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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgattcagtattttctcagtaggtgaccttaacattttcacatgtttttgctcctgcttagcagaatatatctgagttttttggtatcacgtttagatgttttgtgtgtgttgcaactgttttccatgctaatttacagtttttgtgtctttgcagGTTCTATTTCTTATGTATCATTACTTTGCTGCGGCTGAGATATATAATGCAATCAGGGTTTTCATTGCTGCCTACGTCTGGATGACTGGGTTTGGGAACT

Basic information

species Arabidopsis thaliana
transcript AT2G34410.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G34410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g44040.1 (Oryza sativa), 3'ss of exon 6
gtaactgattcagtattttctcagtaggtgaccttaacattttcacatgtttttgctcctgcttagcagaatatatctga-gttttttggtatcacgtttagatgttttgtgtgtgttgcaactgttttccatgctaatttacagtttttgtgtc-----tttgcagGTTCTATTTCTTATGTATCATTACTTTGCTGCGGCTGAGATATATAATGCAATCAGGGTTTTCATTGCTGCCTACGTCTGGATGACTGGGTTTGGGAACT
                                                               | | ||  |   | | | ||   |    || |  || || || | | | |   |  ||||| ||    | |   ||||  |  ||||    |     ||| ||||| || ||| | ||||| || || ||||| ||  |||| ||||| ||||||||  | ||||||||||||||||| |||||||||||||| ||||||||||
-------------------------------------------------------------aatggtagtttccttataatgtcagtcaccattattttcagttgctgtcttt---tgccaacttttaggtaag---atttgtaacttttccacctgctgtttacagGTCCTGTTTTTAATGTACCACTATTTTGCCGCCACTGAAATATACAATGCAATTCGTGTTTTCATTGCTGCCTATGTCTGGATGACTGGATTTGGGAACT

upper sequence: AT2G34410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os05g50510.1 (Oryza sativa), 3'ss of exon 6
gtaactgattcagtattttctcagtaggtgaccttaacattttcacatgtttttgctcctgcttagcagaatatatctgagttttttggtatcacgtttagatgttttgtgtgtgttgcaactgttttccatgctaatttacagtttttgtgtctttgcagGTTCTATTTCTTATGTATCATTACTTTGCTGCGGCTGAGATATATAATGCAATCAGGGTTTTCATTGCTGCCTACGTCTGGATGACTGGGTTTGGGAACT
                                  || || ||| | || | |||    ||| |     | || |||   |   |||| |||    || |    | |||  ||||| |  || | ||||   |||                   |||| |||||  | ||||| ||||| || || || |||||  | || ||||| ||||||||  |||| |||||||||||||| |||||||||||||| || ||||| |
----------------------------------tagcacttttatat-tctttctcgctgtt-----gtat-tatgcaatccttttagtact-tgtatgttggctttaagtgtgctataattattttatctgc-------------------ctttccagGTCTTGTTTCTGATGTACCACTATTTCGCTGCCACAGAAATATACAATGCAATTCGGGTGTTCATTGCTGCCTATGTCTGGATGACTGGATTCGGGAATT

upper sequence: AT2G34410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G458538_T01 (Zea mays), 3'ss of exon 1
gtaactgattcagtattttctcagtaggtgaccttaacattttcacatgtttttgctcctgcttagcagaatatatctgagttttttggtatcacgtttagatgttttgtgtgtgttgcaactgttttccatgctaatttacagtttttgtgtctttgcagGTTCTATTTCTTATGTATCATTACTTTGCTGCGGCTGAGATATATAATGCAATCAGGGTTTTCATTGCTGCCTACGTCTGGATGACTGGGTTTGGGAACT
                                                                                                                                   | ||||||   | |  || ||| ||| |||||  ||||||| ||||| ||||| ||||||||  |||||||||| ||||||||| | || |||||||||  ||| |||||||||||||| |||||||| |
------------------------------------------------------------------------------------------------------------------------------gagtgtactaatt---attcgttctgtgtttccagGTCTTATTTCTGATGTACCATTATTTTGCTGCTTCTGAGATATACAATGCAATCCGTGTGTTCATTGCTTGCTATGTCTGGATGACTGGATTTGGGAATT

upper sequence: AT2G34410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G076394_T01 (Zea mays), 3'ss of exon 6
gtaactgattcagtattttctcagtaggtgaccttaacattttcacatgtttttgctcctgcttagcagaatatatctgagttttttggtatcacgtttagatgttttgtgtgtgttgcaactgttttcca-tgctaatttacagtttttgtgtctttgcagGTTCTATTTCTTATGTATCATTACTTTGCTGCGGCTGAGATATATAATGCAATCAGGGTTTTCATTGCTGCCTACGTCTGGATGACTGGGTTTGGGAACT
                       || |||||  ||| |||     ||  | |||  | || ||| |||   |   | |     | |   ||||||     |  |||| | | |  |    | ||| ||  | |||  | |     ||  | ||   || |||||  | ||||| ||||| || || || |||||  | || ||||| ||||||||| | || |||||||||  ||| |||||||||||||| |||||||| |
-----------------------gttggtgatatta-catcaat-cacttctttagttctccttggcaatgtggttttttagctatctatatcacc----ggagtttggagaggctcttgattgtgttgaaatgcccaatgcattttaatatgcaattccagGTCTTGTTTCTGATGTACCACTATTTCGCTGCCTCGGAAATATACAATGCAATCCGTGTGTTCATTGCTTGCTATGTCTGGATGACTGGATTTGGGAATT

upper sequence: AT2G34410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G25780.2 (Glycine max), 3'ss of exon 7
gtaactgattcagtattttctcagtaggtgaccttaacattttcacatgtttttgctcctgcttagcagaatatatctgagttttttggtatcacgtttagatgttttgtgtgtgttgcaactgttttccatgctaatttacagtttttgtgtctttgcagGTTCTATTTCTTATGTATCATTACTTTGCTGCGGCTGAGATATATAATGCAATCAGGGTTTTCATTGCTGCCTACGTCTGGATGACTGGGTTTGGGAACT
                                                   ||   |      |   | | || ||     |||||  || | |  |||   |||| | | |  ||      |    ||  | | |  ||    || ||   | | | ||||| || ||| | ||||||||||| ||||||||  | |||||||| ||||||||  | |||||||||||||| || || ||||||||||| ||||| ||||
--------------------------------------------------attcattagaaacttagaaactacat-----tttttcagttttaattttgtctgttatttctaagtaatggtt--catctgttcaagctt----ttgttccatttgttcagGTCCTCTTTTTAATGTATCATTATTTTGCTGCAACGGAGATATACAATGCAATACGTGTTTTCATTGCTGCATATGTTTGGATGACTGGATTTGGAAACT

upper sequence: AT2G34410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 7
gtaactgattcagtattttctcagtaggtgaccttaacattttcacatgtttttgctcctgcttagcagaatatatctgagttttttggtatcacgtttagatgttttgtgtgtgttgcaactgttttccatgctaatttacagtttttgtgtctttgcagGTTCTATTTCTTATGTATCATTACTTTGCTGCGGCTGAGATATATAATGCAATCAGGGTTTTCATTGCTGCCTACGTCTGGATGACTGGGTTTGGGAACT
                                                   ||   |      |   | | || ||     | |||  || | |  |||   |||| | | |  ||      |    ||  | | |  ||    || ||   ||| | ||||| || ||| | ||||||||||| ||||||||  | |||||||| ||||||||  | |||||||||||||| || || ||||||||||| ||||| ||||
--------------------------------------------------attcattagaaacttagaaactacat-----tctttcagttttaattttgtctgttatttctaagtaatggtt--catctgttcaagctt----ttgttccatctgttcagGTCCTCTTTTTAATGTATCATTATTTTGCTGCAACGGAGATATACAATGCAATACGTGTTTTCATTGCTGCATATGTTTGGATGACTGGATTTGGAAACT

upper sequence: AT2G34410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 1
gtaactgattcagtattttctcagtaggtgaccttaacattttcacatgtttttgctcctgcttagcagaatatatctgagttttttggtatcacgtttagatgttttgtgtgtgttgcaactgttttccatgct--aatttacagtttttgtgtctttg-cagGTTCTATTTCTTATGTATCATTACTTTGCTGCGGCTGAGATATATAATGCAATCAGGGTTTTCATTGCTGCCTACGTCTGGATGACTGGGTTTGGGAACT
                                                  |||| ||     ||       |||   ||    ||    |  ||   ||| ||  |     |    |  ||   |||||   |||   ||||    | ||| | | |||  |||||||||||||| ||||| || ||||||||||| || |||||||| ||||||||  | || || |||||||| || |||||||||||||| ||||| ||||
-------------------------------------------------gttttactttatttttattatctattattg---cttgcaatgccattgttacatagtgcaatttgcctcaaataattttctgagcttggatttgtcttctttttctttttaacagGTTCTATTTCTAATGTACCACTACTTTGCTGCTGCGGAGATATACAATGCAATTCGTGTCTTTATTGCTGCATATGTCTGGATGACTGGATTTGGAAACT

upper sequence: AT2G34410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S357_34V6.1 (Physcomitrella patens), 3'ss of exon 6
gtaactgattcagtattttctcagtaggtgaccttaacattttcacatgtttttgctcctgcttagcagaatatatctgagttttttggtatcacgtttagatgttttgtgtgtgttgcaactgttttccatgc-taatttacagtttttgtgtctttgcagGTTCTATTTCTTATGTATCATTACTTTGCTGCGGCTGAGATATATAATGCAATCAGGGTTTTCATTGCTGCCTACGTCTGGATGACTGGGTTTGGGAACT
                                                 ||||  |  |  | |   || |||    | |  || |    | ||  |||       ||   |    | ||  |||| | |   | |  |||  | |||||  ||    |||||| || || || |||||||| || || |  ||    ||| | |||||||| ||  | ||||| |||||||||||||| |||||||| |||||||| ||||
-------------------------------------------------ttttcaccgccaccttcgaggataa---taaacttgtacaaagcatatttg------ttacattcacttcatttgttcttctgacatcgtttggatttttttcgt----gcagGTCCTTTTCCTCATGTATCACTATTTCGAAGCTAAAGAGTTTTATAATGCCATTCGAGTTTTTATTGCTGCCTACGTTTGGATGACGGGGTTTGGCAACT

upper sequence: AT2G34410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S74_21V6.1 (Physcomitrella patens), 3'ss of exon 6
gtaactgattcagtattttctcagtaggtgaccttaacattttcacatgtttttgctcctgcttagcagaatatatctgagttttttggtatcacgtttagatgttttgtgtgtgttgcaactgttttccatgctaatttacagtttttgtgtctttgcagGTTCTATTTCTTATGTATCATTACTTTGCTGCGGCTGAGATATATAATGCAATCAGGGTTTTCATTGCTGCCTACGTCTGGATGACTGGGTTTGGGAACT
                                                     |||  ||  | |   |   | |    ||||| | | ||   || |  ||| |    |||    || |  | |  |  |   | ||||||   || | |    || ||||| || || ||||||||||| ||||| |  ||    ||| | || ||||| ||  |||| ||||||||||||||||| |||||||| || ||||| ||||
-----------------------------------------------------tgcgacttgtgaattgttaagaagaaagtttatcgttagttcgat--gatttaacctgttcactgaatttataatgta---ttatttac---ttgtctaaaatttcagGTCCTTTTCCTTATGTATCACTACTTCGAAGCAAAGGAGTTTTACAATGCTATTCGGGTGTTCATTGCTGCCTACGTTTGGATGACGGGTTTTGGCAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgtgtgttgcaactgttttccatgctaatttacagtttttgtgtctttgcagGTTCTATTTCTTATGTATCATTACTTTGCTGCGGCTGAGATATATAATGCAATCAGGGTTTTCATTGCTGCCTACGTCTGGATGACTGGGTTTGGGAACT
                         tgctaat  putative branch site (score: 2)
                                            tgtcttt  putative PPT
                            taatttacagttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactgattcagtattttctcagtaggtgaccttaacattttcacatgtttttgctcctgcttagcagaatatatctgagttttttggtatcacgtttagatgttttgtgtgtgttgcaactgttttccatgctaatttacagtttttgtgtctttgcagGTTCTATTTCTTATGTATCATTACTTTGCTGCGGCTGAGATATATAATGCAATCAGGGTTTTCATTGCTGCCTACGTCTGGATGACTGGGTTTGGGAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC