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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgactaatcgagaggtttactctttcttacaaggctgtagaaactcttaagtacatgttattaatagttccattccatgatggctgttctaatgacagTATGAGAAAGTGGAGAAGATTGGAGAGGGCACATACGGTGTCGTATACAAGGCCCGGGATCGCCTCACTAATGAAACTATTGCTCTGAAAAAAATACGGC

Basic information

species Physcomitrella patens
transcript PP1S25_198V6.5
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S25_198V6.5 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os03g01850.2 (Oryza sativa), 3'ss of exon 1
tatgactaatcgagaggtttactctttcttacaaggctgtagaaactcttaagtacatgttattaatagttccattccatgatggctgttctaatgacagTATGAGAAAGTGGAGAAGATTGGAGAGGGCACATACGGTGTCGTATACAAGGCCCGGGATCGCCTCACTAATGAAACTATTGCTCTGAAAAAAATACGGC---
                   ||  |  |   |     |||     | || |        |  | |    |||    ||| ||    |  ||       ||||| ||| |   ||||||||||||||||||||| ||||| || || |||||||| |||||     |||| || || || || || || || || || ||||   
------------------gtaagcgcttccagcgatctgattcgattcctcttcttgggggactcggggttttgatcc-tgcaaaccttt------gcagTACGAGGA---GGAGAAGATTGGAGAGGGCACGTACGGGGTAGTGTACAAGGCGCGGGACAAGGTCACCAACGAGACGATCGCGCTCAAGAAGATCCGGCTTG

upper sequence: PP1S25_198V6.5 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA15G14390.1 (Glycine max), 3'ss of exon 1
-tatgactaatcgagaggtttactctttcttacaaggctgtagaaactcttaag----tacatgttattaatagttccattccatgatggctgttctaatgacagTATGAGAAAGTGGAGAAGATTGGAGAGGGCACATACGGTGTCGTATACAAGGCCCGGGATCGCCTCACTAATGAAACTATTGCTCTGAAAAAAATACGGC
 |  |    | ||  | |  |  ||| |||| | |   |       |||| ||      || | |  | || | |    ||| ||  |     || |  |  ||||| ||||| ||||||||||| || ||||| |||||||| ||||| |||||||| || || ||| |||| ||||| || || ||||| || || || || |
gttcgtagcaccgcaatgcatcatctctctt-cgattttcagtttcctctcaaaaactcacttttcgtgaaaattggttttcgatttttttgtttttttttgcagTACGAGAAGGTGGAGAAGATAGGCGAGGGAACATACGGCGTCGTTTACAAGGCTCGCGACCGCGTCACCAATGAGACCATCGCTCTCAAGAAGATTCGCC

upper sequence: PP1S25_198V6.5 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA09G03470.1 (Glycine max), 3'ss of exon 1
-----tatgactaatcgagaggtttactctttcttac-aaggctgtagaaactcttaagtacatgttattaatagttccattccatgatggctgttctaatgacagTATGAGAAAGTGGAGAAGATTGGAGAGGGCACATACGGTGTCGTATACAAGGCCCGGGATCGCCTCACTAATGAAACTATTGCTCTGAAAAAAATACGGC
     ||  || | || |    || |||   ||  |  ||   | |      | || | |      |   ||     |  |||| |      | || |  |  ||||| ||||| ||||||||||| || ||||| |||||||| ||||| |||||||| || || |||  ||| ||||| || || |||||||| || || || |
gttcctaccacaattcaatc--ttaacttcatcacattaacattttcttcgattttcactttcctctcacaaactcacttttcctttccattttttttttttgcagTACGAGAAGGTGGAGAAGATAGGCGAGGGAACATACGGCGTCGTTTACAAGGCTCGCGACCGCGCCACCAATGAGACAATCGCTCTGAAGAAGATTCGCC

upper sequence: PP1S25_198V6.5 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ15022 (Selaginella moellendorffii), 3'ss of exon 1
tatgactaatcgagaggtttactctttcttacaaggctgtagaaactcttaagtacatgttattaatagttccattccatgatggctgttctaatg-acagTATGAGAAAGTGGAGAAGATTGGAGAGGGCACATACGGTGTCGTATACAAGGCCCGGGATCGCCTCACTAATGAAACTATTGCTCTGAAAAAAATACGGC
                       ||      |     | |   | ||||   || | ||    |   |  |   |    |   |  | ||     |   |||||||||| |||||||| || || || ||||||||||| ||||| |||||||||||||||||| |||| ||||| || ||||| || || || || || |
--------------------gtactgcgaagccgcattcttcgatctctctcgttcttgccgctctgatcttactgttcttgcgcttcttgcggcgcgtagTATGAGAAGGTGGAGAAAATCGGGGAAGGCACATACGGCGTCGTCTACAAGGCCCGGGATCGCATCACAAATGAGACGATTGCGCTCAAGAAGATCCGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttaagtacatgttattaatagttccattccatgatggctgttctaatgacagTATGAGAAAGTGGAGAAGATTGGAGAGGGCACATACGGTGTCGTATACAAGGCCCGGGATCGCCTCACTAATGAAACTATTGCTCTGAAAAAAATACGGC
                                           ttctaat  putative branch site (score: 2)
                                        ctgttct  CT-rich tract
        tacatgttattaata  TA-rich tract