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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcggtacacaaacctgcactttctaaacgtgtcctaattactttttaaagcttagttaacttttctttgatgcaccatcgtcttggtacttaagacaaatgttgagcttactctttttttttgccagGTTTATGAGCCTGTAGAAGAAGGTTCGTACATCAAAATGATTGATATGGTCAGTGGGAACGGTGGACAGATACAA

Basic information

species Arabidopsis thaliana
transcript AT1G07110.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 11
gtcggtacacaaacctgcactttctaaacgtgtcctaattactttttaaagcttagttaacttttctttgatgcaccatcgtcttggtacttaagacaaatgttgagcttactctttttttttgccagGTTTATGAGCCTGTAGAAGAAGGTTCGTACATCAAAATGATTGATATGGTCAGTGGGAACGGTGGACAGATACAA
              ||| | || | |||  | |  ||| ||    ||| | |  | |  | ||||  |  |   |  || || | | ||  |   | | || ||||    ||  |||        ||||| ||||| || || ||||||||||| ||||| ||||||||||| ||||| |||||||| || || ||  || | 
------------gtctgtaattgccaaat-tatattaaata----ttatatcacaatacattttttgtcaag--aatatagtatagttatatgtaa-acattttgaa---acctttt--------cagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG

upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 14
gtcggtacacaaacctgcactttctaaacgtgtcctaattactttttaaagcttagttaacttttctttgatgcaccatcgtcttggtacttaagacaaatgttgagcttactctttttttttgccagGTTTATGAGCCTGTAGAAGAAGGTTCGTACATCAAAATGATTGATATGGTCAGTGGGAACGGTGGACAGATACAA
                                        | | | ||| |  || ||   |||    |  | ||   |   |||  | |||||    ||||||||         ||   |   ||||||||||||| | ||  | ||||| || ||||| |||||||||||||||||||||||| | |||||||| ||||||
-------------------------------------gcaagtctataacgtgtactt---tttatgattgttcaagctgagctttttccttaaat--aatgttga---------ttccatgcaccagGTTTATGAGACAGTTAATGAAGGATCTTACATAAAAATGATTGATATGGTCAGTGGGCATGGTGGACAAATACAA

upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 15
gtcggtacacaaacctgcactttctaaacgtgtcctaattactttttaaagcttagttaacttttctttgatgcaccatcgtcttggtacttaagacaaatgttgagcttactctttttttttgccagGTTTATGAGCCTGTAGAAGAAGGTTCGTACATCAAAATGATTGATATGGTCAGTGGGAACGGTGGACAGATACAA
                         ||   | | |    |||||||||    |  | || ||    |||                  | |||||    ||||||||         || | |   ||||||||||||| | ||  | ||||| || ||||| |||||||||||||||||||||||| | |||||||| ||||||
-----------------------gcaagtatataccgtgtactttttatgattgtgctagctacctttt------------------tccttaaat--aatgttga---------ttctatgcaccagGTTTATGAGACAGTTAATGAAGGATCTTACATAAAAATGATTGATATGGTCAGTGGGCATGGTGGACAAATACAA

upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 19
gtcggtacacaaacctgcactttctaaacgtgtcctaattactttttaaagcttagttaacttttctttgatgcaccatcgtcttggtacttaagacaaatgttgagcttactctttttttttgccagGTTTATGAGCCTGTAGAAGAAGGTTCGTACATCAAAATGATTGATATGGTCAGTGGGAACGGTGGACAGATACAA
                                                              ||| | ||||    ||    ||  |   ||     ||||  ||       |  ||   |   ||||||||||||| | ||  | ||||| || ||||| |||||||||||||||||||||||| | |||||||| ||||||
----------------------------------------------------------gtactttttatgatttttca--agctgagctttttccttaaataatg------ttgattccatgcaccagGTTTATGAGACAGTTAATGAAGGATCTTACATAAAAATGATTGATATGGTCAGTGGGCATGGTGGACAAATACAA

upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 13
gtcggtacacaaacctgcactttctaaacgtgtcctaattactttttaaagcttagttaacttttctttgatgcaccatcgtcttggtacttaagacaaatgttgagcttactctttttttttgccagGTTTATGAGCCTGTAGAAGAAGGTTCGTACATCAAAATGATTGATATGGTCAGTGGGAACGGTGGACAGATACAA
                         ||   | || ||  ||||||   ||  ||   |  || |||   | ||  |  | |  ||          |  ||||||||         |||  | ||||||||||||||| | ||||||||||| || ||||| ||||||||||| |||| ||||||  | || || || ||||||
-----------------------gcaagtctttcatatgtactttc--aaattttaatggctattcaa-ggtgagcttttgcttta---------aataatgttga---------tttcatatgccagGTTTATGAGACGGTAGAAGAAGGATCTTACATAAAAATGATTGACATGGCCAGTGGACATGGAGGGCAAATACAA

upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 21
gtcggtacacaaacctgcactttctaaacgtgtcctaattactttttaaagcttagttaacttttctttgatgcaccatcgtcttggtacttaagacaaatgttgagcttactctttttttttgccagGTTTATGAGCCTGTAGAAGAAGGTTCGTACATCAAAATGATTGATATGGTCAGTGGGAACGGTGGACAGATACAA-----
                                       |||||||  ||  ||   |  || |||   | ||  |  | |  ||          |  ||||||||         |||  | | ||||||||||||| | ||||||||||| || ||||| ||||||||||| |||| ||||||  | || || || ||||||     
--------------------------------------gtactttt--aaattttaatggctattcaa-ggtgagcttttgcttta---------aataatgttga---------tttcatataccagGTTTATGAGACCGTAGAAGAAGGATCTTACATAAAAATGATTGACATGGCCAGTGGACATGGAGGGCAAATACAAGTAAG

upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA14G37520.3 (Glycine max), 3'ss of exon 13
gtcggtacacaaacctgcactttctaaacgtgtcctaattactttttaaagcttagttaacttttctttgatgcaccatcgtcttggtacttaagacaaatgttgagcttactctttttttttgccagGTTTATGAGCCTGTAGAAGAAGGTTCGTACATCAAAATGATTGATATGGTCAGTGGGAACGGTGGACAGATACAA
                                       |||||||  ||  ||   |  || |||   | ||  |  | |  ||          |  ||||||||         |||  | | ||||||||||||| | ||||||||||| || ||||| ||||||||||| |||| ||||||  | || || || ||||||
--------------------------------------gtactttt--aaattttaatggctattcaa-ggtgagcttttgcttta---------aataatgttga---------tttcatataccagGTTTATGAGACCGTAGAAGAAGGATCTTACATAAAAATGATTGACATGGCCAGTGGACATGGAGGGCAAATACAA

upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 13
gtcggtacacaaacctgcactttctaaacgtgtcctaattactttttaaagcttagttaacttttctttgatgcaccatcgtcttggtacttaa-gacaaatgt-tgagctta-----ctctttttttttgccagGTTTATGAGCCTGTAGAAGAAGGTTCGTACATCAAAATGATTGATATGGTCAGTGGGAACGGTGGACAGATACAA
                                      |   ||  |  |||||| |||  |  |  ||| | |  | || | || ||| ||   || | || | |||   ||      | |  |  | | ||||||||||||||| || |||||||| || |||||||||||||||||||||||  ||||  | | |||||||||||| 
-------------------------------------gtagtttcctggagcttactta--tgatgattggtactac-tcatatttgtattttgtgaaagatttctgaaaataaacaattgtgctcctgtaccagGTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTTGGTGGCCAAGATGGACAGATACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caccatcgtcttggtacttaagacaaatgttgagcttactctttttttttgccagGTTTATGAGCCTGTAGAAGAAGGTTCGTACATCAAAATGATTGATATGGTCAGTGGGAACGGTGGACAGATACAA
                                agcttac  putative branch site (score: 3)
                                  cttactcttttttttt  CT-rich tract
                                   ttactcttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcggtacacaaacctgcactttctaaacgtgtcctaattactttttaaagcttagttaacttttctttgatgcaccatcgtcttggtacttaagacaaatgttgagcttactctttttttttgccagGTTTATGAGCCTGTAGAAGAAGGTTCGTACATCAAAATGATTGATATGGTCAGTGGGAACGGTGGACAGATACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA