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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatattccttgaatcgaaaatgggtatgaacttcagcatcagtgcttagatttggtttcttacaacaatttggatcacattttgggtctgggtttgcagGTTGTGCAGTTGTACTCTTGCTTGGACAAGATTAGCTATGTAGAATGGGCCCCAGATTCGGAGTATCTTCTATGTGGTCTCTTCAAGCGAGCTATTGTTC

Basic information

species Physcomitrella patens
transcript PP1S52_72V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S52_72V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G374969_T01 (Zea mays), 3'ss of exon 1
tcatattccttgaatcgaaaatgg-gtatgaacttcagcatcagtgcttagatttggtttcttacaacaatttggatcacat-tttgggtctgggtttgcagGTTGTGCAGTTGTACTCTTGCTTGGACAAGATTAGCTATGTAGAATGGGCCCCAGATTCGGAGTATCTTCTATGTGGTCTCTTCAAGCGAGCTATTGTTC
   | |  | ||||   | | ||  |||  ||  |  |      |    |||     | |           |    ||  ||  |||        | ||||||| || || || |  || ||| |||||||||| |||| |||||||||||| |||||||| || ||  || ||||||| || | ||||||| | || || |
--gtttggcatgaactcatattgttgtaaaaatatgcgggctcatatcgagacactatattaatgtgtttctaaactcctatacttgaactcaattatgcagGTGGTACAATTATTTTCATGCGTGGACAAGATAAGCTCTGTAGAATGGGCACCAGATTCAGAATACATTTTATGTGGACTTTACAAGCGACCCATGGTGC

upper sequence: PP1S52_72V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA10G33830.1 (Glycine max), 3'ss of exon 1
--tcata---ttccttgaatcga--aaatgggtatgaacttcagcatcagtgcttagatttggtttcttacaacaatttggatcacattttgggtctgggtttgcagGTTGTGCAGTTGTACTCTTGCTTGGACAAGATTAGCTATGTAGAATGGGCCCCAGATTCGGAGTATCTTCTATGTGGTCTCTTCAAGCGAGCTATTGTTC
  ||||    ||  |  |  |||   | ||  || |    | |    || |  |  |  |    ||| |       ||   ||||   |||  | ||   | ||||||||||||||||||  || ||||| ||||||||||||||| | ||||||||||  ||||| || ||| |||| |||||||||| |||     | ||  | |
tgtcatgcgctttttccatccgactcattgattaagctgcttaattccaattatctgcctctagttcctg----gtttgcaatcattctttttggct---tatgcagGTTGTGCAGTTGTTTTCATGCTTAGACAAGATTAGCTATATTGAATGGGCCCTTGATTCTGAATATATTCTTTGTGGTCTCTACAAAAAGCCAATGATAC

upper sequence: PP1S52_72V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA20G33770.1 (Glycine max), 3'ss of exon 1
--tcatattcct--tgaatcgaaaatgggtatgaacttcagcatcagtgcttagatttggtttcttacaacaatttggatcacattttgggtctgggtt-tgcagGTTGTGCAGTTGTACTCTTGCTTGGACAAGATTAGCTATGTAGAATGGGCCCCAGATTCGGAGTATCTTCTATGTGGTCTCTTCAAGCGAGCTATTGTTC
  ||||   | |  |  |||  |       || ||  |    ||      |||  | ||  |       |   |||| | ||  | ||   | ||| || ||||||||||||||||||  || ||||| ||||||||||||||| | ||||||||||  ||||| || ||| |||| || ||||||| |||     | ||  | |
tgtcatgcacatattccatctgactcattgattaagctgcttatttccaatta--tctgcctctagttcatggtttgcaccaattctt---tttggcttatgcagGTTGTGCAGTTGTTTTCATGCTTAGACAAGATTAGCTATATTGAATGGGCCCTTGATTCTGAATATATTCTTTGCGGTCTCTACAAAAAGCCGATGATAC

upper sequence: PP1S52_72V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ17238 (Selaginella moellendorffii), 3'ss of exon 1
tcatattccttgaatcgaaaatgggtatgaacttcagcatcagtgcttagatttggtttcttacaacaa----tttggatcacattttgggtctgggtttg-----cagGTTGTGCAGTTGTACTCTTGCTTGGACAAGATTAGCTATGTAGAATGGGCCCCAGATTCGGAGTATCTTCTATGTGGTCTCTTCAAGCGAGCTATTGTTC
                         | ||| ||    | |   || ||   ||    ||   |   |||    ||||  |     |||||  ||   ||||     ||||| |||||| | ||||||||| | || ||||| ||| ||||||||||||| || || ||||||||| |||| ||||  ||  ||||||| || || || |
---------------------gtactgtgatctctttctttgctggttttgttcttctttccaatgcaagttctttgagtttttctttggaactatttttgtttcacagGTCGTGCAGCTCTACTCTTGCCTCGATAAGATCAGCCATGTAGAATGGGCACCCGACTCGGAGTATGTTCTTTGTGCGCTGGTCAAGCGCGCGATGGTGC

upper sequence: PP1S52_72V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ30936 (Selaginella moellendorffii), 3'ss of exon 1
tcatattccttgaatcgaaaatgggtatgaacttcagcatcagtgcttagatttggtttcttacaacaa----tttggatcacattttgggtctgggtttg-----cagGTTGTGCAGTTGTACTCTTGCTTGGACAAGATTAGCTATGTAGAATGGGCCCCAGATTCGGAGTATCTTCTATGTGGTCTCTTCAAGCGAGCTATTGTTC
                         | ||| ||    | |   || ||   ||    ||   |    ||    ||||  |     |||||  ||   ||||     ||||| |||||| | ||||||||| | || ||||| ||| ||||||||||||| || || ||||||||| |||| ||||  || |||||||| || || || |
---------------------gtactgtgatctctttctttgctggttttgttcttctttccaatgtaagttctttgagtttttctttggaactatttttgtttcacagGTCGTGCAGCTCTACTCTTGCCTCGATAAGATCAGCCATGTAGAATGGGCACCCGACTCGGAGTATGTTCTTTGTGCGCTGTTCAAGCGCGCGATGGTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttagatttggtttcttacaacaatttggatcacattttgggtctgggtttgcagGTTGTGCAGTTGTACTCTTGCTTGGACAAGATTAGCTATGTAGAATGGGCCCCAGATTCGGAGTATCTTCTATGTGGTCTCTTCAAGCGAGCTATTGTTC
            ttcttac  putative branch site (score: 2)
                   aacaattt  TA-rich tract