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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT

Basic information

species Arabidopsis thaliana
transcript AT3G15980.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 13
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacatttta-ttttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
                                                 |    |||| |||   |  |||| | ||||   |||   ||  |    | || | |  |  |||| |     || |  |   |  |||| ||||||| |||||||| || ||||||||||||||  | ||||| ||||| || ||||||||||| ||||||||||||
------------------------------------------------gtgagtaattttgttcctggatttaaatttttttttgcgtgtcatttggaatattatgat-gctaaataggatctgctttctta--tttgtagAATCTCTATTGGGCCGATAGTGGTGATTTAGTGACAATTGCAAGTGACACCTCATTCTACATTTTGAAGTACAAT

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 4
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
                                                 |    |||| |||   |  |||  | |||   |||   ||  |    | || | |  |  |||| |      |||  |     ||||| ||||||| |||||||| || ||||||||||||||  | ||||| ||||| || ||||||||||| ||||||||||||
------------------------------------------------gtgagtaattttgttcatggattcaaatttattttgcgtgtcatttggaatattatgat-gctaaatag--gatccgctttcttatttgtagAATCTCTATTGGGCCGATAGTGGTGATTTAGTGACAATTGCAAGTGACACCTCATTCTACATTTTGAAGTACAAT

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttg-tcccaattagtgtctttactaactctttactcccatgaa-aaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
                                                       | ||     |||  | ||  | |   | ||  | |  |   ||  | | || |    || |   || |    | |    ||||  |||| |||||||||||||| || |||||  |||| || || || |||||||| |||||||||||  |||||||||| 
----------------------------------------------------gtgagtcaaatattatctattgatatttatagattgatacttttaacgaatttcatactgaaataactagttttgtcactgtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 13
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaa-gttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
                     ||  || ||| ||     | | |   || || |||  || |  |||||||    |  || |||||| ||||| ||| | |     | |      |||||                || |||||||||| |||||||| ||||||||||||||| | ||||| |||||||||||||||||||| ||||| || |||
---------------------gtaatg-gaatttg----ttaccttattatttcaaacctttttttacattca--tgccatttgaaatgttgtgccactcaaaacatgt-----ttctttg---------------tgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 13
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagt-tgaaagttgtcccaattagtgtctttactaactctttactcc---catgaaaaatt-tgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
                     ||  ||| |  ||  ||||  |  | || |   | |||   | |    ||  |||| || | |||| ||  |  || ||    | |  | |        |||     ||||     || || |||||||||| |||||||| ||||||||||||||| | ||||| |||||||||||||||||||| ||||| || |||
---------------------gtaatgacat-ttgacatttgttgccttata--atttcaaacctggttttgcatttccaatgtgaaggtaatggcatttgacatttgaaatgttgtgccactgaagacatgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 13
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagtt-gtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
                                                       | ||    ||   |||||   ||  || |||| || ||    || ||| |   || ||||  |||  |   || |    |||  ||||| |||| |||||||| ||||||||  |||| || || || |||||||| |||||||||||| | |||||||||
----------------------------------------------------gtgagtcaaaagtattatttttccttgggtggaaattttgtatgtatgagt-ttaatattaaccttttgttt--atcatgtgtttatagAATGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 14
gtatccaattaccttgtctctgttgtgagaagttagcattcatcactttt-ttccaattctgtcgttacattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
                                     | || | ||||||  | ||    ||      |||  | | ||   || |   || |     |||  | |  |   || |  ||||||   ||     |  | ||||| | ||||||||||| ||||||||||| ||  | || || || ||| ||||||||||||| ||||||||||||
----------------------------------gtgagtcgttacttttgcttcagcaatggatacccatcatgtgtt---tttactcttttttgccttaacgccactgg-aattgattactcttgtgcctggt--gtagAATGTATATTGGGCTGACAGTGGTGATTTGGTGACAATAGCAAGCGATTCGTCATTCTACATTTTGAAGTACAAT

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 12
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
                                      |  ||||  | ||    ||| | || ||   |   | |||    || ||  |||    || ||| |   || ||||  |||  |   || |   ||||  ||||  |||| |||||||| ||||||||  |||| || || || |||||||| |||||||||||| | |||||||||
-------------------------------------gtgaatcaagtatt----attttttc-ttgggtggaaattttgtatgtaaaatgt----atgagt-ttactattaaccttttcttt--atcatgcatttatagAACGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 13
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
                        || || | || |  |   | || | |    |  |      || | | |||||           |||||   | ||| | |  ||| | |   | |                  ||||| || || |||||||| ||||||||| ||||| | |||||||||||||| |||||||||||  |||||||||||
------------------------gtaagtactttgattaggtgacatctagttatctgctcttttccttcttattc----------gttgtttaatttaattttgttatttatcttgtgt----------------cagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGTGATACATCATTCTACATTCTGAAGTACAAT

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 2
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
                             ||||  || | ||| |  |     ||  | | |  ||  ||||  | ||           |||  |  ||  |   |||  |||   ||| ||    |          ||||| || || |||||||| ||||||||| ||||  | |||||||||||||| |||||||| ||| |||||||||||
---------------------------gtaagt--gcttgcatgaggtgacatcagctttctgcttttatttcttctt---------actgtttc--ttgttaattttgttaaaatttt-cttgtgt----------cagAACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAAT

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttg-cagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
                                          | | |  |||   |||  ||    ||||||  || || | |        ||  | | | ||| |    ||| | | |      || ||   | || ||||| || || |||||||| ||||||||| ||||| | |||||||| ||||| |||||||||||  |||||||||||
-----------------------------------------gtaagtacttt--gattaggtg---acatttagttatctgctcttttccttcttattcattgtttaatataattttgt-----tattaatcttgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 13
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgtta-cattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
                                          | | |  || |      || | | | | || |  ||| | ||     |  | |   ||  | | |||  ||| | ||| ||    |          ||||| || || |||||||| || |||||||||||  | |||||||||||||| |||||||| ||| | |||||||||
-----------------------------------------gtaagtgcttgcatgaggtggcatcagctttctgcttttatttct---tcttactgtttcttatttttgttaaattttt-cttgtgt----------cagAACCTGTACTGGGCTGATAGCGGTGATTTAGTGACGATTGCTAGTGATACATCATTCTATATCCTTAAGTACAAT

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 13
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
                        || || |  || |||  ||  | | ||  | |   ||   ||   ||| ||       || | |       | | | |||   |  |  || ||   |    |  |  |||| ||||| || ||||||||||| ||||| ||||| || |||||||| |||||||| ||||| |||||| |||||||||||
------------------------gtaagca-ctaacatg-atggcctgttggctaccgtggtattgt-tttcatgccacactgcagg--aattgattaaatgttccttttttcttttctttttttttcactattt-cagAACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACATCATTTTACATCCTGAAGTACAAT

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 13
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
                                           ||  || |   ||  ||  | | |||    |||  ||| |     | | | ||   |   |  |   | | |  ||       |   ||  || |||||||||||||||||||| |||||||||||||| || ||||| |||||| | ||||| |||||||| |||||||||
------------------------------------------gcatgttctcaaaaagcttacttcaca----attaccaggt---tttggccacagagaaactaatagttcatttctttgggtggtttcaatatttcagAATCTTTATTGGGCTGATAGTGGTGATTTAGTGGCAATTGCAAGTGATTCATCATTTTACATCTTAAAGTACAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
                      tactaac  putative branch site (score: 0)
                                        atgaaaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG