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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctgctcccacggcatggaccgttgtaattccgatagtttcagggccgtccattatttcactgtgattccaagttccgcactggtttctgctgatttagcttcccttccggccaagccgaagtaacttcttccactgtgcagCTGGCGGCGAGGATTGCTGTCTCCAATTTGCACAAAAACACCAAGAAATCCTTCTCTGAGACTGTGAAGGATATGTATCGCCATGTGAACGCCAGATCTG

Basic information

species Physcomitrella patens
transcript PP1S195_46V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S195_46V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 1
gtaagctgctcccacggcatggaccgttgtaattccgatagtttcagggccgtccattatttcactgtgattccaagttccgcactggtttctgctgatttagcttcccttccggccaagccgaagtaacttcttccactgtgcagCTGGCGGCGAGGATTGCTGTCTCCAATTTGCACAAAAACACCAAGAAATCCTTCTCTGAGACTGTGAAGGATATGTATCGCCATGTGAACGCCAGATCTG
                                           | |  |||    |  | ||||| ||  ||     ||  |  |    ||| | |  |      || | ||| | || |  ||         | |   |||| |||| |||||||||||||| || |||||  ||||||| ||||||||||| |||||||| |||||                                      
------------------------------------------gtaacagccactga--acttcaccgttgttggtttttttgttccccattcgg-tagtaccttgtctcctcctgacatgtgga--------ttgctgttgtgaagCTCGCGGCGAGGATTGCGGTTTCCAACCTGCACAAGAACACCAAGAAGTCCTTCTCGGAGAC--------------------------------------

upper sequence: PP1S195_46V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 1
gtaagctgctc-ccacggcatggaccgttgtaattccgatagtttcagggccgtccattatttcactgtgattccaagttccgcactggtttctgctgatttagcttcccttccggccaagccgaagtaacttcttccactgtgcagCTGGCGGCGAGGATTGCTGTCTCCAATTTGCACAAAAACACCAAGAAATCCTTCTCTGAGACTGTGAAGGATATGTATCGCCATGTGAACGCCAGATCTG
|| ||   | | || ||  ||   ||       |  |  | |||||||  |       | | |  ||||  |||     || |  |||   |  | |   ||  |     |  | | |        || | |         ||| |||||||||||||||||||||| || ||  ||||||| ||||| ||||| |||||||| |||||                                      
gtgagtaacccaccccgaaatcctcctcccctctggccttggtttcagctctcctgtctgtctgtctgtctttctg---tctgtgctgacgtggggttggttgcccctgttctctgtc--------gtgattc--------gtgaagCTGGCGGCGAGGATTGCTGTGTCGAACCTGCACAAGAACACAAAGAAGTCCTTCTCGGAGAC--------------------------------------

upper sequence: PP1S195_46V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 1
gtaagctgctcccacggcatggaccgttgtaattccgatagtttcagggccgtccatta--tttcactgtgattccaagttccgcactggtttctgctgatttagcttcccttccggccaagccgaagtaacttcttccactgtgcagCTGGCGGCGAGGATTGCTGTCTCCAATTTGCACAAAAACACCAAGAAATCCTTCTCTGAGACTGTGAAGGATATGTATCGCCATGTGAACGCCAGATCTG
                                          |   |  ||  || | |  |  | |  || || ||| |  |      || | || ||   |  | |    |  ||      |         || |     ||| || ||||||||||||||||||| || ||  ||||||| ||||| ||||| |||||||| |||||                                      
-----------------------------------------gtgaggaacccaccgtgaaatccccccttggtttcaactctcatgtctgtctttgttgtcctgacgtggggtt-ggtttcctctcttctctatcgtgattcgtgaagTTGGCGGCGAGGATTGCTGTGTCTAACCTGCACAAGAACACAAAGAAGTCCTTCTCGGAGAC--------------------------------------

upper sequence: PP1S195_46V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 1
gtaagctgctcccacggcatggaccgttgtaattccgatagtttcagggccgtccattatttcactgtgattccaagttccgcactggtttctgctgatttagcttcccttccggccaagccgaagtaacttcttccactgt-gcagCTGGCGGCGAGGATTGCTGTCTCCAATTTGCACAAAAACACCAAGAAATCCTTCTCTGAGACTGTGAAGGATATGTATCGCCATGTGAACGCCAGATCTG
                                                        ||| ||| ||   ||| | | | |   | | | |     ||  |    |        ||   |    |||| | ||  |    ||| |||| |||| || |||||||| || || ||| ||||||| |||||||||||||||||||| |||||                                      
-------------------------------------------------------gttagttccctcaaatttctattcc---atttgatgaaattgtgtgtcttggatggatggattattgtaagtgattttgtttgttgttgcagTTGGCTGCTAGGATTGCCGTTTCGAATCTGCACAAGAACACCAAGAAATCCTTCTCCGAGAC--------------------------------------


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgctgatttagcttcccttccggccaagccgaagtaacttcttccactgtgcagCTGGCGGCGAGGATTGCTGTCTCCAATTTGCACAAAAACACCAAGAAATCCTTCTCTGAGACTGTGAAGGATATGTATCGCCATGTGAACGCCAGATCTG
                                aagtaac  putative branch site (score: 2)
                                      cttcttccact  CT-rich tract
      attta  TA-rich tract