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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcactattttttaacagacccttttagtatttaaaaagaaagagaaaaagaagagaaagaagttaaattccaaaacctcaaggcttacatgaacgtgcgtaagacttctgacatactaggattacttacctgctccggtacttcgaaatgcttctgacaaaagggataattggcctgcagGTTTGTGGATTTGATTTGCTTCGATCGCAAGGCCGGTCATATGTGTGTGACGTTAATGGGTGGAGTTTTGTTAAGAACTCTTACAA

Basic information

species Physcomitrella patens
transcript PP1S70_284V6.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S70_284V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: LOC_Os03g48300.3 (Oryza sativa), 3'ss of exon 10
gtgagcactattttttaacagacccttttagtatttaaaaagaaagagaaaaagaagagaaagaagttaaattccaaaacctcaaggcttacatgaacgtgcgtaagacttctgacatactaggattacttacctgctccggtacttcgaaatgcttctgacaaaa---gggataattgg--cctgcagGTTTGTGGATTTGATTTGCTTCGATCGCAAGGCCGGTCATATGTGTGTGACGTTAATGGGTGGAGTTTTGTTAAGAACTCTTACAA
                                                                                      | || | ||    | | |     ||     |||   |  || | |   |      ||| |||  |||  | ||   |      |  || | | |   |   |||||||||| |||||| |  |  | |   | ||  | |||||||| |||||||||||||| ||||| ||||| |||||||| |||||
--------------------------------------------------------------------------------------gtttgcttgcttct-catcttcttttcatgataaccgccttgcgt--ttatcatagtatttcctaatattcctattatgttctgatatgacttgtttccatagGTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAA

upper sequence: PP1S70_284V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 11
gtgagcactattttttaacagacccttttagtatttaaaaagaaagagaaaaagaagagaaagaagttaaattccaaaacctcaaggcttacatgaacg--tgcgtaagacttctgacatactaggattacttacctgctccggtacttcgaaatgcttctgacaaaagggataattggcctgcagGTTTGTGGATTTGATTTGCTTCGATCGCAAGGCCGGTCATATGTGTGTGACGTTAATGGGTGGAGTTTTGTTAAGAACTCTTACAA
                                                                                      | ||   |||| |  ||  || ||  | |    |||  |||  | ||           || |    ||||| | |     ||    |     | ||||||||||| || |||||| | || |||||  | ||  | |||||||| |||||||| ||||| ||||||||||| |||||||| || ||
---------------------------------------------------------------------------------gtgtagtttgtttgaaggaatgattacgaaatgttgt-tacctggaaaagttgaagatat---tattgtataatgcat-tagtggaattattttcatgtctgcagGTTTGCGGTTTTGATCTCCTACGATCTGAGGGAAGTTCATATGTTTGTGACGTAAATGGATGGAGTTTTGTGAAGAACTCCTATAA

upper sequence: PP1S70_284V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 11
gtgagcactattttttaacagacccttttagtatttaaaaagaaagagaaaaagaagagaaagaagttaaattccaaaacctcaaggcttacatgaacgtgcgtaagacttctgacatactaggattacttacctgctccggtacttcgaaatgcttctgacaaaagggataattggcctgcagGTTTGTGGATTTGATTTGCTTCGATCGCAAGGCCGGTCATATGTGTGTGACGTTAATGGGTGGAGTTTTGTTAAGAACTCTTACAA
                                                     | |      |||   ||    |     ||||     | | || | |  |||||  | |   | ||  || | |  || |  |  | |  |    || | |  ||    ||| |    | |      | ||||| ||||| |||||| | || |||||  | ||| | |||||||| ||||| || ||||| ||||||||||| |||||||| |||||
-----------------------------------------------------gtatgttgtgaatccaatcctccggctctcattatgt-cttgcagggccgtaatcccttata-atggtacgtt--ctgatttcgtgcaatga--cgtagtaatttcttcaacatttttcac--atttccagGTCTGTGGGTTTGATCTTCTACGATCTGAGGGCTGTTCATATGTTTGTGATGTCAATGGATGGAGTTTTGTGAAGAACTCATACAA

upper sequence: PP1S70_284V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 10
gtgagcactattttttaacagacccttttagtatttaaaaagaaagagaaaaagaagagaaagaagttaaattccaaaacctcaaggcttacatgaacgtgcgta-agacttctgacatactaggattacttacc-tgctccggtacttcgaaatgcttctgacaaaagggataattggcctgcagGTTTGTGGATTTGATTTGCTTCGATCGCAAGGCCGGTCATATGTGTGTGACGTTAATGGGTGGAGTTTTGTTAAGAACTCTTACAA
                                                                                    | ||   |||  |  |   |  | | |  |    || |  ||| | ||    |     | ||  ||    | ||  | | |      ||| |  || ||||||||||||| |||||| |  | || |   | || || |||||||| ||||| || ||||| ||||||||||| ||||||||| ||||
------------------------------------------------------------------------------------acgcaaccatacatatatttgtaaattctttctttattgagatgagttgttgttaaatgttatgtctttgttctatttatattttccatatt--gcttgcagGTTTGTGGGTTTGATCTCTTGCGTTGTGAGGGACGCTCATATGTCTGTGATGTGAATGGATGGAGTTTTGTGAAGAACTCTCACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacctgctccggtacttcgaaatgcttctgacaaaagggataattggcctgcagGTTTGTGGATTTGATTTGCTTCGATCGCAAGGCCGGTCATATGTGTGTGACGTTAATGGGTGGAGTTTTGTTAAGAACTCTTACAA
                                        ataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcactattttttaacagacccttttagtatttaaaaagaaagagaaaaagaagagaaagaagttaaattccaaaacctcaaggcttacatgaacgtgcgtaagacttctgacatactaggattacttacctgctccggtacttcgaaatgcttctgacaaaagggataattggcctgcagGTTTGTGGATTTGATTTGCTTCGATCGCAAGGCCGGTCATATGTGTGTGACGTTAATGGGTGGAGTTTTGTTAAGAACTCTTACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC