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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttaactgaatgtttcttgacattatactttaaggaagttttcaattctttcgagtcgcattggggtttgatagttcatttcgtgttttttttcttgcagTCATCATATGGATTTGTTGACTACTTGGACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAAT

Basic information

species Physcomitrella patens
transcript PP1S84_50V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S84_50V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 3
------tttaactgaatgtttcttgacattatactttaaggaagttttcaattctttcgagtcgcattggggtttgatagttcatttcgtgtttttt---ttcttgcagTCATCATATGGATTTGTTGACTACTTGGACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAAT
      |||        |    |     || || |  || |||| |||    ||  | | ||  | |||     | |    |      |  | ||||    | |||||||||||||||||||||||| ||||||| || |  |  | ||||    | ||  |||  ||||| || || || |  ||
gtagagttttggaacccgcccttctgttttttattcgaatgaagcttt----tcggtagtgtt-ctttgaaagctaacttctagacatgaatgttttacacttttgcagTCATCATATGGATTTGTTCACTACTTTGATCGAAGATGTGCTAGTATGGCTATAATGACTCTTAACGGAAGGCATAT

upper sequence: PP1S84_50V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT3G14100.1 (Arabidopsis thaliana), 3'ss of exon 3
------------------------------------------------------------------------------------tttaactgaatgtttcttgacatt--atactttaaggaagtt--ttcaatt-ctttcgagtcgcattggggtttgatagttcatttcgtgttttttttcttgcagTCATCATATGGATTTGTTGACTACTTGGACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAAT
                                                                                      || || ||   ||    |  ||  |||||||||||||  |  |  | || ||    | |   | |||  |   | ||      || | ||| |||  |||||||||||||||||||||||| ||||||| || |  |  |  |||||  | ||  ||    |||| || || || |   |
gtagttagattctaaaatccacctgatttctactttattgtgaaagtgaccctcttatatagtagctttcttgttttggacgagcatacctcaacaattgcacatttttaatactttaaggaaactactctacttgctgcttactaaaaatggactcataaagcatgcatctt-tttatttatttgcagTCATCATATGGATTTGTTCACTACTTTGATCGAAGATCCGCTGCTCTGGCTATACTGTCTCTGAACGGAAGGCATCT
















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|100356992|gb|BY983639.1|BY983639
EST:     TTTCTAACATTGGGCCGTTGGAGGGTTGCAAACTTATCAGGAAAGAGAAG                         TCATCATATGGATTTGTTGACTACT
genomic: TTTCTAACATTGGGCCGTTGGAGGGTTGCAAACTTATCAGGAAAGAGAAGgtaactgtgg ... tttcttgcagTCATCATATGGATTTGTTGACTACT
EST: gi|208376147|gb|DC910999.1|DC910999
EST:     TTTCTAACATTGGGCCGTTGGAGGGTTGCAAACTTATCAGGAAAGAGAAG                         TCATCATATGGATTTGTTGACTACTTGGACCATATTTATGCTGCAGTAGCA
genomic: TTTCTAACATTGGGCCGTTGGAGGGTTGCAAACTTATCAGGAAAGAGAAGgtaactgtgg ... tttcttgcagTCATCATATGGATTTGTTGACTACTTGGACCATATTTATGCTGCAGTAGCA
EST: gi|162258161|gb|FC433943.1|FC433943
EST:     TTTCTAACATTGGGCCGTTGGAGGGTTGCAAACTTATCAGGAAAGAGAAG                         TCATCATATGGATTTGTTGACTACTTGGACCATATTTATGCTGCAGTAGCA
genomic: TTTCTAACATTGGGCCGTTGGAGGGTTGCAAACTTATCAGGAAAGAGAAGgtaactgtgg ... tttcttgcagTCATCATATGGATTTGTTGACTACTTGGACCATATTTATGCTGCAGTAGCA
EST: gi|100420202|gb|BY975968.1|BY975968
EST:     TTTCTAACATTGGGCCGTTGGAGGGTTGCAAACTTATCAGGAAAGAGAAG                         TCATCATATGGATTTGTTGACTACTTGGACCATATT
genomic: TTTCTAACATTGGGCCGTTGGAGGGTTGCAAACTTATCAGGAAAGAGAAGgtaactgtgg ... tttcttgcagTCATCATATGGATTTGTTGACTACTTGGACCATATT
EST: gi|208368756|gb|DC940051.1|DC940051
EST:     TTTCTAACATTGGGCCGTTGGAGGGTTGCAAACTTATCAGGAAAGAGAAG                         TCATCATATGGATTTGTTGACTACTTGGACCATATTTATGCTGCAGTAGCA
genomic: TTTCTAACATTGGGCCGTTGGAGGGTTGCAAACTTATCAGGAAAGAGAAGgtaactgtgg ... tttcttgcagTCATCATATGGATTTGTTGACTACTTGGACCATATTTATGCTGCAGTAGCA
EST: gi|100450649|gb|CJ974369.1|CJ974369
EST:     TTTCTAACATTGGGCCGTTGGAGGGTTGCAAACTTATCAGGAA-GAGAAG                         TCATCATATGGATTNGTTGACTACTTGGAC-ATATTTATGCTGCAGTAGCA
genomic: TTTCTAACATTGGGCCGTTGGAGGGTTGCAAACTTATCAGGAAAGAGAAGgtaactgtgg ... tttcttgcagTCATCATATGGATTTGTTGACTACTTGGACCATATTTATGCTGCAGTAGCA
EST: gi|162254430|gb|FC430656.1|FC430656
EST:     TTTCTAACATTGGGCCGTTGGAGGGTTGCAAACTTATCAGGAAAGAGAAG                         TCATCATATGGATTTGTTGACTACTTGGACCATATTTATGCTGCAGTAGCA
genomic: TTTCTAACATTGGGCCGTTGGAGGGTTGCAAACTTATCAGGAAAGAGAAGgtaactgtgg ... tttcttgcagTCATCATATGGATTTGTTGACTACTTGGACCATATTTATGCTGCAGTAGCA
EST: gi|208391587|gb|DC933836.1|DC933836
EST:     TTTCTAACATTGGGCCGTTGGAGGGTTGCAAACTTATCAGGAAAGAGAAG                         TCATCATATGGATTTGTTGACTACTTGGACCATATTTATGCTGCAGTAGCA
genomic: TTTCTAACATTGGGCCGTTGGAGGGTTGCAAACTTATCAGGAAAGAGAAGgtaactgtgg ... tttcttgcagTCATCATATGGATTTGTTGACTACTTGGACCATATTTATGCTGCAGTAGCA
EST: gi|162277159|gb|FC453381.1|FC453381
EST:     GTTGGAGGGTTGCAAACTTATCAGGAAAGAGAAG                         TCATCATATGGATTTGTTGACTACTTGGACCATATTTATGCTGCAGTAGCA
genomic: GTTGGAGGGTTGCAAACTTATCAGGAAAGAGAAGgtaactgtgg ... tttcttgcagTCATCATATGGATTTGTTGACTACTTGGACCATATTTATGCTGCAGTAGCA
EST: gi|100409806|gb|BY956113.1|BY956113
EST:     TTTCTAACATTGGGCCGTTGGAGGGTTGCAAACTTATCAGGAAAGAGAAG                         TCATCATATGGATTTGTTGACTACTTGGACCATATTTATGCTGCAGTAGCA
genomic: TTTCTAACATTGGGCCGTTGGAGGGTTGCAAACTTATCAGGAAAGAGAAGgtaactgtgg ... tttcttgcagTCATCATATGGATTTGTTGACTACTTGGACCATATTTATGCTGCAGTAGCA
EST: gi|162152881|gb|FC328975.1|FC328975
EST:     TTTCTAACATTGGGCCGTTGGAGGGTTGCAAACTTATCAGGAAAGAGAAG                         TCATCATATGGATTTGTTGACTACTTGGACCATATTTATGCTGCAGTAGCA
genomic: TTTCTAACATTGGGCCGTTGGAGGGTTGCAAACTTATCAGGAAAGAGAAGgtaactgtgg ... tttcttgcagTCATCATATGGATTTGTTGACTACTTGGACCATATTTATGCTGCAGTAGCA

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: 28 (upstream exon), 14 (downstream exon)
Score: 4

CGTAGGCAACATACACACGAAAGTTACAGAGGCGCTTCTTGCCGAAGTTTTTTCTAACATTGGGCCGTTGGAGGGTTGCAAACTTATCAGGAAAGAGAAGgtaactgtgg ... tttcttgcagTCATCATATGGATTTGTTGACTACTTGGACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttcgagtcgcattggggtttgatagttcatttcgtgttttttttcttgcagTCATCATATGGATTTGTTGACTACTTGGACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAAT
                    gtttgat  putative branch site (score: 4)
                             ttcatttcgtgttttt  putative PPT
                                        ttttttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttaactgaatgtttcttgacattatactttaaggaagttttcaattctttcgagtcgcattggggtttgatagttcatttcgtgttttttttcttgcagTCATCATATGGATTTGTTGACTACTTGGACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG