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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttttttaatctcttctgctcttttgttttctgttgtgttaatagcgaagattaatcttgtatttgccatatccgttacttggggaaaattgttttaacattcctatgcccctggttttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTGGACAGCCAACCCGAGATCCCGAACCACGTGAATGATGAACGCGCCTGAG

Basic information

species Arabidopsis thaliana
transcript AT2G14740.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G14740.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os10g20630.1 (Oryza sativa), 3'ss of exon 11
gtaagcttttttaatctcttctgctcttttgttttctgttgtgttaatagcgaagattaatcttgtatttgccatatccgttacttggggaaaattgttttaacattcctatgcccctggttttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTGGACAGCCAACCCGAGATCCCGAACCACGTGAATGATGAACGCGCCTGAG
| | | | | | | | | | | | || || | ||||| | ||| | | | | | | | ||| | | || ||| |||||||||||| ||||||||||| || |||||||||||||||||| ||||||| ||| ||| | || || || ||||||||| |
-----------------------atgatcagacctttttcatttcgagatcagaaatgtccaccacatctt---tatccatagcttatgacctgctaatattaatcccgtgtgctgtt--tctttcagTCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTGGACAGTCAAGGGGAGGTGCCAAATCATACAAATGATGAAGAACACCATT

upper sequence: AT2G14740.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA01G45380.1 (Glycine max), 3'ss of exon 11
gtaagcttttttaatctcttctgctcttttgttttctgttgtgttaatagcgaagattaatcttgtatttgccatatccgttacttggggaaaattgttttaacattcctatgcccctggttttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTGGACAGCCAACCCGAGATCCCGAACCACGTGAATGATGAACGCGCCTGAG
| || ||||| || |||| || | |||| | ||| | | | ||| || || | | | || ||||||| |||||||||||||| ||||| |||||||| || ||||| || || ||||| |||||||||||| | || | || || || || |||||| || | || |||
----------------------------aaatcagaacacaagtgaatagtgatgattcatttgtaatttaacttattcagttttataggataaaaaattaatggtatttttgttggtggttttgcagCAATACATGGATTCAGAAATCAGAGCAATCATGGCGCAATATATGCCCTTGGACAGCCAAGCAGAAGTTCCAAATCATGTCAATGATCAAAGAGCATGAA

upper sequence: AT2G14740.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA10G40340.1 (Glycine max), 3'ss of exon 11
------------------------------------------gtaagcttttttaatctcttctgctctt---ttgttttctgttgtgtta-atagcgaa--gattaa-tcttgtat----------ttgccatatccgttacttggggaaaattgt-tttaacatt--------cctatgcccctggttttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTGGACAGCCAACCCGAGATCCCGAACCACGTGAATGATGAACGCGCCTGAG
| || | ||| | | ||| ||| || | | ||||| | | ||| |||||| | | |||| ||| | | | | | | ||| || ||| |||| | || || |||| ||| ||| ||||| || || ||||||||||| ||||||||||| ||||| |||||||||||| || || || ||||||| || ||| | || | |
gtaagctttatcacattctcagtttggtgatgctatttgatatttagatgccttattttattcaattctaaaattatatagcattgtggcatgcaatgaaatgattaaatttcgtatcatctgagacttgttagaaactcaaatatgagaacatgacgtttgccatttaccggtatttttgttggtgtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTGGACAGCCAAGGAGAAATTGTAAATCACGTGAGCGAAGAAAGAGCGTAAA

upper sequence: AT2G14740.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA20G27000.1 (Glycine max), 3'ss of exon 11
-----------------------------------------------gtaagcttttttaatctcttctgctcttttgttttctgttgtgtta-atagcgaaga----ttaatcttgtatt-tgccatatccgtta----------cttggg-----gaaaattgt--tttaacatt-cctatgcccctggttttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTGGACAGCCAACCCGAGATCCCGAACCACGTGAATGATGAACGCGCCTGAG
| ||||||| || |||| |||| | | ||||| | | ||| | | ||| |||| | | | |||| || | |||| ||| |||| | | | || || |||| ||| ||| ||||| || || ||||||||||| ||||||||||| ||||| |||||||||||| || | || |||||| | || ||| | || |||
gtaagctttgtcacattttcagtttggtgatgctattagatatttagatgcctttttttattcaattctaaa-ttttatatagcattgtggcatgcaacgagaagcattaaattcggtatcatctgagacttgttagaaactcaaatatgagaacatgaaatttgcaatttaccggtatttttgttggtgtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTGGACAGCCAAGGAGAAGTTGTAAATCACGTGCACGAAGAAAGAGCGTGAA

upper sequence: AT2G14740.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA11G00370.1 (Glycine max), 3'ss of exon 11
---------------------------------------gtaagcttttttaatctcttctgctcttttgttttctgttgtgttaatagcgaagattaatcttgtatttgccatatccgttacttggggaaaattgttttaacattcctatgcccctggttttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTGGACAGCCAACCCGAGATCCCGAACCACGTGAATGATGAACGCGCCTGAG
| | |||| | ||||| || || || ||| | | | | | || ||| | | | ||| || ||| | | | ||||||| |||||||||||||| || || || ||||| || ||||| || || ||||| |||||||||||| | || | || || || || |||||| || | || |||
gtaagctcttctgctttctctcattttggtggtgttattggatgcttaatgctgaaattctgtagcattagagcgtgctgagttgccgtcatgattcatttgtaatttaaatttattcagttttataggataaaaatttagtggtatttttattggtggttttgcagCAATACATGGATTCCGAAATTAGAGCAATCATGGCGCAATATATGCCCTTGGACAGCCAAGCAGAAGTTCCAAATCATGTCAATGATCAAAGAGCATGAA

upper sequence: AT2G14740.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv03s0091g00740.t01 (Vitis vinifera), 3'ss of exon 11
gtaagcttttttaatctcttctgctcttttgttttctgttgtgttaatagcgaagattaatcttgtatttgccatatccgttacttggggaaaattgttttaacattcctatgcccctggttttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTGGACAGCCAACCCGAGATCCCGAACCACGTGAATGATGAACGCGCCTGAG
|| | | || || | | ||| ||| || | |||||| | | |||| ||| |||| || | || | ||| || |||| ||| |||||||||||| ||||||||||| ||||||||||| |||||||| ||||||||||| | || |||| || || || ||| || | || |||
-------------------aatgttttaatgagttgagaaattgcaatg--taaggttgaca--atatttgttggttttgc-acttttggattattgatt-gatgtttc-atggt--tgctttttcagTCATACATGGACTCGGAGATCAGAGCTATAATGGCACAATACATGCCCCTGGACAGCCAAACGGAAGTCCCAAATCATGTCTCTGAGGATCATGCATGAA

upper sequence: AT2G14740.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S227_69V6.1 (Physcomitrella patens), 3'ss of exon 13
gtaagcttttttaatctcttctgctcttttgttttctgttgtgttaatagcgaagattaatcttgtatttgccatatccgttacttggggaaaattgttttaacattcctatgcccctggttttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTGGACAGCCAACCCGAGATCCCGAACCACGTGAATGATGAACGCGCCTGAG-
|| |||| | | | ||| |||| || | || | | | |||| | || || || | |||| | | | ||| || |||| |||||||||||| ||||| || || |||||||| |||||||||||| | |||||| | || | |||| ||| || ||| |||
-------ttgcatgtctccacaaatggagatctctcttttgtactagtt-cgtaaagtg--cttgaacttatttgatt--------------aacggatttagcttgtcggtgct----gtggaacagTCATACATGGACTCGGAGATAAGGGCAATAATGGCGCAGTACATGCCACTCGACAGCTCAAGTGAAGTTAATCACCATCTGACCGAGGAA-GCGTAAAGAC

upper sequence: AT2G14740.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: EFJ30872 (Selaginella moellendorffii), 3'ss of exon 11
gtaagcttttttaatctcttctgctcttttgttttctgttgtgttaatagcgaagattaatcttgtatttgccatatccgttacttggggaaaattgttttaacattcctatgcccctggttttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTGGACAGCCAACCCGAGATCCCGAACCACGTGAATGATGA-ACGCGCCTGAG
|||| | ||| | || | | | | | ||| || | | | | | | | || |||||||| || ||||| ||||| || ||||||||||||||||| | ||||||||| ||| | | ||||| || | || || | | ||
--------------------------------------------------------gtaatatca-attcgtgat-tgcttgatccagcaaaacttaacgttctctactggaaacttt--tcctgtagTCTTACATGGATTCGGAGATTAGAGCTATCATGGCACAGTACATGCCGCTCGACAGCCAAAACGATGTGCATCACCACTTGCAAGAGGATGCTTGATTGT-

upper sequence: AT2G14740.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: EFJ22768 (Selaginella moellendorffii), 3'ss of exon 11
gtaagcttttttaatctcttctgctcttttgttttctgttgtgttaatagcgaagattaatcttgtatttgccatatccgttacttggggaaaattgttttaacattcctatgcccctggttttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTGGACAGCCAACCCGAGATCCCGAACCACGTGAATGATGA-ACGCGCCTGAG
|| || ||| | || | || |||| | ||| || | | | | | | | || |||||||| || ||||| ||||| || ||||||||||||||||| | ||||||||| ||| | | ||||| || | || || | | ||
--------------------------------------------------gtaatatcaat-tcgtgctcgcttgatccagca-------aaacttaacgttctctactggaaacttt--tcctgtagTCTTACATGGATTCGGAGATTAGAGCTATCATGGCACAGTACATGCCGCTCGACAGCCAAAACGACGTGCATCACCACTTGCAAGAGGATGCTTGATTGT-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatccgttacttggggaaaattgttttaacattcctatgcccctggttttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTGGACAGCCAACCCGAGATCCCGAACCACGTGAATGATGAACGCGCCTGAG
                        ttttaac  putative branch site (score: 2)
 aaaattgttttaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcttttttaatctcttctgctcttttgttttctgttgtgttaatagcgaagattaatcttgtatttgccatatccgttacttggggaaaattgttttaacattcctatgcccctggttttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTGGACAGCCAACCCGAGATCCCGAACCACGTGAATGATGAACGCGCCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC