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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaggcgttcagacgtccatattgcatgacaattgagtttatttgcaccagtaaatcagttattctcttccttgcagggcaatttaagttgctgtttgtctttgttgtctgctttacattacaagtatcggtttagaaaccgtcgcgtttgatttatcagaatttggacgtgttgcgcagGGACACTGCTGGACAGGAGAGGTTTAGGAGTTTGATTCCCAGCTACATCCGGGATTCGTCCGTGGCAGTGGTTGTCTATGATGTTTCCA

Basic information

species Physcomitrella patens
transcript PP1S39_147V6.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S39_147V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os03g09140.1 (Oryza sativa), 3'ss of exon 2
gtaaaggcgttcagacgtccatattgcatgacaattgagtttatttgcaccagtaaatcagttattctcttccttgcagggcaatttaagttgctgtttgtctttgttgtctgctttacattacaagtatcggtttagaaaccgtcgcgtttgatttatcagaatttggacgtgttgcgcagGGACACTGCTGGACAGGAGAGGTTTAGGAGTTTGATTCCCAGCTACATCCGGGATTCGTCCGTGGCAGTGGTTGTCTATGATGTTTCCA
                                                                          || |  | |||        |        |  | |    |    |  |   | || |     ||| ||    || |   | |||||    ||       |  || ||||||| || ||||| |||||||||||  |||| ||||| || || |||||| ||||||| || ||||||||| |||| || |||||  |  
--------------------------------------------------------------------------tgaactgaaatcacgcgcacaagacaattcagcta---gtgaaaactgggaggttttcagctagtaaaaaccgggagagttttatggtgatg-----ataatgtgcagGGATACAGCTGGGCAGGAGAGGTTCCGGAGCTTGATCCCAAGTTACATCAGGGATTCTTCTGTGGCAGTGATTGTTTACGATGTGACTG

upper sequence: PP1S39_147V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G128771_T01 (Zea mays), 3'ss of exon 2
gtaaaggcgttcagacgtccatattgcatgacaattgagtttatttgcaccagtaaatcagttattctcttccttgcagggcaatttaagttgctgtttgtctttgttgtctgctttacattacaagtatcggtttagaaaccgtcgcgtttgatttatcagaatttggacgtgttgcgcagGGACACTGCTGGACAGGAGAGGTTTAGGAGTTTGATTCCCAGCTACATCCGGGATTCGTCCGTGGCAGTGGTTGTCTATGATGTTTCCA
                                                                                       |  || || ||||  |||  ||   |||||   |||     ||    || || |      |  ||    | |||    |||  | || ||  |||||| ||||| ||||||||||||||||||||| | ||||| ||||||||| |||| || || || || |||||||| |||||||| ||||
-------------------------------------------------------------------nnnnnnnnnnnnnnnnnnncacattactatttgagttt--tggtagctttg--tta-gttcattttcttggaga-----acagttagcatttca----ttgttcttgctgt-cagGGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA

upper sequence: PP1S39_147V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ30542 (Selaginella moellendorffii), 3'ss of exon 2
gtaaaggcgttcagacgtccatattgcatgacaattgagtttatttgcaccagtaaatcagttattctcttccttgcagggcaatttaagttgctgtttgtctttgttgtctgctttacattacaagtatcggtttagaaaccgtcgcgtttgatttatcagaatttggacgtgttgcgcagGGACACTGCTGGACAGGAGAGGTTTAGGAGTTTGATTCCCAGCTACATCCGGGATTCGTCCGTGGCAGTGGTTGTCTATGATGTTTCCA
                                                                                                                               |   ||||    | |      |  || ||| | |  | |      |   |  |||||| |||||||| |||||| | ||  |||||||||||||||||||||| |||||||||||||||||||| || || || |||||  | |
----------------------------------------------------------------------------------------------------------------------------gtatgctggttct--agcttcaaaggatggttttttacgagtctatttttacgtccagGGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGA

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|208346149|gb|DC917102.1|DC917102
EST:     CTCTCCAAGACCATGTATCNTGAGGATCGCACTGTTAGACTACAGCTCTG                         GGACACTGCTGGACAGGAGAGGTTTAGGAGTTTGATTCCCAGCTACATCCG
genomic: CTCTCCAAGACCATGTATCTTGAGGATCGCACTGTTAGACTACAGCTCTGgtaaaggcgt ... tgttgcgcagGGACACTGCTGGACAGGAGAGGTTTAGGAGTTTGATTCCCAGCTACATCCG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcggtttagaaaccgtcgcgtttgatttatcagaatttggacgtgttgcgcagGGACACTGCTGGACAGGAGAGGTTTAGGAGTTTGATTCCCAGCTACATCCGGGATTCGTCCGTGGCAGTGGTTGTCTATGATGTTTCCA
                     gtttgat  putative branch site (score: 5)
                          atttatcagaattt  TA-rich tract