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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgtcattttctttcaaatcggtcattttcagatagtatctgtgtttggcagtacctgcctactaggactgaatcgtgattttcctgttatctttcagATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCTGATCTTCCATAAGATTCGTGCTGTTTTTGGTTTTGGGCTGTAACTTCGT

Basic information

species Physcomitrella patens
transcript PP1S454_1V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S454_1V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA19G33140.1 (Glycine max), 3'ss of exon 2
ttttgtcattttctttcaaatcggtcattttcagatagtatctgtgtttggcagtacctgcctactaggactgaatcgtgattttcctgttatctttcagATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCTGATCTTCCATAAGATTCGTGCTGTTTTTGGTTTTGGGCTGTAACTTCGT
   ||     ||  ||   || |||  | |  |  |  | | | |||||    ||    |  |  || |   |  | |   | ||| || ||     ||| ||||| ||||| || |||||||| |||||||||||||||||||| ||||| || ||||| | ||| ||||| ||||||||||||||  | | |  |  |
--gtgagtggttgattggtattggttttgtggaagttttgtttttgttt--ttgt-ttggtttgttaaggtgggtttgatttgttcttgata-----cagGTATGGGAATGCTACCGTGGTGGAGAACACGGAAAGGGGATGGCGGGATCTTATTTTCCAGAGGATACGTGCGGTTTTTGGTTTTGGAATTTGATATTTT

upper sequence: PP1S454_1V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA03G30230.1 (Glycine max), 3'ss of exon 2
ttttgtcattttctttcaaatcggtcatt--ttcagatagtatctgtgtttggcagtacctgcctactaggactgaat--cgtgatt--ttcctg---ttatctttcagATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCTGATCTTCCATAAGATTCGTGCTGTTTTTGGTTTTGGGCTGTAACTTCGT
  |     |||  ||   |||  |  | |  ||  |  |   | ||| ||||        ||  |  |  |      |   ||||||  ||| ||    | | || ||| ||||| ||||| || |||||||| |||||||||||||| ||||| ||||| || ||||| | ||| ||||||||||||||||||||  | | |  |  |
-gtgagtgtttgattgagaatttgggaatggtttggggaagttttgtttttgttttcttttgtttggtttgttaaggtggtgtgatttgttcttgaatctgtattacagGTATGGGAATGCTACTGTGGTGGAGAACACGGAAAGGGGGTGGCGGGATCTTATTTTCCAGAGGATACGTGCTGTTTTTGGTTTTGGAATTTGAGATTTT

upper sequence: PP1S454_1V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA02G28830.3 (Glycine max), 3'ss of exon 2
ttttgtcattttctttcaaatcggt-cattttcagatagtatctgtgtttggcagtacctgcctactaggactgaatcgtgattttcctgttatct--ttcagATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCTGATCTTCCATAAGATTCGTGCTGTTTTTGGTTTTGGGCTGTAACTTCGT
    || | |   | |  ||||| | |  |||  | | | |  || |||| ||   | |    ||||  |  |   | ||   || | || |  |   | ||||||||| |||||||| |||||||| ||||| || ||||||||||| ||||| || ||||| | ||| ||  |||  ||||                    
----gtgagtcggtgtttaatcgtttcggtttgggtttggaattg-gttttgctcaatcgagttactgaggatatgtggttgcttgcttgcttgcaaatgcagATATGGAAATGCAACTGTGGTGGAGAACACAGAGAGGGGATGGCGGGATCTCATTTTCCAAAGGATACGGACTGCGTTTG--------------------

upper sequence: PP1S454_1V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA02G28830.1 (Glycine max), 3'ss of exon 2
ttttgtcattttctttcaaatcggt-cattttcagatagtatctgtgtttggcagtacctgcctactaggactgaatcgtgattttcctgttatct--ttcagATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCTGATCTTCCATAAGATTCGTGCTGTTTTTGGTTTTGGGCTGTAACTTCGT
    || | |   | |  ||||| | |  |||  | | | |  || |||| ||   | |    ||||  |  |   | ||   || | || |  |   | ||||||||| |||||||| |||||||| ||||| || ||||||||||| ||||| || ||||| | ||| ||  |||                          
----gtgagtcggtgtttaatcgtttcggtttgggtttggaattg-gttttgctcaatcgagttactgaggatatgtggttgcttgcttgcttgcaaatgcagATATGGAAATGCAACTGTGGTGGAGAACACAGAGAGGGGATGGCGGGATCTCATTTTCCAAAGGATACGGACTGC-------------------------

upper sequence: PP1S454_1V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA02G28830.2 (Glycine max), 3'ss of exon 2
ttttgtcattttctttcaaatcggt-cattttcagatagtatctgtgtttggcagtacctgcctactaggactgaatcgtgattttcctgttatc--tttcagATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCTGATCTTCCATAAGATTCGTGCTGTTTTTGGTTTTGGGCTGTAACTTCGT
    || | |   | |  ||||| | |  |||  | | | |  || |||| ||   | |    ||||  |  |   | ||   || | || |  |   | ||||||||| |||||||| |||||||| ||||| || ||||||||||| ||||| || ||||| | ||| ||  |||  |||||||||||  | | |  |  |
----gtgagtcggtgtttaatcgtttcggtttgggtttggaattg-gttttgctcaatcgagttactgaggatatgtggttgcttgcttgcttgcaaatgcagATATGGAAATGCAACTGTGGTGGAGAACACAGAGAGGGGATGGCGGGATCTCATTTTCCAAAGGATACGGACTGCGTTTGGTTTTGGAATTTGAGCTTTT

upper sequence: PP1S454_1V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA09G16680.1 (Glycine max), 3'ss of exon 3
ttttgtcattttctttcaaatcggtcattttcagatagtatctgtgtttggcagtacctgcctactaggactgaatcgtgattttcctgttatct-----ttcagATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCTGATCTTCCATAAGATTCGTGCTGTTTTTGGTTTTGGGCTGTAACTTCGT
                  | || ||  ||     ||    | || |||||  | |   ||  |     ||  || |     || |   ||||  |     | ||||||||| |||||||| |||||||| ||||| || ||||| ||||| ||||| || ||||| | ||| ||  |||  |||||||||||  | | |  |  |
---------------gtgagtcagtgtttaatcaattcagtttgggtttgaaatt---tgttttgctcgatcgagttaccgttatgtggttacttgcaaatgcagATATGGAAATGCAACTGTGGTGGAGAACACAGAGAGGGGTTGGCGGGATCTCATTTTCCAAAGGATACGAACTGCGTTTGGTTTTGGAATTTGAGATTTT

upper sequence: PP1S454_1V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT3G12050.1 (Arabidopsis thaliana), 3'ss of exon 2
ttttgtcattttctttcaaatcggtcattttcagatagtatctgtgtttggcagtacctgccta-ctaggactgaatcgtgattttcctgttatcttt-cagATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCTGATCTTCCATAAGATTCGTGCTGTTTTTGGTTTTGGGCTGTAACTTCGT
   || | | |   || | ||  || | |     |  ||  ||   | ||     |      || |||    |   |  || || |||  |  |   | |||||| || ||||| || |||||||||||||| || || |||||| ||||||| || ||||||| ||| ||||| ||||| || |||||  | | |  |  |
--atggcctgtgtcttaagatgagtgagtgattcaatgttgctaaatgtgaggacattgatgtaactactgttatctgatgtttatccaatggttgatgcagATACGGGAATGCGACTGTGGTGGAAAACACTGAGAGAGGATGGAGAGATCTTATATTCCATAGGATCCGTGCAGTTTTCGGATTTGGAATATGAACTTAT

upper sequence: PP1S454_1V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv08s0007g06710.t01 (Vitis vinifera), 3'ss of exon 2
ttttgtcattttctttcaaatcggtcattttcagatagt---atctgtgtttggcagtacctg-----cctactaggactgaatcgtgattttcctgttatct-----ttcagATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCTGATCTTCCATAAGATTCGTGCTGTTTTTGGTTTTGGGCTGTAACTTCGT
    ||   ||||| |  | | | |  |||| |  | ||    | | ||||    ||   |||     |  ||| |       | ||||||    || ||| |     | ||||||||| |||||||||||||| || ||||| ||||| || ||| | ||||| || ||||| |||||  | || || |||||||||||  | | | ||  |
----gttggtttctgttga-tggcttgttttgattttgttctgtttttgttcctaaggctctgtgattctgacttgtggctgtttgtgattgctttggtatttcattatgcagATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCTCATTTTCCACAAGATAAGAGCAGTGTTTGGTTTTGGAATATGAATTTTT

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|19788714|gb|BQ040872.1|BQ040872
EST:     GGCCTGACCATCGTGAAACTGACTCAGACCGACGTTCCAGACGAGGACAG                         ATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCT
genomic: GGCCTGACCATCGTGAAACTGACTCAGACCGACGTTCCAGACGAGGACAGgtacactagg ... tatctttcagATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCT
EST: gi|2956970|gb|AJ225533.1|AJ225533
EST:     GGCCTGACCATCGTGAAACTGACTCAGACCGACGTTCCAGACGAGGACAG                         ATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCT
genomic: GGCCTGACCATCGTGAAACTGACTCAGACCGACGTTCCAGACGAGGACAGgtacactagg ... tatctttcagATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCT
EST: gi|161982432|gb|EE296441.1|EE296441
EST:     GGCCTGACCATCGTGAAACTGACTCAGACCGACGTTCCAGACGAGGACAG                         ATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCT
genomic: GGCCTGACCATCGTGAAACTGACTCAGACCGACGTTCCAGACGAGGACAGgtacactagg ... tatctttcagATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCT
EST: gi|161982440|gb|EE296444.1|EE296444
EST:     GGCCTGACCATCGTGAAACTGACTCAGACCGACGTTCCAGACGAGGACAG                         ATATGGCAATGCAACAGTGGTGGAAAACACGGAAGGGGGACGGCGAGATCT
genomic: GGCCTGACCATCGTGAAACTGACTCAGACCGACGTTCCAGACGAGGACAGgtacactagg ... tatctttcagATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCT
EST: gi|208389397|gb|DC953235.1|DC953235
EST:     GGCCTGACCATCGTGAAACTGACTCAGACCGACGTTCCAGACGAGGACAG                         ATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCT
genomic: GGCCTGACCATCGTGAAACTGACTCAGACCGACGTTCCAGACGAGGACAGgtacactagg ... tatctttcagATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCT
EST: gi|162241050|gb|FC416681.1|FC416681
EST:     GGCCTGACCATCGTGAAACTGACTCAGACCGACGTTCCAGACGAGGACAG                         ATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCT
genomic: GGCCTGACCATCGTGAAACTGACTCAGACCGACGTTCCAGACGAGGACAGgtacactagg ... tatctttcagATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCT
EST: gi|162205259|gb|FC380941.1|FC380941
EST:     GGCCTGACCATCGTGAAACTGACTCAGACCGACGTTCCAGACGAGGACAG                         ATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCT
genomic: GGCCTGACCATCGTGAAACTGACTCAGACCGACGTTCCAGACGAGGACAGgtacactagg ... tatctttcagATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCT
EST: gi|161982434|gb|EE296443.1|EE296443
EST:     GGCCTGACCATCGTGAAACTGACTCAGACCGACGTTCCAGACGAGGACAG                         ATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCT
genomic: GGCCTGACCATCGTGAAACTGACTCAGACCGACGTTCCAGACGAGGACAGgtacactagg ... tatctttcagATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCT
EST: gi|162171880|gb|FC349004.1|FC349004
EST:     GGCCTGACCATCGTGAAACTGACTCAGACCGACGTTCCAGACGAGGACAG                         ATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCT
genomic: GGCCTGACCATCGTGAAACTGACTCAGACCGACGTTCCAGACGAGGACAGgtacactagg ... tatctttcagATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCT

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: 14 (upstream exon), 32 (downstream exon)
Score: 6

GTAATTTTATCTTTCGAGGAACCTGAAGTTGGCCTGACCATCGTGAAACTGACTCAGACCGACGTTCCAGACGAGGACAGgtacactagg ... tatctttcagATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCTGATCTTCCATAAGATTCGTGCTGTTTTTGGTTTTGGGCTGTAACTTCGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttggcagtacctgcctactaggactgaatcgtgattttcctgttatctttcagATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCTGATCTTCCATAAGATTCGTGCTGTTTTTGGTTTTGGGCTGTAACTTCGT
                                    ttttcctgttatcttt  CT-rich tract
                                            ttatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgtcattttctttcaaatcggtcattttcagatagtatctgtgtttggcagtacctgcctactaggactgaatcgtgattttcctgttatctttcagATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCTGATCTTCCATAAGATTCGTGCTGTTTTTGGTTTTGGGCTGTAACTTCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT