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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtaccttgatgcttatttgaatggttgaacttttaagacaaggataaaagatataatggtgttctttgatgcagCTGCTTTGGGTCAACCTTATCATGGATACTCTTGGAGCACTTGCACTAGCTACAGAGCCACCAACCGATCATCTTATGCATAGAACCCCTGTTGGAAGAA

Basic information

species Arabidopsis thaliana
transcript AT3G21180.1
intron # 26
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 27
------gttagtaccttgatgcttatt--tgaatggttgaacttttaagacaaggataaaagatataatggt---gttctttgat--gcagCTGCTTTGGGTCAACCTTATCATGGATACTCTTGGAGCACTTGCACTAGCTACAGAGCCACCAACCGATCATCTTATGCATAGAACCCCTGTTGGAAGAA
| | ||| || | ||| | | || ||| | | || | | || | | | ||| |||||| || ||||| ||||| |||||||||||||| || || |||||||| || ||||| ||||| || || ||||||||||| ||| | || ||||| ||||
gtttgagctcatactctgtttgttactgatagataacacggaagttatggttaatattctctctcttttgcttgggcttgttggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAA

upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: GLYMA08G23760.1 (Glycine max), 3'ss of exon 29
-------gttagtaccttgatgcttatttgaatggttgaacttttaagacaaggataaaagatata------------atg---gtgttctttgatgcagCTGCTTTGGGTCAACCTTATCATGGATACTCTTGGAGCACTTGCACTAGCTACAGAGCCACCAACCGATCATCTTATGCATAGAACCCCTGTTGGAAGAA
| | | | || | | | || | ||| || ||||| |||| ||| || |||| | | ||||| | ||||| ||||||||||||||||| ||||| || |||||||| ||||| || |||||||| || | || ||||| ||| | || ||||| |||
ataaaaaactgactgataattacgtacaagggcagattaaaatcatcatcaatgaaaaaaggtatatcttggtttttcatgttcatgctcttgggtacagCTTTTGTGGGTTAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCACCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAA

upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 26
----gttagtaccttgatgcttatttgaatggttgaacttttaagac-----aaggataaaagatata------------atg---gtgttctttgatgcagCTGCTTTGGGTCAACCTTATCATGGATACTCTTGGAGCACTTGCACTAGCTACAGAGCCACCAACCGATCATCTTATGCATAGAACCCCTGTTGGAAGAA
|| || |||| ||| | | || | | | || | | | | ||||| |||| ||| || |||| | | ||||| | ||||||||||||||||||||||| ||||| || |||||||| ||||| || || ||||| || | || ||||| ||| | || ||||| |||
aaaaactaagac--tgatagttacgtacaagggtagattaaaaacatcatcaatgaaaaaaaggtatattttggtttttgatgttcatgctcttgggtacagCTTTTGTGGGTCAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCGCCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAA

upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: GLYMA13G44990.1 (Glycine max), 3'ss of exon 28
-----------------gttagtaccttgatgc-ttatttgaat----ggttgaacttttaagacaaggataaaagatataatggtgttctttgatgcagCTGCTTTGGGTCAACCTTATCATGGATACTCTTGGAGCACTTGCACTAGCTACAGAGCCACCAACCGATCATCTTATGCATAGAACCCCTGTTGGAAGAA
|| | | || | ||| ||| | | || |||| || | || | | |||| | |||||||||||||||||||| || ||||| || |||||||| ||||| || || ||||| || | |||||||| ||| | || ||||| |||
gtaccctgccctctaatattgttgaatgaatatatgattcaaattacagatagagtcacatttacaatacctgcgtttacccctctcttactgtgtatagCTTTTGTGGGTCAACCTTATCATGGACACACTTGGGGCTCTTGCACTGGCTACGGAACCGCCAACAGACAACCTTATGCACAGATCACCAGTTGGCCGAA

upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 28
-----------gttagtaccttg-atgcttatttgaatggttgaactt---------ttaagacaagg-ataaaagatataatggtgttctttgatgcagCTGCTTTGGGTCAACCTTATCATGGATACTCTTGGAGCACTTGCACTAGCTACAGAGCCACCAACCGATCATCTTATGCATAGAACCCCTGTTGGAAGAA
| | | || ||| | || ||| || || |||| | | | | | | | | | ||| | ||||| || ||||| ||||||||||||||||||||||||||||||||| | ||||| || |||||||| |||||||||||| | ||| | || ||||| |||
gcagtgtgaaaaatgttgcttttcatggtctttcaaataaccaaatttagggattatttaattcttcttacatcactttttcttttctcacttggtacagCTTCTATGGGTTAACCTTATCATGGATACTCTTGGAGCACTTGCATTGGCTACTGAACCACCAACTGATCATCTTATGGAAAGATCTCCAGTTGGTCGAA

upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: PP1S8_288V6.1 (Physcomitrella patens), 3'ss of exon 28
----------------------------------------------------gttagtaccttgat-gcttatttga-atggt----tgaacttttaag--acaaggataaaagatataatggtgttctt-tgatgc----agCTGCTTTGGGTCAACCTTATCATGGATACTCTTGGAGCACTTGCACTAGCTACAGAGCCACCAACCGATCATCTTATGCATAGAACCCCTGTTGGAAGAA
| || ||||| || ||| || |||| ||| |||| ||| | || | || ||| || | | ||| || || | |||||||| | |||||||| ||| | |||||||||||||| ||||| |||||||| || ||| |||||||| || | | || ||||||||||
gtttgtaccttaatctttttaatatgggaaatttagtaacagtgtagtgtcggcgagaaccttaatcatttaactgttatggcgtcatgagattttgcattacataacttaaggttactgatgtgctcatgttgtgctggtagTTGTTATGGGTCAATTTGATCATGGACACTTTGGGAGCACTTGCACTTGCTACTGAGCCACCTACAGATGATCTTATGGATCGGAAACCAGTTGGAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatggttgaacttttaagacaaggataaaagatataatggtgttctttgatgcagCTGCTTTGGGTCAACCTTATCATGGATACTCTTGGAGCACTTGCACTAGCTACAGAGCCACCAACCGATCATCTTATGCATAGAACCCCTGTTGGAAGAA
                                            ctttgat  putative branch site (score: 5)
 tgttcttt  CT-rich tract
 ataaaagatataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtaccttgatgcttatttgaatggttgaacttttaagacaaggataaaagatataatggtgttctttgatgcagCTGCTTTGGGTCAACCTTATCATGGATACTCTTGGAGCACTTGCACTAGCTACAGAGCCACCAACCGATCATCTTATGCATAGAACCCCTGTTGGAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA