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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtatctgccttctttctcaacattttatggatgccatctggctttttcctgttatgtaaggactctataacgatgatgatgtggggtgcttgatgggtccattttgggtgttaattatacacgatgcatgaaaaattaattatatggagtggaacattttgcagCGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATGACATGGATACTTCTGCTGCAGATGGTGCTTATGACAATTAGTATTTGTT

Basic information

species Physcomitrella patens
transcript PP1S83_162V6.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S83_162V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: AT5G37340.1 (Arabidopsis thaliana), 3'ss of exon 16
gtgcgtatctgccttctttctcaacattttatggatgccatctggctttttcctgttatgtaaggactctataacgatgatgatgtggggtgcttgatgggtccattttgggtgttaatt-atacacgatgcatgaaaaattaattatatggagtggaacattttgcagCGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATGACATGGATACTTCTGCTGCAGATGGTGCTTATGACAATTAGTATTTGTT
                                                                  || ||||| ||    ||  ||   |    |  | |   || |    |   | |  |  |  |  |    |  ||  |||  | | | ||     |   | |||  ||||| || ||  |  |||  |||||||||||||| |||||||| || ||||| ||||||||| | || |||| |||||||||        |      
------------------------------------------------------------------ctgtataatgaaatcgacttgaatta---ggagtgaatatgtcaattagaactggagtcttggggttcaagtaacaaatgttgttgtgttttttaaactacagTTGAAGAGTACGAGAGATCATGGGAGCAAAACGAGGAGTTGGGTCTCAACGACATTGATACTTCTTCAGCTGATGCTGCTTATGAGTCCACAGAGCCAAC

upper sequence: PP1S83_162V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: AT5G22480.1 (Arabidopsis thaliana), 3'ss of exon 16
-----gtgcgtatctgccttctttctcaacattt--------tatggatgccatct----ggctttttcctgttatgtaaggactctataacga------tgatgatgtggggtgcttgat--gggtccattttgggtgttaattatacacgatgcatgaaaaattaattatatggagtggaacattt----tgcagCGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATGACATGGATACTTCTGCTGCAGATGGTGCTTATGACAATTAGTATTTGTT
      | |   | | || |   | |  |   ||        |||| || | | ||       | ||     ||||  |     |   | | ||      | ||||    | |   |  ||  ||   || |     ||| |||||   ||    | ||     | ||| | | |   ||  |  |||    | |||  ||||| || ||  |  |||  || ||||||||||| |||||||| || ||||| ||||||||| | || |||| |||||||||        |   |  
gtaagttactcgtttaccctgcctatgtagccttaagtgggatatgaatacgaactaaacaaatattcagacttatccattcctttcttgatgaattttataatgaaactgagacataaattaggactcaatcaatatgtgaattagg-acaggacttgggttttgaataacaagttttgttatgtttgaactacagTTGAAGAGTACGAGAGGTCATGGGATCAAAACGAGGAGTTGGGTCTCAACGACATAGATACTTCTTCAGCTGATGCTGCTTATGAATCCACAGAGACGAC
















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|37852112|gb|BJ610120.1|BJ610120
EST:     TTTCATAGCACCAGCAACCGATGACTTCGAAGCTGATTCACAATTATCAT                         CGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATG
genomic: TTTCATAGCACCAGCAACCGATGACTTCGAAGCTGATTCACAATTATCATgtgcgtatct ... cattttgcagCGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATG
EST: gi|162231693|gb|FC408273.1|FC408273
EST:     TTTCATAGCACCAGCAACCGATGACTTCGAAGCTGATTCACAATTATCAT                         CGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATG
genomic: TTTCATAGCACCAGCAACCGATGACTTCGAAGCTGATTCACAATTATCATgtgcgtatct ... cattttgcagCGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATG
EST: gi|37833064|gb|BJ591076.1|BJ591076
EST:     TTTCATAGCACCAGCAACCGATGACTTCGAAGCTGATTCACAATTATCAT                         CGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATG
genomic: TTTCATAGCACCAGCAACCGATGACTTCGAAGCTGATTCACAATTATCATgtgcgtatct ... cattttgcagCGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATG
EST: gi|208383459|gb|DC923611.1|DC923611
EST:     TTTCATAGCACCAGCAACCGATGACTTCGAAGCTGATTCACAATTATCAT                         CGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATG
genomic: TTTCATAGCACCAGCAACCGATGACTTCGAAGCTGATTCACAATTATCATgtgcgtatct ... cattttgcagCGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATG
EST: gi|37828455|gb|BJ586467.1|BJ586467
EST:     TTTCATAGCACCAGCAACCGATGACTTCGAAGCTGATTCACAATTATCAT                         CGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATG
genomic: TTTCATAGCACCAGCAACCGATGACTTCGAAGCTGATTCACAATTATCATgtgcgtatct ... cattttgcagCGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATG
EST: gi|37824807|gb|BJ582873.1|BJ582873
EST:     TTTCATAGCACCAGCAACCGATGACTTCGAAGCTGATTCACAATTATCAT                         CGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATG
genomic: TTTCATAGCACCAGCAACCGATGACTTCGAAGCTGATTCACAATTATCATgtgcgtatct ... cattttgcagCGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATG
EST: gi|162167397|gb|FC343100.1|FC343100
EST:     TTTCATAGCACCAGCAACCGATGACTTCGAAGCTGATTCACAATTATCAT                         CGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATG
genomic: TTTCATAGCACCAGCAACCGATGACTTCGAAGCTGATTCACAATTATCATgtgcgtatct ... cattttgcagCGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATG
EST: gi|37836032|gb|BJ594040.1|BJ594040
EST:     TTTCATAGCACCAGCAACCGATGACTTCGAAGCTGATTCACAATTATCAT                         CGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATG
genomic: TTTCATAGCACCAGCAACCGATGACTTCGAAGCTGATTCACAATTATCATgtgcgtatct ... cattttgcagCGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATG
EST: gi|18337553|gb|BJ169577.1|BJ169577
EST:     TTTCATAGCACCAGCAACCGATGACTTCGAAGCTGATTCACAATTATCAT                         CGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATG
genomic: TTTCATAGCACCAGCAACCGATGACTTCGAAGCTGATTCACAATTATCATgtgcgtatct ... cattttgcagCGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATG
EST: gi|208396068|gb|DC924534.1|DC924534
EST:     TTTCATAGCACCAGCAACCGATGACTTCGAAGCTGATTCACAATTATCAT                         CGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATG
genomic: TTTCATAGCACCAGCAACCGATGACTTCGAAGCTGATTCACAATTATCATgtgcgtatct ... cattttgcagCGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATG
EST: gi|162189275|gb|FC366758.1|FC366758
EST:     TTTCATAGCACCAGCAACCGATGACTTCGAAGCTGATTCACAATTATCAT                         CGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATG
genomic: TTTCATAGCACCAGCAACCGATGACTTCGAAGCTGATTCACAATTATCATgtgcgtatct ... cattttgcagCGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATG
EST: gi|162240587|gb|FC419364.1|FC419364
EST:     TTTCATAGCACCAGCAACCGATGACTTCGAAGCTGATTCACAATTATCAT                         CGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATG
genomic: TTTCATAGCACCAGCAACCGATGACTTCGAAGCTGATTCACAATTATCATgtgcgtatct ... cattttgcagCGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATG
EST: gi|37835488|gb|BJ593500.1|BJ593500
EST:     TTTCATAGCACCAGCAACCGATGACTTCGAAGCTGATTCACAATTATCAT                         CGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATG
genomic: TTTCATAGCACCAGCAACCGATGACTTCGAAGCTGATTCACAATTATCATgtgcgtatct ... cattttgcagCGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATG

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: 35 (upstream exon), 32 (downstream exon)
Score: 8

AAAGTGGAAGAAGAGTTTACACTAATTTTGGATGATGCTCTCGCAAACTCTTTCATAGCACCAGCAACCGATGACTTCGAAGCTGATTCACAATTATCATgtgcgtatct ... cattttgcagCGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATGACATGGATACTTCTGCTGCAGATGGTGCTTATGACAATTAGTATTTGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaattatacacgatgcatgaaaaattaattatatggagtggaacattttgcagCGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATGACATGGATACTTCTGCTGCAGATGGTGCTTATGACAATTAGTATTTGTT
                        aattaat  putative branch site (score: 8)
              atgcatgaaaaattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtatctgccttctttctcaacattttatggatgccatctggctttttcctgttatgtaaggactctataacgatgatgatgtggggtgcttgatgggtccattttgggtgttaattatacacgatgcatgaaaaattaattatatggagtggaacattttgcagCGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATGACATGGATACTTCTGCTGCAGATGGTGCTTATGACAATTAGTATTTGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG