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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggccaaagtttcgcaacattagtcggtattaacttcaaaatcgttgacgaggattcagaagttttagaaacgttggctgacagacatgaccctggttgtggttgtttcgcagTGGACATGGGCTGCAACGATTCTCCAGAGTTCCAATGTGGCCTGGCAGTATGGAGTAAGCGGTCCCTTCTGGTATGCAAGTGGCGCCACCGTGCAGGTGT

Basic information

species Physcomitrella patens
transcript PP1S257_108V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S257_108V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AC202439.3_FGT006 (Zea mays), 3'ss of exon 2
gtaggccaaagtttcgcaacattagtcggtattaacttcaaaatcgttgacgaggattcagaagttttagaaacgttggctgacagacatgaccctggttgtggttg-tttcgcagTGGACATGGGCTGCAACGATTCTCCAGAGTTCCAATGTGGCCTGGCAGTATGGAGTAAGCGGTCCCTTCTGGTATGCAAGTGGCGCCACCGTGCAGGTGT
                                  ||    |  ||  |||       |||      || ||   ||       |||       |     | |      |   ||||||||||||||| |||||||| || ||||| || || ||||| |||||||| || || ||||| || ||||                              
--------------------------------gtacacatacttcactgagattttctcatttcccttcgatttgtctttcttcagTTTCAGTCACATGTATATCGAATCGAGCAGTGGACATGGGCGGCAACGATCCTGCAGAGCTCGAACGTGGCGTGGCAGTACGGCGTGAGCGGGCCTTTCT------------------------------

upper sequence: PP1S257_108V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA04G14790.1 (Glycine max), 3'ss of exon 2
gtaggccaaagtttcgcaacattagtcggtattaacttcaaaatcgttga--cgaggattcagaagttttagaaacgttggctgacagacatgaccctggttgtggttgtttcg--cagTGGACATGGGCTGCAACGATTCTCCAGAGTTCCAATGTGGCCTGGCAGTATGGAGTAAGCGGTCCCTTCTGGTATGCAAGTGGCGCCACCGTGCAGGTGT
                    | | |     | || | ||| | |   |     || ||  | ||  ||  |      ||   | ||     |   | |  ||  | |  ||| |  ||||||||||||||||| || || || || || || ||||| || ||| |||||||||| || || || ||||||||||| |                     
------------------gtaatggattcaaatagcctcatagttaatactttgatgaacctgagattcca------ttttttcacgtctcttttctttattacgatgattttgtgcagTGGACATGGGCTGCTACAATCCTGCAAAGCTCTAATGTTGCATGGGAGTATGGAGTTAGTGGACCTTTCTGGTATGCTA---------------------

upper sequence: PP1S257_108V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv02s0033g01370.t01 (Vitis vinifera), 3'ss of exon 2
gtaggccaaagtttcgcaacattagtcggtattaacttcaaaatcgttgacgaggattcagaagttttagaaacgttggctgacagacatgaccctggttgtggttgtttcgcagTGGACATGGGCTGCAACGATTCTCCAGAGTTCCAATGTGGCCTGGCAGTATGGAGTAAGCGGTCCCTTCTGGTATGCAAGTGGCGCCACCGTGCAGGTGT
               | ||  |          |  |||   | |  |  | | | |||||||  ||  | || | |    |  |    |     |||               |||||||| |||||||| || ||  | || || |||||||| || |||||||||||||| ||||| || ||||||||||| ||||| || ||| | |||    
---------------gtaatgtctaatatcgcttcctttgtagttctacatg-gaattcaga--ttcaataagcttatattttcgagtaccggtctg-------------tacagTGGACTTGGGCTGCCACAATCTTGCAAAGCTCCAATGTAGCATGGCAGTATGGAGTTAGCGGCCCTTTCTGGTATGCCAGTGGAGCTACCATCCAG----

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|18327642|gb|BJ159645.1|BJ159645
EST:     CGGGACGAAACATCAAAACTGGGCTGATCGCCAGCGTCATTGTTTCTCAG                         TGGACATGGGCTGCAACGATTCTCCAGAGTTCCAATGTGGCCTGGCAGTAT
genomic: CGGGACGAAACATCAAAACTGGGCTGATCGCCAGCGTCATTGTTTCTCAGgtaggccaaa ... tgtttcgcagTGGACATGGGCTGCAACGATTCTCCAGAGTTCCAATGTGGCCTGGCAGTAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagttttagaaacgttggctgacagacatgaccctggttgtggttgtttcgcagTGGACATGGGCTGCAACGATTCTCCAGAGTTCCAATGTGGCCTGGCAGTATGGAGTAAGCGGTCCCTTCTGGTATGCAAGTGGCGCCACCGTGCAGGTGT
                 ggctgac  putative branch site (score: 3)
                                            ttgtttc  putative PPT
     tttagaaa  TA-rich tract