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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagcttattttcgattggttgaactagttccgtggttcatttgatttgttgtttttgatatcatttggttttagagcaattcgtggcttctgattccgacaacatctaaatgattttcgtgttcttacagCCAAGACGCAGTGACTTGGATATGAACCAGCATGTGAACAACGTGAAGTACATTGGTTGGATGATGGAG

Basic information

species Physcomitrella patens
transcript PP1S3_298V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S3_298V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os06g05130.1 (Oryza sativa), 3'ss of exon 5
gtcagcttattttcgattggttgaactagttccgtggttcatttgatttgttgtttttgatatcatttggttttagagcaattcgtggcttctgattccgacaacatctaa--atgattttcgtgttctta-cagCCAAGACGCAGTGACTTGGATATGAACCAGCATGTGAACAACGTGAAGTACATTGGTTGGATGATGGAG
                                 ||   ||| || || | |  || ||    |||||   |||         | |||| |||| || |  | ||  ||| |  | |  |    ||||| |  ||||| |   | |||||| | ||| | ||||||||||||||||| |||||||| |||||||||||  | |||
---------------------------------gtaagtcagttaatat-tgcttgttaccgtcattcatttt-------gctggtgg-ttctcatgcataaaatttctcatgagggatcctttgttcatgtcagCCGAAGTGGAGTGACCTTGATGTCAACCAGCATGTGAACAATGTGAAGTATATTGGTTGGATACTTGAG

upper sequence: PP1S3_298V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G017382_T01 (Zea mays), 3'ss of exon 4
gtcagcttattttcgattggttgaactagttccgtggttcatttgatttgttgtttttgatatcatttggttttagagcaattcgtggcttctgatt---ccgacaacatctaaatgattttcgtgttcttacagCCAAGACGCAGTGACTTGGATATGAACCAGCATGTGAACAACGTGAAGTACATTGGTTGGATGATGGAG-------------------------------
                                                        |    |  |   |     |   |   ||||  | |||| ||   |||    || || ||  | ||       | | ||||| ||  | |||||| ||||  | |||||||| ||||||||||| |||||||| ||||||||  | |||                               
-------------------------------------------------------gtaaggaggagcagaccagaacacctctcgtcccgtctggttggaccgctctcaactgaaaaacttgttccccccttcagCCCAGGTGGAGTGACATGGACGTCAACCAGCACGTGAACAACGTCAAGTACATCGGTTGGATCCTCGAGAGCGTGCCGCTGGACGTGCTGGAGGATTACC

upper sequence: PP1S3_298V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ13354 (Selaginella moellendorffii), 3'ss of exon 4
gtcagcttattttcgattggttgaactagttccgtggttcatttgatttgttgtttttgatatcatttggttttagagcaattcgtggcttctgattccgacaacatctaaatgattttcgtgttcttacagCCAAGACGCAGTGACTTGGATATGAACCAGCATGTGAACAACGTGAAGTACATTGGTTGGATGATGGAG
                                                 ||   | |  || ||| ||   |||    |  ||    ||   |  ||   | |  |||      || || |  ||  | |||||||| |   | |||||||| ||||||||||| ||||||||||| |||||||| || |||||| | |||
-------------------------------------------------gtgagtatccatctcactttccttt----ctctttcctgcgctt--tttttaaagtatc------atctttgcatt--tgcagCCAAGGCATGGAGACTTGGACATGAACCAGCACGTGAACAACGTAAAGTACATCGGATGGATGCTCGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaattcgtggcttctgattccgacaacatctaaatgattttcgtgttcttacagCCAAGACGCAGTGACTTGGATATGAACCAGCATGTGAACAACGTGAAGTACATTGGTTGGATGATGGAG
                            atctaaa  putative branch site (score: 3)
                                            tgttctt  putative PPT
                            atctaaatgatttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagcttattttcgattggttgaactagttccgtggttcatttgatttgttgtttttgatatcatttggttttagagcaattcgtggcttctgattccgacaacatctaaatgattttcgtgttcttacagCCAAGACGCAGTGACTTGGATATGAACCAGCATGTGAACAACGTGAAGTACATTGGTTGGATGATGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA