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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaggagttatatttaccttttatgcaggtttttgtacacgtcgtaatgagcgcatacacattgttttatcatccggatttgcgagtcttggcgacctggaaatgtgcgtaattcatgatttttgctgcatattctacgaagacatcaagggtctctgcatctgactgtttttgttgcattggaatagGCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCTGTTGGTTGGAGGCGAGAAGGTCTTGTTTACAAGAAAAATGAG

Basic information

species Physcomitrella patens
transcript PP1S54_156V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA11G04600.1 (Glycine max), 3'ss of exon 4
gtaacaggagttatatttaccttttatgcaggtttttgtacacgtcgtaatgagcgcatacacattgttttatcatccggatttgcgagtcttggcgacctggaaatgtgcgtaattcatgatttttgctgcatattctacgaagacatcaagggtctctgcatctgactgtttttgttgcattggaatagGCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCTGTTGGTTGGAGGCGAGAAGGTCTTGTTTACAAGAAAAATGAG
                                                                                      |  | |||  ||  |   | | |   ||||   |  | ||   || |||||  || ||  | |    | ||    |||||         || |     |||| || ||  |||||   | ||      |||||||||  | |||||||| || |||||||||||| || ||||||| ||||| ||||| || ||||||
--------------------------------------------------------------------------------------gttttttgttgagtttacattttt--taatatgttgtgttgtttgaatatttcaccaatcctttt--gttcatctcatctcgtgtgcaatgct-tgggggaacagCCCTCAGATA---GACCTATTCCAAATGCAACTTTACAAGTTACCGGTGCTGTTGGTTGGCGGAGAGAAGGCCTTGTATACAAAAAGAATGAG

upper sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA17G16630.3 (Glycine max), 3'ss of exon 4
gtaacaggagttatatttaccttttatgcaggtttttgtacacgtcgtaatgagcgcatacacattgttttatcatccggatttgcgagtcttggcgacctggaaatgtgc---gtaattcatgatttttgctgcatattctacgaagacatcaagggtctctgcatctgactgt-ttttgt-tgcattggaatagGCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCTGTTGGTTGGAGGCGAGAAGGTCTTGTTTACAAGAAAAATGAG
                                                                                                 | ||| | || |      ||| | |  |||||| |    |  | |  |   |   |        ||     ||||| | || ||| ||||||| |  |   || | |  |||| ||      |||||||||  | |||||||| || |||||||||||| || ||||||| ||||| ||||| || ||||||
-------------------------------------------------------------------------------------------------atctgtatatatattttttaacttaatatttttaccctctggtgt-tgggtattcctttaaatccttttcttgactatattctgtgtgcattgaataaaagCCCACA-GATAGACCTGTTCCAAATGCAACTTTACAAGTTACTGGTGCTGTTGGTTGGCGGAGAGAAGGGCTTGTGTACAAAAAGAATGAG

upper sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA05G23670.2 (Glycine max), 3'ss of exon 4
gtaacaggagttatatttaccttttatgcaggtttttgtacacgtcgtaatgagcgcatacacattgttttatcatccggatttgcgagtcttggcgacctggaaatgtgcgtaattcatgatttttgctgcatattctacgaagacatcaagggtctctgcatctgactgt-ttttgt-tgcattggaatagGCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCTGTTGGTTGGAGGCGAGAAGGTCTTGTTTACAAGAAAAATGAG
                                                                                 | ||    | ||    |  |  || |     || ||      || || ||  |||||        ||| ||     | ||    ||||| | || ||| ||||||| |  |   || | |  |||| ||      |||||||||  | |||||||| || |||||||||||| || ||||||| ||||| ||||| || ||||||
---------------------------------------------------------------------------------tctgtatattttt---attttcaacttaatatatttaccctgttgtgttgagtattc--------cattaaatccttttgt---tgactatgttctgtgtgcattgaataaaagCCCACA-GATAGACCTGTTCCAAATGCAACTTTACAAGTTACTGGTGCTGTTGGTTGGCGGAGAGAAGGGCTTGTGTACAAAAAGAATGAG

upper sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv02s0012g00910.t01 (Vitis vinifera), 3'ss of exon 4
gtaacaggagttatatttaccttttatgcaggtttttgtacacgtcgtaat--gagcgcat-acacattgttttatcatccggatttgcgagtcttggc--gacctggaaatgtgcgtaattca--tgatttttgctgcatattctacgaagac----atcaagggtctctgcat-ctgactgtttttgttgcattggaata-----gGCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCTGTTGGTTGGAGGCGAGAAGGTCTTGTTTACAAGAAAAATGAG
         |||| || |   |||||   |    |||    |  | |||||  ||||  || |  ||||    |    | |  | |||    |  |||       |  || | | | | ||| |  |||   || ||  |||||  |   |       ||  | | |  ||  || ||   | | |||  ||      ||||      ||| |     |||  |||      ||||||||  | |||||||| || ||||||||||||||| |||| || |||||||| || || ||||||
---------gttagatgtttattttagctatacattttggaatctagtaatttgagcagatgaggcattaccgtggatttctaagttgtacttaatggtttatattttaagtatacattattaaaatgaagattcctttatattaaagtgaattttttattgaagattccttaatactatttttctttaatgtgccaaaatataaatagCCTTCAG--ATAAACCAGTCCCCAATGCAACTTTACAAGTTACAGGTGCTGTTGGTTGGAGGAGAGAGGGCCTTGTTTATAAAAAGAATGAG

upper sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ22278 (Selaginella moellendorffii), 3'ss of exon 4
gtaacaggagttatatttaccttttatgcaggtttttgtacacgtcgtaatgagcgcatacacattgttttatcatccggatttgcgagtcttggcgacctggaaatgtgcgtaattcatgatttttgctgcatattctacgaagacatcaagggtctctgcatctgactgtttttgttgcattggaatagGCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCTGTTGGTTGGAGGCGAGAAGGTCTTGTTTACAAGAAAAATGAG
                                                                                                                                            ||| |   |  |  | ||       | || |  ||| |  | ||     || || ||||||  || || |||  |||||| || || ||||| || || || || || |||||  |||| ||||||||||||||||||||||||
----------------------------------------------------------------------------------------------------------------------------------------gtagcgatgtgttgcattgcctggctggttaacagaatttatctctttc---cagCCCATAGATACAAGACCCCCAGCAAATGCTACTCTCCAAGTCACCGGTGCAGTGGGATGGAGAAGAGAGGGTCTTGTTTACAAGAAAAATGAG

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|100401870|gb|BY954751.1|BY954751
EST:     TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAG                         GCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCT
genomic: TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAGgtaacaggag ... attggaatagGCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCT
EST: gi|162280315|gb|FC456332.1|FC456332
EST:     TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAG                         GCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCT
genomic: TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAGgtaacaggag ... attggaatagGCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCT
EST: gi|100404582|gb|BY973650.1|BY973650
EST:     TGAAACTTTATATTACTCAAGAAAGTGTTCGTTCTCCATTTTCATCCAAG                         GCCCTAGATAATAGGGCACCAATAAATGCAACCCTTCAAGTTACGGGAGCT
genomic: TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAGgtaacaggag ... attggaatagGCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCT
EST: gi|162233608|gb|FC409367.1|FC409367
EST:     TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAG                         GCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCT
genomic: TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAGgtaacaggag ... attggaatagGCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCT
EST: gi|208385555|gb|DC937100.1|DC937100
EST:     TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAG                         GCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCT
genomic: TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAGgtaacaggag ... attggaatagGCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCT
EST: gi|100429936|gb|BY978164.1|BY978164
EST:     TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAG                         GCCCTAGATAATAGGCCACCAANNTAA-TGCA-CCCTTCA-GTTACGGNAG
genomic: TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAGgtaacaggag ... attggaatagGCCCTAGATAATAGGCCACCAA--TAAATGCAACCCTTCAAGTTACGGGAG
EST: gi|67572605|gb|BJ945429.1|BJ945429
EST:     TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAG                         GCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCT
genomic: TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAGgtaacaggag ... attggaatagGCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCT
EST: gi|208361334|gb|DC935063.1|DC935063
EST:     TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAG                         GCCCTAGATAATAGGCCACC
genomic: TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAGgtaacaggag ... attggaatagGCCCTAGATAATAGGCCACC
EST: gi|100384770|gb|BY950760.1|BY950760
EST:     TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAG                         GCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCT
genomic: TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAGgtaacaggag ... attggaatagGCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCT
EST: gi|162223092|gb|FC399983.1|FC399983
EST:     TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAG                         GCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCT
genomic: TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAGgtaacaggag ... attggaatagGCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCT
EST: gi|162178167|gb|FC354885.1|FC354885
EST:     CCATTTTCATCCAAG                         GCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCT
genomic: CCATTTTCATCCAAGgtaacaggag ... attggaatagGCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCT
EST: gi|100407158|gb|BY974039.1|BY974039
EST:     TGGAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAG                         GCCCTAGANTA-TAGGCCACCAANTAA-TGCAACCCTTCAAGTTACGGGAG
genomic: TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAGgtaacaggag ... attggaatagGCCCTAGA-TAATAGGCCACCAA-TAAATGCAACCCTTCAAGTTACGGGAG
EST: gi|100387570|gb|BY988441.1|BY988441
EST:     TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAG                         GCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCT
genomic: TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAGgtaacaggag ... attggaatagGCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCT
EST: gi|67578518|gb|BJ950685.1|BJ950685
EST:     TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAG                         GCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCT
genomic: TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAGgtaacaggag ... attggaatagGCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCT
EST: gi|208393441|gb|DC904059.1|DC904059
EST:     TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAG                         GCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCT
genomic: TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAGgtaacaggag ... attggaatagGCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCT
EST: gi|100415400|gb|BY975297.1|BY975297
EST:     TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCA-G                         GCCCTAGANTA-TAGGCCACCAANNTAA-TGCA-CCCTTCAAGTTACGGGA
genomic: TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAGgtaacaggag ... attggaatagGCCCTAGA-TAATAGGCCACCAA--TAAATGCAACCCTTCAAGTTACGGGA
EST: gi|100450131|gb|CJ974109.1|CJ974109
EST:     TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCNAG                         GCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCGAGTTACGGGAGCT
genomic: TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAGgtaacaggag ... attggaatagGCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCT
EST: gi|100364351|gb|BY984569.1|BY984569
EST:     TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAG                         GCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCT
genomic: TGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAGgtaacaggag ... attggaatagGCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCT

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: 29 (upstream exon), 25 (downstream exon)
Score: 11

AGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAGgtaacaggag ... attggaatagGCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCTGTTGGTTGGAGGCGAGAAGGTCTTGTTTACAAGAAAAATGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctacgaagacatcaagggtctctgcatctgactgtttttgttgcattggaatagGCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCTGTTGGTTGGAGGCGAGAAGGTCTTGTTTACAAGAAAAATGAG
                          atctgac  putative branch site (score: 11)
                                   tttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacaggagttatatttaccttttatgcaggtttttgtacacgtcgtaatgagcgcatacacattgttttatcatccggatttgcgagtcttggcgacctggaaatgtgcgtaattcatgatttttgctgcatattctacgaagacatcaagggtctctgcatctgactgtttttgttgcattggaatagGCCCTAGATAATAGGCCACCAATAAATGCAACCCTTCAAGTTACGGGAGCTGTTGGTTGGAGGCGAGAAGGTCTTGTTTACAAGAAAAATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA