaac  putative branch site (score: 3)
                                      ttaacttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtactccaccatttccactaaaatctgttttccatctgtgatcataatagcctttggtaaactagtatgtgcttagaatgagatgagttaacttattggcgcagGTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA