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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggattatacacttttatcaagtagtggagcatcgaaattcattatactcagtttttttcttttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT

Basic information

species Arabidopsis thaliana
transcript AT5G43810.2
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 14
gtaaggattatacacttttatcaagtagtggagcatcgaaattcattatac---tcagtttttttcttttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
|||||| | |  || || |||    ||   |  ||||    ||  ||  ||   | |   | | |  |  | |   |  |||||||||| |||||||||||||| ||||| ||||| ||||| || || || |||||||| |||||  ||||||| || || |||||| | || || ||||
gtaaggctga-gcatttctat-ggttacatggccatcattttttttttaacctcttaccctctctaataagctgcatgcagGTTGTTGCATCTCAAGACTGGCCAGAAGTTACAAAGTATGCTGGATTGGTGTGTGCTCAGGCTCATCGGCAAGAGCTCATTCAAGATCTTTACAAGACAT

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 13
----------------------------gtaaggattatacacttttatcaagtagtgga-gcatcgaaattcattat--actcagtttttttcttttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
                            | |   |     ||  || ||||||   || |    |     ||  || |  ||| | | |   || | || |      ||||||||||||||||||| ||||| ||||| ||||| ||||| || || ||||||||||| || ||| ||||||| || || || ||  | || |||||||
gtaaggctcattactactttccatttctgcatcaacatgtcatattcatcaagatatgcacatctttgtcttggttttggactta-tctcactcatatgctgctgacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTTTGTGCTCAGGCACACCGGCAAGAGCTCATTCAGGACCTTTACAAAACAT

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 14
----------------------------gtaaggattata-cacttttatcaagtagtggagcatcgaaattcat----tatactcagtttttttcttttgttttctt-tagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
                             | |  | |||  ||| || |||| |   || | ||||   |||  |       ||| |  | | | | | | | | ||   ||||||||||||||||||| ||||| ||||| ||||| ||||| || || ||||||||||| || ||| ||||||| || || |||||  | || |||||||
gtaaggctcgttactactttgccatttcttcatcaatatgtcacattcatcaggatatgca-catccttatttttgttccgaacttatctgtctgcctctttctgctcacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTTTGTGCTCAGGCACACCGGCAAGAGCTCATTCAAGACCTTTACAAAACAT

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 14
---------------gtaaggattatacacttttatcaagtagtggagcatcgaaattcattatactcagtttttttctt----ttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
                |  |  ||  |   ||| ||   | | |||  || |||   |  |  ||     | | | |  |    |||   ||| |||||||| || ||||||||||||||||||||||| |||||||| |||||||| |||||||||||||| || || ||||| |||||||||||||| ||||  |
gtacacttatgatccatttgtcttg-attttttaatattgcaatggttca-cgagggttttggtagctgatatctattgtgcaattgcaatctatagGTTGTAGCATCTCAAGACTGGCCTGAAGTGACGAAATATGCCGGTTTAGTGTGTGCTCAAGCTCATAGACAGGAACTCATACAAGATTTGTACAAAATGT

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA10G38770.1 (Glycine max), 3'ss of exon 15
------gtaaggattatacacttttatcaagtagtggagcat--cgaaattcattata--ctcagtttttttcttttgttt------tctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
       |     ||||  |  |||||   ||  |  |||||  ||| | |||||      |  |     |  |  |||||      ||| ||||| || || || || |||||||| ||||||||||||||||| |||||||| |||||||||||||| ||||| |||||||||||||||||||| ||||| |
gtatttttctaatttatttatctttattt-gttttatagcattgcgatagtcattgagggttttggaaactgataatgtttacccaatctatagGTAGTCGCATCCCAGGACTGGCCCGAAGTGACAAAATATGCCGGTTTAGTATGTGCTCAAGCTCATAGGCAGGAACTTATACAAGATTTGTACAAAACTT

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA10G00530.1 (Glycine max), 3'ss of exon 6
gtaagg--attatacacttttatcaagtagtggagcatcgaaattcattatactcagtttttttcttttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
||| |   || || || || | |  | |  |  |   |  |       |  |     | | | ||  |   |   |  |||| || || |||||||||||||||||| ||||||||||||| |||||||| |||||||||||||| || || ||||| |||||||||||||| ||||  |
gtacgcttatgatccatttgtcttgattttttaattttgcagtggttcttgagctgatatctatcgctcaatacgt--agGTAGTAGCATCTCAAGACTGGCCTGAACTGACAAAATATGCTGGTTTAGTGTGTGCTCAAGCTCATAGACAGGAACTCATACAAGATTTGTACAAAATGT

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 15
------gtaaggattatacacttttatcaagtagtggagcatcgaaattcattatactcagtttt-----tttcttttgttt------tctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
       |     ||||  |  |||||   ||  |  ||||| | |||   | ||     |||||      |  |  |||||      |||  |||| || || || || |||||||| ||||||||||||||||| ||||| || || || |||||||| ||||| |||||||||||||||||||| ||||| |
gtacttatctaatttatttatctttattt-gttttatagcattgcaata-gtcatcgagggttttggaaactcataatgtttacccaatctacagGTAGTAGCATCCCAGGACTGGCCCGAAGTGACAAAATATGCCGGTTTGGTATGCGCCCAAGCTCATAGGCAGGAACTTATACAAGATTTGTACAAAACTT

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 12
gtaaggattataca-cttttatcaag--tagtggagcatcg--------aaattcattat------actcagttttt------ttcttttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
||||   || |  | ||  ||||| |  |  | || | | |        ||| |  ||||      |||  |||  |      || || | ||   | ||||| || |||||||| |||||||||||||| ||||||||||| || || ||||||||||| |||||||| || ||||| ||||||||||| || || ||||
gtaaaatttctttaactgatatcatgcttcctagaaccttgtttttcctaaagtggttattgaggaactttgttgctgatagattgttgtattaattgtagGTAGTAGCTTCTCAGGACTGGCCTGAAGTCACAAAATATGCAGGATTGGTTTGTGCTCAGGCTCACAGACAGGAACTGATACAAGATTTATACAAGACAT

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: EFJ24991 (Selaginella moellendorffii), 3'ss of exon 15
gtaaggattatacacttttatcaagtagtggagcatcgaaattcattatactcagtttttttcttttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
                        ||| ||  ||       | |  |  |  | ||     ||  ||| | | | ||||||||||| || ||||| ||||| || ||||| || |||||||| ||||||||||||||||| ||  | |||||||| ||||||||| | || || || |
------------------------gta-tgctgctct----tccgctgcagcc-gtgaaactcaattgctgt-tatagGTTGTTGCATCGCAAGATTGGCCCGAGGTGACGAAGTATGCGGGATTAGTTTGTGCTCAAGCACATCGTCAAGAACTGATACAAGATCTCTACAAGACCT

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: EFJ19862 (Selaginella moellendorffii), 3'ss of exon 14
gtaaggattatacacttttatcaagtagtggagcatcgaaattcattatactcagtttttttctt--ttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
                           ||       |||  ||  || |  |  || | |   |    ||  |  |  ||||||| |||||||| || ||||| ||||| || ||||| || ||| |||| || |||||||||||||| |||||  | || |||||||||||||||||||
---------------------------gtaagtgtacgatttttcttttcgtgtgtctctcaataagctgcctgttacagGTTGTCGCTTCTCAGGATTGGCCAGAAGTAACGAAATACGCAGGTCTAGTCTGCGCTCAAGCTCACAGACAAGAGTTGATCCAAGATTTGTATAAAACAT

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: EFJ15357 (Selaginella moellendorffii), 3'ss of exon 15
gtaaggattatacacttttatcaagtagtggagcatcgaaattcattatactcagtttttttcttttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
                        ||| ||  || |     | |  || | || ||     ||  ||| | | | ||||||||||| || ||||| ||||| || ||||| || |||||||| ||||||||||||||||| ||  | |||||||| ||||||||| | || || || |
------------------------gta-tgctgcttt----tccgctacagtc-gtgaaactcaattgctgt-tatagGTTGTTGCATCGCAAGATTGGCCCGAGGTGACGAAGTATGCGGGATTAGTTTGTGCTCAAGCACATCGTCAAGAACTGATACAAGATCTCTACAAGACCT

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 14
gtaaggattatacacttttatcaagtagtggagcatcgaaattcattatactcagtttttttct----tttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
                           ||       |||  ||  || |  |  || | |   |    | ||  |  |  ||||||| |||||||| || ||||| ||||| || ||||| || ||| |||| || |||||||||||||| |||||  | || |||||| ||||||||||||
---------------------------gtaagtgtacgatttttcttttcgtgtgtctctaaataagctgtgcctgttacagGTTGTCGCTTCTCAGGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTGTGCGCTCAAGCTCACAGACAAGAGTTGATCCAAGATCTGTATAAAACAT

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: EFJ19863 (Selaginella moellendorffii), 3'ss of exon 14
gtaaggattatacacttttatcaagtagtggagcatcgaaattcattatactcagtttttttctt--ttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT---------------
                                | | |||  ||  || |  |  || | |   |    ||  |  |   |||||| |||||||| || ||||| ||||| || ||||| || ||| |||| || |||||||||||||| |||||  | || |||||||||||||||||||               
--------------------------------gta-cgatttttcttttcgtgtgtctctaaataagctgcctgttaccggttgtcgcttctcagGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTGTGCGCTCAAGCTCACAGACAAGAGTTGATCCAAGATTTGTATAAAACATGGGTTGATCCTCAGA

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|47828868|gb|CK118552.1|CK118552
EST:     ACGTGACTCACCCAGAGAACGGGGAAGAGTCAAGCCCTTCAATCGCTGCT                         GTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTT
genomic: ACGTGACTCACCCAGAGAACGGGGAAGAGTCAAGCCCTTCAATCGCTGCTgtaaggatta ... ttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtagtggagcatcgaaattcattatactcagtttttttcttttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
                         tactcagtttttttct  CT-rich tract
                                tttttttcttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggattatacacttttatcaagtagtggagcatcgaaattcattatactcagtttttttcttttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC