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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctgatgtggtaaagatagctgtttttaaaggtagtgtggcaacaagcccgttggttttaaaggtgttgatacatggtaattcgtggttgtactgaatagGTGGTGGAGTTGCCAATGTTGCATCCTGAGAAGTTCGTGAAATTGGGAATTGATCCGCCCAAAGGAGTCCTTTGCTATGGCCCTCCCGGAACTGGCAAGA

Basic information

species Physcomitrella patens
transcript PP1S49_256V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os02g54340.1 (Oryza sativa), 3'ss of exon 6
-------------------gctgatgtggtaaagatagctgtttttaaaggtagtgtggcaacaagcccgttggttttaaaggtgt--tgatacatggtaattcgtggttgtactg----aatagGTGGTGGAGTTGCCAATGTTGCATCCTGAGAAGTTCGTGAAATTGGGAATTGATCCGCCCAAAGGAGTCCTTTGCTATGGCCCTCCCGGAACTGGCAAGA
                   | | || |          ||    ||         |||| || || ||  ||| |||||  |  | |  || ||  |  |  ||  |  || |  |      |||||| || ||| | || ||| | || || |||||||| || ||  | || |||||||| || || || |||||||||||||||||||| ||||||||||| |
gtatactaatcttttttcagttcatatcccttgtcgtgcaaacttgctcatccttgtg-catcaggctagttagttttggacttattttgctatttactgtttgctaattattgtttgttcatagGTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATTGATCCTCCAAAGGGGGTCCTTTGCTATGGCCCTCCTGGAACTGGCAAAA

upper sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 6
gctgatgtggta-aagatagctgtttttaaaggtagtgtggcaacaagcccgttggttttaaaggtgttgata-catggtaattc-gtggttgtac----tgaatagGTGGTGGAGTTGCCAATGTTGCATCCTGAGAAGTTCGTGAAATTGGGAATTGATCCGCCCAAAGGAGTCCTTTGCTATGGCCCTCCCGGAACTGGCAAGA
         |||   |||   | ||| |    ||    |||||   |   | |     |||     |    ||   |||| | || ||| ||||||    |    |||| || ||  | || ||| | || || || ||||| || ||  | || |||||||| || ||||| ||||||||||||||||| || || ||||||||||
---------gtatgtgatccttttttcttcttgtgagctggcacatactgcatcatagttagttacgggactagtttggttactctgtgcttgtaccttttttgcagGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATTGATCCTCCAAAAGGCGTCCTTTGCTATGGCCCACCTGGCACTGGCAAGA

upper sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ13722 (Selaginella moellendorffii), 3'ss of exon 6
gctgatgtggtaaagatagctgtttttaaaggtagtgtggcaacaagcccgttggttttaaaggtgttgatacatggtaattcgtggttgtactga-atagGTGGTGGAGTTGCCAATGTTGCATCCTGAGAAGTTCGTGAAATTGGGAATTGATCCGCCCAAAGGAGTCCTTTGCTATGGCCCTCCCGGAACTGGCAAGA
                                       | ||| |  || ||  ||  |   |  ||  |    |   ||      || |||  | |||||| || ||| | || ||| | ||||||||||||||  | ||  | ||||| ||||| ||||||||||| |||||||| |||||||| |||||||| || |
---------------------------------------gtaactacaccatt--ttacatttggtttcctcgtcgacgatcttaacttttacgcatatagGTTGTAGAGCTTCCTATGCTCCATCCTGAGAAGTTTATCAAGCTTGGAATCGATCCTCCCAAAGGAGTTCTTTGCTACGGCCCTCCGGGAACTGGGAAAA

upper sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ29161 (Selaginella moellendorffii), 3'ss of exon 6
gctgatgtggtaaagatagctgtttttaaaggtagtgtggcaacaagcccgttggttttaaaggtgttgatacatggtaattcgtggttgtactga-atagGTGGTGGAGTTGCCAATGTTGCATCCTGAGAAGTTCGTGAAATTGGGAATTGATCCGCCCAAAGGAGTCCTTTGCTATGGCCCTCCCGGAACTGGCAAGA
                                       | ||| |  || ||  ||  |   |  ||  |    |   ||      || |||  | |||||| || ||| | || ||| | || ||||| |||||  | ||  | ||||| ||||| ||||||||||| |||||||| |||||||| |||||||| || |
---------------------------------------gtaactacaccatt--ttacatttggttttctcgtcgacgatcttaacttttacgcatatagGTTGTAGAGCTTCCTATGCTCCACCCTGAAAAGTTTATCAAGCTTGGAATCGATCCTCCCAAAGGAGTTCTTTGCTACGGCCCTCCGGGAACTGGGAAAA

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|208386966|gb|DC956935.1|DC956935
EST:     CCTACAATGATATTGGTGGCTGTAAAGAGCAAATAGAAAAGATGCGTGAG                         GTGGTGGAGTTGCCAATGTTGCATCCTGAGAAGTTCGTGAAATTGGGAATT
genomic: CCTACAATGATATTGGTGGCTGTAAAGAGCAAATAGAAAAGATGCGTGAGgtaaatgaaa ... tactgaatagGTGGTGGAGTTGCCAATGTTGCATCCTGAGAAGTTCGTGAAATTGGGAATT
EST: gi|208348229|gb|DC905485.1|DC905485
EST:     CCTACAATGATATTGGTGGCTGTAAAGAGCAAATAGAAAAGATGCGTGAG                         GTGGTGGAGTTGCCA-TGTTGCATCCTGAGAAGTTCGTGAAATTGGGAATT
genomic: CCTACAATGATATTGGTGGCTGTAAAGAGCAAATAGAAAAGATGCGTGAGgtaaatgaaa ... tactgaatagGTGGTGGAGTTGCCAATGTTGCATCCTGAGAAGTTCGTGAAATTGGGAATT
EST: gi|67727435|gb|BJ977694.1|BJ977694
EST:     CAAATAGAAAAGATGCGTGAG                         GTGGTGGAGTTGCCAATGTTGCATCCTGAGAAGTTCGTGAAATTGGGAATT
genomic: CAAATAGAAAAGATGCGTGAGgtaaatgaaa ... tactgaatagGTGGTGGAGTTGCCAATGTTGCATCCTGAGAAGTTCGTGAAATTGGGAATT
EST: gi|67507498|gb|BJ940380.1|BJ940380
EST:     CCTACAATGATATTGGTGGCTGTAAAGAGCAAATAGAAAAGATGCGTGAG                         GTGGTGGAGTTGCCAATGTTGCATCCTGAG
genomic: CCTACAATGATATTGGTGGCTGTAAAGAGCAAATAGAAAAGATGCGTGAGgtaaatgaaa ... tactgaatagGTGGTGGAGTTGCCAATGTTGCATCCTGAG
EST: gi|208375716|gb|DC936656.1|DC936656
EST:     CCTACAATGATATTGGTGGCTGTAAAGAGCAAATAGAAAAGATGCGTGAG                         GTGGTGGAGTTGCCAATGTTGCATCCTGAGAAGTTCGTGAAATNGGGAATT
genomic: CCTACAATGATATTGGTGGCTGTAAAGAGCAAATAGAAAAGATGCGTGAGgtaaatgaaa ... tactgaatagGTGGTGGAGTTGCCAATGTTGCATCCTGAGAAGTTCGTGAAATTGGGAATT
EST: gi|100445251|gb|BY982880.1|BY982880
EST:     CTACA-TGATNAT-GGTGGCTGTAAAGAGCAAATAGAAAAGATGCGTGAG                         GGTGGTGGAGTTGCCAA
genomic: -TACAATGAT-ATTGGTGGCTGTAAAGAGCAAATAGAAAAGATGCGTGAGgtaaatgaaa ... tactgaatagG-TGGTGGAGTTGCCAA
EST: gi|100385842|gb|BY951036.1|BY951036
EST:     CCTACAATGATATTGGTGGCTGTAAAGAGCAAATAGAANAGATGCGTGAG                         GTGGTGGAGTTGCCAATGTTGCATCCTGAGAAGTTCGTGAAATTGGGAATT
genomic: CCTACAATGATATTGGTGGCTGTAAAGAGCAAATAGAAAAGATGCGTGAGgtaaatgaaa ... tactgaatagGTGGTGGAGTTGCCAATGTTGCATCCTGAGAAGTTCGTGAAATTGGGAATT
EST: gi|208397607|gb|DC912225.1|DC912225
EST:     CCTACAATGATATTGGTGGCTGTAAAGAGCAAATAGAAAAGATGCGTGAG                         GTGGTGGANTTGCCAATGTTGCATCCTGA
genomic: CCTACAATGATATTGGTGGCTGTAAAGAGCAAATAGAAAAGATGCGTGAGgtaaatgaaa ... tactgaatagGTGGTGGAGTTGCCAATGTTGCATCCTGA
EST: gi|208387130|gb|DC941302.1|DC941302
EST:     CTACAATGAATATTGGTGGCTGTAAAGAGCAAATAGAAAAGATGCGTGAG                         GTGGTGGAGTTGCCA-TGTTGCATCCTGAGAN-TTCGTGAA-TTGGNANT-
genomic: CTACAATGA-TATTGGTGGCTGTAAAGAGCAAATAGAAAAGATGCGTGAGgtaaatgaaa ... tactgaatagGTGGTGGAGTTGCCAATGTTGCATCCTGAGAAGTTCGTGAAATTGGGAATT
EST: gi|100352668|gb|BY945387.1|BY945387
EST:     CCTACAATGATATTGGTGGCTGTNAAGAGCAAATAGAAAAGATGCGTGAG                         GTGGTGGAGTTGCCAATGTTGCATCCTGAGAAGTTCGTGAAATTGGGAATT
genomic: CCTACAATGATATTGGTGGCTGTAAAGAGCAAATAGAAAAGATGCGTGAGgtaaatgaaa ... tactgaatagGTGGTGGAGTTGCCAATGTTGCATCCTGAGAAGTTCGTGAAATTGGGAATT
EST: gi|100352747|gb|BY945428.1|BY945428
EST:     CCTACNATGATATTGGTGGCTGTNAAGAGCAAATAGAAAAGATGCGTGAG                         GTGGTGGAGTTGCCAATGTTGCATCCTGAGAAGTTCGTGAAATTGGGGATT
genomic: CCTACAATGATATTGGTGGCTGTAAAGAGCAAATAGAAAAGATGCGTGAGgtaaatgaaa ... tactgaatagGTGGTGGAGTTGCCAATGTTGCATCCTGAGAAGTTCGTGAAATTGGGAATT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 32 (upstream exon), 34 (downstream exon)
Score: 11

GATTGACCCCAGCGTTACAATGATGACAGTGGAGGAAAAGCCAGATGTCACCTACAATGATATTGGTGGCTGTAAAGAGCAAATAGAAAAGATGCGTGAGgtaaatgaaa ... tactgaatagGTGGTGGAGTTGCCAATGTTGCATCCTGAGAAGTTCGTGAAATTGGGAATTGATCCGCCCAAAGGAGTCCTTTGCTATGGCCCTCCCGGAACTGGCAAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcccgttggttttaaaggtgttgatacatggtaattcgtggttgtactgaatagGTGGTGGAGTTGCCAATGTTGCATCCTGAGAAGTTCGTGAAATTGGGAATTGATCCGCCCAAAGGAGTCCTTTGCTATGGCCCTCCCGGAACTGGCAAGA
                   tgttgat  putative branch site (score: 11)
          ttttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctgatgtggtaaagatagctgtttttaaaggtagtgtggcaacaagcccgttggttttaaaggtgttgatacatggtaattcgtggttgtactgaatagGTGGTGGAGTTGCCAATGTTGCATCCTGAGAAGTTCGTGAAATTGGGAATTGATCCGCCCAAAGGAGTCCTTTGCTATGGCCCTCCCGGAACTGGCAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA