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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaggagtcatttatttaagtttgaaacctgcttgtttccatatgaaaaaaagaagtaatttcttgtgtacaacatacttggtatttggatgcaagcatctaatcattctctggattagttgatggaatcaatatctaactcttataattttactatgtatgtgaatggtagGATTTTGATTTCGAAGAGCTTGAAGAAGTTTTGCAATACTATCCTCAAGGCTATCATGGAGTTGATAAGGAAGGAAGACCTGTCTACATTGAAAGACTTG

Basic information

species Arabidopsis thaliana
transcript AT1G55690.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G55690.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G459982_T01 (Zea mays), 3'ss of exon 2
gttaggagtcatttatttaagtttgaaacctgcttgtttccatatgaaaaaaagaagtaatttcttg-tgtacaacatacttggtatttggatgcaagcatctaatcattctctggattagttgatggaatcaatatctaactcttataattttactatgtatgtgaatggtagGATTTTGATTTCGAAGAGCTTGAAGAAGTTTTGCAATACTATCCTCAAGGCTATCATGGAGTTGATAAGGAAGGAAGACCTGTCTACATTGAAAGACTTG
||  |  ||  | || |  ||    |||  || |        |||   |||      | || | | | ||||    | |     | | ||| | | |  || |  ||||  | ||  || |   |   |  | ||  ||        ||  || ||| |    ||  |    |||||||||| ||  | || || || || ||  ||||||| |||||||| || || ||||| ||||| ||||||||||| ||||||||||||||    ||||
gtaggatgttgtctactctag----aaagttgatctcaaagttatatgaaactctgctgatatatagatgtatt-tacatgcactctatggcttctaagat-tgttcatcatatgattttgcaaaactatgccatgccttttaacagtagctt-actgtactcgttga----agGATTTTGAATTTCATGAACTAGAGGAGGTCCTGCAATATTATCCTCATGGTTACCATGGGGTTGACAAGGAAGGAAGGCCTGTCTACATTGAGTTGCTTG

upper sequence: AT1G55690.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G452580_T03 (Zea mays), 3'ss of exon 4
gttaggagtcatttatttaagtttgaaacctgcttgtttccatatgaaaaaaagaagtaatttcttg-tgtacaacatacttggtatttggatgcaagcatctaatcattctctggattagttgatggaatcaatatctaactcttataattttactatgtatgtgaatggtagGATTTTGATTTCGAAGAGCTTGAAGAAGTTTTGCAATACTATCCTCAAGGCTATCATGGAGTTGATAAGGAAGGAAGACCTGTCTACATTGAAAGACTTG
||  |  ||  | || |  |     |||  || |        |||   |||      | || | | | ||||    | |     | | ||| | | |  || |  ||||  | ||  |  |   |   |    ||   ||       ||  || ||| |    ||  |    |||||||||| ||  | || || || || ||  ||||||| |||||||| || || ||||| ||||| ||||||||||| ||||||||||||||    ||||
gtaggatgttgtctactctaa----aaagttgatctcaaagttatatgaaactctgctgatatatagatgtatt-tacatgcactctatggcttctaagat-tgttcatcatatgattctgcaaaactatgtcatgcatattaacagtagctt-actgtactcgttga----agGATTTTGAATTTCATGAACTAGAGGAGGTCCTGCAATATTATCCTCATGGTTACCATGGGGTTGACAAGGAAGGAAGGCCTGTCTACATTGAGTTGCTTG

upper sequence: AT1G55690.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G48060.1 (Glycine max), 3'ss of exon 4
gttaggagtcatttatttaagtttgaaacctgcttgtttccatatgaaaaaaagaagtaatttcttgtgtacaacatacttggtatttggatgcaagcatctaatc-attctctggattagttgatggaatcaatatctaactcttataattttactatgtatgtgaatggtagGATTTTGATTTCGAAGAGCTTGAAGAAGTTTTGCAATACTATCCTCAAGGCTATCATGGAGTTGATAAGGAAGGAAGACCTGTCTACATTGAAAGACTTG
                                                                        ||  |  |   |||||       ||||| |  || || ||       |  | ||| |     ||| |  || |  |    ||    ||    ||  ||  |||||||||| || | |||||| |||||||| ||||| || ||||||||||| || |||||||||||||||||||| || || ||||||||||| |||||||
------------------------------------------------------------------------aatct-ttgaatatttcagcatcagcatattttctatgctagaagacaccttatgtatgttttattttgctttggtgtgattgtggtgataatgtttga-agGATTTTGAATTTGGAGAGCTGGAAGAAGTATTGCAGTATTATCCTCAAGGGTACCATGGAGTTGATAAGGAAGGTAGGCCAGTCTACATTGAGAGACTTG

upper sequence: AT1G55690.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G12450.1 (Glycine max), 3'ss of exon 4
gttaggagtcatttatttaagtttgaaacctgcttgtttccatatgaaaaaaagaagtaatttcttgtgtacaacatacttggtatttggatgcaagcatctaatcattctctggattagttgatggaatcaatatctaactcttataattttactatgtatgtgaatggtagGATTTTGATTTCGAAGAGCTTGAAGAAGTTTTGCAATACTATCCTCAAGGCTATCATGGAGTTGATAAGGAAGGAAGACCTGTCTACATTGAAAGACTTG
                                                                   |      | |  ||  | |||| ||         | | |||  | |  ||  | |    ||  |   ||  |  | ||||  |||   |  || | |   | | |||||||||| || | |||||| |||||||| ||||| || ||||||||||| || |||||||||||||||||||| || || || |||||||| |||||||
------------------------------------------------------------------attatttgcttttttaatctttgaatatttcagcatcagcatattttcaat--gctagaagacaccggatacatgttttat--tttggttgggtgttt---ttgaagGATTTTGAATTTGGAGAGCTGGAAGAAGTATTGCAGTATTATCCTCAAGGGTACCATGGAGTTGATAAGGAAGGTAGGCCAGTTTACATTGAGAGACTTG

upper sequence: AT1G55690.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G17830.1 (Glycine max), 3'ss of exon 3
gttaggagtcatttatttaagtttgaaacctgcttgtttccatatgaaaaaaagaagtaatttcttgtgtacaacatacttggtatttggatgcaagcatctaatcattctctgga-ttagttgatggaatcaatatctaactcttataattttactatgtatgtgaatggtagGATTTTGATTTCGAAGAGCTTGAAGAAGTTTTGCAATACTATCCTCAAGGCTATCATGGAGTTGATAAGGAAGGAAGACCTGTCTACATTGAAAGACTTG
                                                                 ||| |  | | |  |    |||| ||  || |  |   ||  |    || | ||  |  |||   |   |   ||| ||| ||   | | ||    || ||||     ||||||||| || |||||||| |||||||| |||||  | || |||||||| |||||||||||||| |||||||| || || || ||||||||||| ||||
-----------------------------------------------------------------tgtttgta-cgt-ttcaaaatttaga-acatgtgttctatgctaggatgcacttgatacatgatttggttggttaagtctaatgtctgttctg-acatttgaa-----gGATTTTGAATTTGAAGAGCTGGAAGAAGTGTTGCAGCATTACCCTCAAGGGTATCATGGAGTTGACAAGGAAGGTAGGCCAGTTTACATTGAAAGGCTTG

upper sequence: AT1G55690.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv19s0015g01160.t01 (Vitis vinifera), 3'ss of exon 4
gttaggagtcatttatttaagtttgaaacctgcttgtttccatatgaaaaaaagaagtaat-ttcttgtgtacaacatacttggtatttggatgcaagcatctaatcattctctggattagttgatggaatcaatatctaactcttataattttactatgtatgtgaatggtagGATTTTGATTTCGAAGAGCTTGAAGAAGTTTTGCAATACTATCCTCAAGGCTATCATGGAGTTGATAAGGAAGGAAGACCTGTCTACATTGAAAGACTTG
                                                         || |  |||||  |     | | | | |  ||      ||   | |  |  || |||| |    ||         | |  ||||  || |       ||| | ||   |||  | |||| ||||| ||| ||||||| || || || || |||||||| |||||||| || ||||||||||||||||||||||| || || |||||||| |||||||
---------------------------------------------------------tactgctcttggcttttctacaatggatgatttatgagaaatgttt--ttgttttctgaac--atta-------tattgcctaatcctaac------actgtataatcgaaatgaagGACTTTGAATTCAAAGAGCTGGAGGATGTCTTACAATACTACCCTCAAGGATACCATGGAGTTGATAAGGAAGGAAGGCCAGTTTACATTGAGAGACTTG

upper sequence: AT1G55690.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S307_16V6.1 (Physcomitrella patens), 3'ss of exon 4
gttaggagtcatttatttaagtttgaaacctgcttgtttccatatgaaaaaaagaagtaatttcttgtgtacaacatacttggtatttggatgcaagcatctaatcattctctggattagttgatggaatcaatatctaactcttataattttactatgtatgtgaatggtagGATTTTGATTTCGAAGAGCTTGAAGAAGTTTTGCAATACTATCCTCAAGGCTATCATGGAGTTGATAAGGAAGGAAGACCTGTCTACATTGAAAGACTTG
                                                      | ||  ||        |  ||||||| | | | ||   |   |||| || |   ||| |  || |   |||          ||| | ||  | | || |  |  ||  ||       |||| ||  | ||   |||  ||||  ||||   | | |||||||||||||| |||||||| || ||||| ||||| || ||||| |||||||||||| |||
-----------------------------------------------------tacgtgcttcgacac-cagtacatact-gatttatgtgagggggcatatattgtctctttatatca--cgat----------tcttattcgca-agttgtgattcgttcgtt-----cagGACTTCAAATTTACAGAAATTGACAAAGTGAGGAATTACTATCCTCAAGGGTATCATGGGGTGGATAAAGAAGGCAGGCCTGTGTACATTGAAAGAATTG

upper sequence: AT1G55690.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S169_81V6.1 (Physcomitrella patens), 3'ss of exon 3
gttaggagtcatttatttaagtttgaaacctgcttgtttccatatgaaaaaaagaagtaatttcttgtgtacaacatacttggtatttggatgcaagcatctaatc--attctctggattagttgatggaatca-atatctaactcttataattt-tactatgtatgtgaatggt--agGATTTTGATTTCGAAGAGCTTGAAGAAGTTTTGCAATACTATCCTCAAGGCTATCATGGAGTTGATAAGGAAGGAAGACCTGTCTACATTGAAAGACTTG
                                                                               ||||| || |||| |  | |  |  |   |     |||  |  || |      || || |  |||  || | |||  |  ||| | | |   |  |  |||| || | |||    ||  ||||  ||||   | | |||||||||||||| ||||||||||| ||||| ||||| |||||||| || ||||||||  |||
-------------------------------------------------------------------------------ttggttttaggatactggaacatgcttcgagatattggggtgctttacatgcccacatgtacaacggttctcattgatgatatttgtttcgtttcttcagGACTTCGTTTTTACTGAAATTGACAAAGTGAGGAATTACTATCCTCAAGGGTATCATGGAGTGGATAAAGAAGGCAGACCTGTGTATATTGAAAGGATTG

upper sequence: AT1G55690.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S47_303V6.1 (Physcomitrella patens), 3'ss of exon 2
gttaggagtcatttatttaagtttgaaacctgcttgtttccatatgaaaaaaagaagtaatttcttgtgtacaacatacttggtatttggatgcaagcatctaatcattctctggattagttgatggaatcaatatctaactcttataattttactatgtatgtgaatggtagGATTTTGATTTCGAAGAGCTTGAAGAAGTTTTGCAATACTATCCTCAAGGCTATCATGGAGTTGATAAGGAAGGAAGACCTGTCTACATTGAAAGACTTG
                                 |||  |||   ||     | ||  ||   |||| ||||      | ||  | ||  ||| |   ||  | | ||   | |  |  | ||   |||              || |   |  |  |||| ||||  |    |||| ||  | |||   ||  | ||   ||||    ||||||||||||||||  | ||||| ||||| || |||||||||||||| || |||||     | |
------------------------------gttttggatcc---tggtgccatgatttagcatcttttgta------atttacttttaagattcctacacatgaacaaaatttacaggaatttgcgga------------tactgaggctcctgttatg-atgttga--acagGACTTCCAGTTCACCGAATTGGATTCAGTTCGAAAATACTATCCTCAAGGACACCATGGTGTTGACAAAGAAGGAAGACCTGTTTATATTGAGCAGATAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttgatggaatcaatatctaactcttataattttactatgtatgtgaatggtagGATTTTGATTTCGAAGAGCTTGAAGAAGTTTTGCAATACTATCCTCAAGGCTATCATGGAGTTGATAAGGAAGGAAGACCTGTCTACATTGAAAGACTTG
                atctaac  putative branch site (score: 2)
         aatcaatatctaactc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaggagtcatttatttaagtttgaaacctgcttgtttccatatgaaaaaaagaagtaatttcttgtgtacaacatacttggtatttggatgcaagcatctaatcattctctggattagttgatggaatcaatatctaactcttataattttactatgtatgtgaatggtagGATTTTGATTTCGAAGAGCTTGAAGAAGTTTTGCAATACTATCCTCAAGGCTATCATGGAGTTGATAAGGAAGGAAGACCTGTCTACATTGAAAGACTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA