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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gccaatgatctcgacatctcgctgagttgaaggtgaaggagatcaagaacggttgtttgacaatgtattccacgttcggattctttgttcagGCTATCGTCACTGGAAAGAGACCCTTGGAGAACCTGAGCGACTATCTTGCAGATCCCGGTACCAACAACGCCTGGGCATACACCACCAACTTCACCCCCG

Basic information

species Physcomitrella patens
transcript PP1S169_127V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S169_127V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA16G27990.1 (Glycine max), 3'ss of exon 1
-----------------------------------------------------------------gccaatgatctcgaca-tctcgctgagttgaaggtgaaggagatcaagaacggttgtttgacaatgtattccacgttcggattctttgttcagGCTATCGTCACTGGAAAGAGACCCTTGGAGAACCTGAGCGACTATCTTGCAGATCCCGGTACCAACAACGCCTGGGCATACACCACCAACTTCACCCCCG
                                                                 ||  |||| |  ||   | | |||||| |||||||||||||| ||||||| ||| | ||| | ||||  |||| ||| ||||||||||||||||| || || || |||||| ||||||| || ||||                                                                  
gtgggcctcttggtgaggtgactgatccaatctatccaggtggcagctttgacccattgggtcttgctgatgacccagaggcttttgctgagCTGAAGGTGAAGGAGCTCAAGAATGGTAGGTTGGCCATGTTCTCCATGTTTGGATTCTTTGTTCAGGCAATTGTGACAGGAAAGGGACCCTTAGAAAACC------------------------------------------------------------------

upper sequence: PP1S169_127V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EDP01724 (Chlamydomonas reinhardtii), 3'ss of exon 4
gccaatgatctcgacatctcg-ctgagttgaaggtg-aaggagatcaagaacggttgtttgacaatgtattc-cacgtt-cggattctttgttcagGCTATCGTCACTGGA----AAGAGACCCTTGGAGAACCTGAGCGACTATCTTGCAGATCCCGGTACCAACAACGC-CTG--GGCATACACCACCAACTTCACCCCCG
||||  |    |  | |   | |||  |     ||    ||     | |  | ||    ||   | | |||  | ||   | | | |    | || ||      | ||| |           | || ||   |||| ||  ||  ||  | || ||||  |||  |   |  |||  ||   |    | |||   |  || | 
gccacgggctgctgcgtaaagactgtatcctttgtccgtggccgaaaggtgctgtaccctgctgacgcatttgctcgccgctgctcccacatgcacgcagGACCCCCTGTACCCCGGCGAGTCGTTCGACCCCCTGGGC--CTGGCTGAC-GACCCCGACACCTTCGCTGAGCTGAAGGTGAAGGAGATCAAGAACGGCCGCC

upper sequence: PP1S169_127V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EDO98358 (Chlamydomonas reinhardtii), 3'ss of exon 3
--------------------------------------------------gccaatgatctcgacatctcgctgagttgaaggtgaagga--gatcaagaacggt-tgtttgacaatgtattccacgttcggattctttg---ttcagGCTATCGTCACTGGAAAGAGACCCTTGGAGAACCTGAGCGACTATCTTGCAGATCCCGGTACCAACAACGC-CTG--GGCATACACCACCAACTTCACCCCCG
                                                  |     | |   |   ||| | || ||     |  | | |  | ||  | ||| | ||  || ||   |   ||||  | |    ||  |   | ||||  |   |           |  | || ||   |||| ||  ||  ||  | || ||||  |||  |   |  |||  ||   |    | |||   |  || | 
gtgagtgcggttcgctgtgaagggaagcttccctcaaaacacatgggacagtttcggtttgtgttgtctggttgcgtcagtagcaatgcacggttcgtggacgttgtgcatggcatcattgcccacccttgctccctccgcgttgcagGACAAGCTGTACCCCGGTGGCTCGTTCGACCCCCTGGGC--CTGGCTGAC-GACCCCGACACCTTCGCTGAGCTGAAGGTGAAGGAGATCAAGAACGGCCGCC

upper sequence: PP1S169_127V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EDP00188 (Chlamydomonas reinhardtii), 3'ss of exon 5
gccaatgatctcgacatctcgctgagttgaaggtgaaggagat---caagaacg-gttgtt-tg-acaatgtattccacgt--tcggattctttgttcagGCTATCGTCACTGGAAA-GAGACCCTTGGAGAACCTGA-GCGACTATCTTGCAGATCCCGGTACCAACAACGCCTGGGCATACACCACCAACTTCACCCCCG------------------------------
|  | || |  || ||    | |  ||     |||| || | |    | | ||  | || | || | ||| ||   || |   |   ||   |||||   |||| | | | ||     |  ||||    || ||  |  ||  |      ||   | |    |||  |   ||||||      ||| || |      | | |                              
gtgagtgcttgcggcaaaagggttggtgatgtgtgatggggctgcgtatgtacacgctgctgtgcataatttaggtcatggaatgatatagcttgtt---gctaacctgaatgctttcgtaaccccaacagGACAAGCTGCACCCCGGCGGCCAGTTCTTCGACCCCCTGGGCCTGGCTGAGGACC-CCGATGCTTTCGCTGAGCTGAAGGTGAAGGAGATCAAGAACGGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagatcaagaacggttgtttgacaatgtattccacgttcggattctttgttcagGCTATCGTCACTGGAAAGAGACCCTTGGAGAACCTGAGCGACTATCTTGCAGATCCCGGTACCAACAACGCCTGGGCATACACCACCAACTTCACCCCCG
                 gtttgac  putative branch site (score: 4)
                                           ttctttgttc  putative PPT
                        aatgtatt  TA-rich tract