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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttcccgcacttcttttatacaatcaaattgttggcagtatagaattcgcaatatttgacaccaggacggaatctgataccagttgtagtcacttctgggtattttattaagtgtgcagcgtgcattacacaggcatttggtggtcctcgaagcttacagttatcttttttcttgcagCTCATAAATGAAAAGCCACAAATTGTACAAGAGTACGAGTCAGGGAAAGCAATTCCCAACCAACAGATCATATCGAAATTGGAACGTGTGCTTGGTACGA

Basic information

species Physcomitrella patens
transcript PP1S35_215V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S35_215V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os08g27850.2 (Oryza sativa), 3'ss of exon 3
gttttcccgcacttcttttatacaatcaaattgttggcagtatagaattcgcaatatttgacaccaggacggaatctgataccagttgtagtcacttctgggtattttattaagtgtgcagcgtgcattacacaggcatttggtggtcctcgaagcttacagttatcttttttcttgcagCTCATAAATGAAAAGCCACAAATTGTACAAGAGTACGAGTCAGGGAAAGCAATTCCCAACCAACAGATCATATCGAAATTGGAACGTGTGCTTGGTACGA
                                                               ||  | |  |   |     || || |||  | |||   |  ||  ||||| | |  | |       || |   |||    |   | || |     | |       |||| |   ||| | || ||||| ||||| ||  |  | || |||||||||||||| ||||| ||||| ||||| ||||||||   |||  | ||| | |  ||||| || |
------------------------------------------------------------gtgccctgtccaaccata----caattttaga-atttcctagcgttacattaacttt-taccaca-gccactcgcacatacactaaccttcaactaaaatatggtgtgttttgcaaacagATGATCAATGAGAAGCCCCAGGTGATCCAGGAGTACGAGTCAGGTAAAGCTATTCCGAACCAGCAGATCATCGGGAAGCTTGAAAGGGCTCTTGGAACAA

upper sequence: PP1S35_215V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G101480_T01 (Zea mays), 3'ss of exon 3
gttttcccgcacttcttttatacaatcaaattgttggcagtatagaattcgcaatatttgacaccaggacggaatctgataccagttgtagtcacttctgggtattttattaagtgtgcagcgtgcattacacaggcatttggtggtcctcgaagcttacagttatcttttttcttgcagCTCATAAATGAAAAGCCACAAATTGTACAAGAGTACGAGTCAGGGAAAGCAATTCCCAACCAACAGATCATATCGAAATTGGAACGTGTGCTTGGTACGA
                                                                        | ||| || |  ||||| ||      | | |   ||  ||  || | ||   || | |  |  |   ||||      |   || | |  | |||  | ||  |||||| | || ||||| ||||||||  |  | || ||||| |||||||| || |||||||||||||| ||||||||    ||  | ||  | |  || || ||||
----------------------------------------------------------------------aaagtct-atgct-gttgttgtag----tagttccattgatagctgggaagta-gcttgatccttgg--ttggcctctttatgagatga-ggatatggtgttcattgcagATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCAATTCCCAACCAGCAGATCATTGGCAAGCTCGAGAGGGCCCTGGGAACGA

upper sequence: PP1S35_215V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT3G58680.1 (Arabidopsis thaliana), 3'ss of exon 3
gttttcccgcacttcttttatacaatcaaattgttggcagtatagaattcgcaatatttgacaccaggacggaatctgataccagttgtagtcacttctgggtattttattaagtgtgcagcgtgcattacacaggcatttggtggtcctcgaagct-tacagttatcttttttcttgcagCTCATAAATGAAAAGCCACAAATTGTACAAGAGTACGAGTCAGGGAAAGCAATTCCCAACCAACAGATCATATCGAAATTGGAACGTGTGCTTGGTACGA
                                                                                             ||||     | |||   |   | |    | | | ||  || | | || |   ||  | |||    |    |    |||  |  || |||| || ||||| ||||||||| |  | ||||| |||||||| |||||||||||||| || ||||||||| | || ||  ||||  | |  |||||| | |
-------------------------------------------------------------------------------------------gtactttca--tttttctctgtatctttctctttcttt-tactgtctttcgtcagtaattgaattcattgtatgggttttgattctgtagCTGATCAATGAGAAGCCACAAGTGATCCAAGAATACGAGTCTGGGAAAGCAATTCCGAATCAACAGATCCTTTCAAAGCTGGAGAGGGCACTTGGTGCTA

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|7286491|gb|AW598978.1|AW598978
EST:     GGCTCAACTTGCACAG                         CTCATAAATGAAAAGCCACAAATTGTACAAGAGTACGAGTCAGGGAAAGCA
genomic: GGCTCAACTTGCACAGgttttcccgc ... tttcttgcagCTCATAAATGAAAAGCCACAAATTGTACAAGAGTACGAGTCAGGGAAAGCA
EST: gi|67507609|gb|BJ940490.1|BJ940490
EST:     TTATGCAGGCTCGGTTGGATAAGAAGATGACACAGGCTCAACTTGCACAG                         CTCATAAATGAAAAGCCACAAATTGTACAAGAGTACGAGTCAGGGAAAGCA
genomic: TTATGCAGGCTCGGTTGGATAAGAAGATGACACAGGCTCAACTTGCACAGgttttcccgc ... tttcttgcagCTCATAAATGAAAAGCCACAAATTGTACAAGAGTACGAGTCAGGGAAAGCA
EST: gi|208380149|gb|DC927428.1|DC927428
EST:     TTATGCAGGCTCGGTTGGATAAGAAGATGACACAGGCTCAACTTGCACAG                         CTCATAAATGAAAAGCCACAAATTGTACAAGAGTACGAGTCAGGGAAAGCA
genomic: TTATGCAGGCTCGGTTGGATAAGAAGATGACACAGGCTCAACTTGCACAGgttttcccgc ... tttcttgcagCTCATAAATGAAAAGCCACAAATTGTACAAGAGTACGAGTCAGGGAAAGCA
EST: gi|162220358|gb|FC396350.1|FC396350
EST:     TTATGCAGGCTCGGTTGGATAAGAAGATGACACAGGCTCAACTTGCACAG                         CTCATAAATGAAAAGCCACAAATTGTACAAGAGTACGAGTCAGGGAAAGCA
genomic: TTATGCAGGCTCGGTTGGATAAGAAGATGACACAGGCTCAACTTGCACAGgttttcccgc ... tttcttgcagCTCATAAATGAAAAGCCACAAATTGTACAAGAGTACGAGTCAGGGAAAGCA
EST: gi|208349962|gb|DC913670.1|DC913670
EST:     TTATGCAGGCTCGGTTGGATAAGAAGATGACACAGGCTCAACTTGCACAG                         CTCATAAATGAAAAGCCACAAATTGTACAAGAGTACGAGTCAGGGAAAGCA
genomic: TTATGCAGGCTCGGTTGGATAAGAAGATGACACAGGCTCAACTTGCACAGgttttcccgc ... tttcttgcagCTCATAAATGAAAAGCCACAAATTGTACAAGAGTACGAGTCAGGGAAAGCA

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), 24 (downstream exon)
Score: 13

ACGAGAAAGTGCCCACAGAACTCAAGAGAAAAATTATGCAGGCTCGGTTGGATAAGAAGATGACACAGGCTCAACTTGCACAGgttttcccgc ... tttcttgcagCTCATAAATGAAAAGCCACAAATTGTACAAGAGTACGAGTCAGGGAAAGCAATTCCCAACCAACAGATCATATCGAAATTGGAACGTGTGCTTGGTACGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattacacaggcatttggtggtcctcgaagcttacagttatcttttttcttgcagCTCATAAATGAAAAGCCACAAATTGTACAAGAGTACGAGTCAGGGAAAGCAATTCCCAACCAACAGATCATATCGAAATTGGAACGTGTGCTTGGTACGA
                            agcttac  putative branch site (score: 13)
                                     ttatcttttttcttgc  putative PPT
                                     ttatcttttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttcccgcacttcttttatacaatcaaattgttggcagtatagaattcgcaatatttgacaccaggacggaatctgataccagttgtagtcacttctgggtattttattaagtgtgcagcgtgcattacacaggcatttggtggtcctcgaagcttacagttatcttttttcttgcagCTCATAAATGAAAAGCCACAAATTGTACAAGAGTACGAGTCAGGGAAAGCAATTCCCAACCAACAGATCATATCGAAATTGGAACGTGTGCTTGGTACGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA