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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcacttgccttctttttgtgcgtttaattaagttggacggctgctattattttgaaaggagattttattgctctatgcgtttggggttgtcttgatgagtacaattgtgtgctgagtgtggacattctctccggaagtggcattgctgatttcattcttgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAG

Basic information

species Physcomitrella patens
transcript PP1S49_154V6.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S49_154V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 15
gtaagttcacttgccttctttttgtgcgtttaattaagttggacggctgctattattttgaaaggagattttattgctctatgcgtttggggttgtcttgatgagtacaattgtgtgctgagtgtggacattctctccggaagtggcattgctgatttcattcttgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAG
                                                            ||  || |||       | | |    ||    || ||||    | ||||  ||                      | ||  |||| |||   | |||  |||        |||||||||||| |||||||| ||||||||   ||| |||||||| ||||||||||| |  |||||||||
----------------------------------------------------------gtaagtgaaattcatccattttgtagccttacatttatcttttctattacatctgc--------------------tttcgtgagtg-catacttaattctatttaataaatgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAAGGAAGCACATTGAAG

upper sequence: PP1S49_154V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 15
gtaagttcacttgccttctttttgtgcgtttaattaagttggacggctgctattattttgaaaggagattttattgctctatgcgtttggggttgtcttgatgagtacaattgtgtgctgagtgtggacattctctccggaagtg-gcattgctgatttcattcttgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAG
                                                                                 |  ||     |     ||      |  || | | || |   |||||   || |     | |||| ||  |||| | ||  |    | | | ||||||||||| |||||||| ||||||||   ||| |||||||| ||||||||||| || || ||||||
--------------------------------------------------------------------------------gtaagtaaaatgaaaatttaccttttttaaatatctgtt---tgtgg---ttgtaaaaagtagtgagccatgcttactttttgaacgattg-cagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAG

upper sequence: PP1S49_154V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA02G01930.2 (Glycine max), 3'ss of exon 15
gtaagttcacttgccttctttttgtgcgtttaattaagttggacggctgctattattttgaaaggagattttattgctctatgcgtttggggttgtcttgatgagtacaattgtgtgctgagtgtggacattctctccggaagtggcattgctgatttcattcttgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAG
                                                                                           |||  ||  ||   |||   ||     |   |||   ||   |||   |||   | |  | | |||| | | ||      |||||||| ||||||||||| || ||| ||  ||| |||| |||||||||||| ||||||||  | |||
-------------------------------------------------------------------------------------------gtttcctctattt-tactcctgaaacttccttgttttcacattcttttgaaactgaa--gttaatttgactgttc-----cagAAAATCGGTTATGACAAGGCAGCAACAGTTGCCAAGACAGCTCACAAAGAGGGGACTACTCTTAAG

upper sequence: PP1S49_154V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA02G01930.1 (Glycine max), 3'ss of exon 15
gtaagttcacttgccttctttttgtgcgtttaattaagttggacggctgctattattttgaaaggagattttattgctctatgcgtttggggttgtcttgatgagtacaattgtgtgctgagtgtggacattctctccggaagtggcattgctgatttcattcttgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAG
                                                                                           |||  ||  ||   |||   ||     |   |||   ||   |||   |||   | |  | | |||| | | ||      |||||||| ||||||||||| || ||| ||  ||| |||| |||||||||||| ||||||||  | |||
---------------------------------------------------------------------------------------gtaagtttcctctattt-tactcctgaaacttccttgttttcacattcttttgaaactgaa--gttaatttgactgttc-----cagAAAATCGGTTATGACAAGGCAGCAACAGTTGCCAAGACAGCTCACAAAGAGGGGACTACTCTTAAG

upper sequence: PP1S49_154V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: AT2G47510.1 (Arabidopsis thaliana), 3'ss of exon 16
gtaagttcacttgccttctttttgtgcgtttaattaagttggacggctgctattattttgaaaggagattttattgctctatgcgtttggggttgtcttgatgagtacaattgtgtgctgagtgtggacattctctccggaagtggcattgctgatttcat-tcttgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAG
                                                    | | | |  ||        |||||  ||  || |||   ||  ||    | |  |  |   | | || |   || |  | || |   || |  |  ||   || | | | || | ||   |||||||| || |||||||| |||||||||  ||| ||||||||||||||||||||   ||||||||||
---------------------------------------------------gtaagtctctaaa-------tattgaactccgcctttttagtcatccgttttaccattaggat-tactaa---tgaatgtacttt---gatgctgagttttggaatccttatcctctttaccagAAAATCGGGTATGACAATGCTGCAGCAGTTGCCAAGAAAGCTCACAAAGAAGGATGTACATTGAAG

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|37846628|gb|BJ604636.1|BJ604636
EST:     TCGCTAATGCTTGTGACTGCGCTCAACCCT                         AAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
genomic: TCGCTAATGCTTGTGACTGCGCTCAACCCTgtaagttcac ... tgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
EST: gi|162193052|gb|FC371476.1|FC371476
EST:     TCGCTAATGCTTGTGACTGCGCTCAACCCT                         AAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
genomic: TCGCTAATGCTTGTGACTGCGCTCAACCCTgtaagttcac ... tgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
EST: gi|162199788|gb|FC375861.1|FC375861
EST:     TCGCTAATGCTTGTGACTGCGCTCAACCCT                         AAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
genomic: TCGCTAATGCTTGTGACTGCGCTCAACCCTgtaagttcac ... tgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
EST: gi|37822641|gb|BJ580707.1|BJ580707
EST:     TCGCTAATGCTTGTGACTGCGCTCAACCCT                         AAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
genomic: TCGCTAATGCTTGTGACTGCGCTCAACCCTgtaagttcac ... tgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
EST: gi|37848238|gb|BJ606246.1|BJ606246
EST:     TCGCTAATGCTTGTGACTGCGCTCAACCCT                         AAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
genomic: TCGCTAATGCTTGTGACTGCGCTCAACCCTgtaagttcac ... tgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
EST: gi|67724429|gb|BJ974688.1|BJ974688
EST:     TCGCTAATGCTTGTGACTGCGCTCAACCCT                         AAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
genomic: TCGCTAATGCTTGTGACTGCGCTCAACCCTgtaagttcac ... tgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
EST: gi|162169177|gb|FC345144.1|FC345144
EST:     TCGCTAATGCTTGTGACTGCGCTCAACCCT                         AAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
genomic: TCGCTAATGCTTGTGACTGCGCTCAACCCTgtaagttcac ... tgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
EST: gi|37845743|gb|BJ603751.1|BJ603751
EST:     TCGCTAATGCTTGTGACTGCGCTCAACCCT                         AAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
genomic: TCGCTAATGCTTGTGACTGCGCTCAACCCTgtaagttcac ... tgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
EST: gi|37848321|gb|BJ606329.1|BJ606329
EST:     TCGCTAATGCTTGTGACTGCGCTCAACCCT                         AAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
genomic: TCGCTAATGCTTGTGACTGCGCTCAACCCTgtaagttcac ... tgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
EST: gi|162170411|gb|FC347609.1|FC347609
EST:     TCGCTAATGCTTGTGACTGCGCTCAACCCT                         AAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
genomic: TCGCTAATGCTTGTGACTGCGCTCAACCCTgtaagttcac ... tgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
EST: gi|18340439|gb|BJ172467.1|BJ172467
EST:     TCGCTAATGCTTGTGACTGCGCTCAACCCT                         AAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
genomic: TCGCTAATGCTTGTGACTGCGCTCAACCCTgtaagttcac ... tgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
EST: gi|37844446|gb|BJ602454.1|BJ602454
EST:     TCGCTAATGCTTGTGACTGCGCTCAACCCT                         AAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
genomic: TCGCTAATGCTTGTGACTGCGCTCAACCCTgtaagttcac ... tgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
EST: gi|37830591|gb|BJ588603.1|BJ588603
EST:     TCGCTAATGCTTGTGACTGCGCTCAACCCT                         AAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
genomic: TCGCTAATGCTTGTGACTGCGCTCAACCCTgtaagttcac ... tgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
EST: gi|37850973|gb|BJ608981.1|BJ608981
EST:     TCGCTAATGCTTGTGACTGCGCTCAACCCT                         AAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
genomic: TCGCTAATGCTTGTGACTGCGCTCAACCCTgtaagttcac ... tgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
EST: gi|208369492|gb|DC955905.1|DC955905
EST:     TCGCTAATGCTTGTGACTGCGCTCAACCCT                         AAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
genomic: TCGCTAATGCTTGTGACTGCGCTCAACCCTgtaagttcac ... tgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
EST: gi|162152401|gb|FC327964.1|FC327964
EST:     TCGCTAATGCTTGTGACTGCGCTCAACCCT                         AAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
genomic: TCGCTAATGCTTGTGACTGCGCTCAACCCTgtaagttcac ... tgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
EST: gi|162169176|gb|FC345143.1|FC345143
EST:     TCGCTAATGCTTGTGACTGCGCTCAACCCT                         AAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
genomic: TCGCTAATGCTTGTGACTGCGCTCAACCCTgtaagttcac ... tgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
EST: gi|37844732|gb|BJ602740.1|BJ602740
EST:     TCGCTAATGCTTGTGACTGCGCTCAACCCT                         AAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
genomic: TCGCTAATGCTTGTGACTGCGCTCAACCCTgtaagttcac ... tgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
EST: gi|18335537|gb|BJ167557.1|BJ167557
EST:     TCGCTAATGCTTGTGACTGCGCTCAACCCT                         AAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
genomic: TCGCTAATGCTTGTGACTGCGCTCAACCCTgtaagttcac ... tgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
EST: gi|162170412|gb|FC347610.1|FC347610
EST:     TCGCTAATGCTTGTGACTGCGCTCAACCCT                         AAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
genomic: TCGCTAATGCTTGTGACTGCGCTCAACCCTgtaagttcac ... tgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
EST: gi|162193053|gb|FC371477.1|FC371477
EST:     TCGCTAATGCTTGTGACTGCGCTCAACCCT                         AAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
genomic: TCGCTAATGCTTGTGACTGCGCTCAACCCTgtaagttcac ... tgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
EST: gi|18334072|gb|BJ166088.1|BJ166088
EST:     TCGCTAATGCTTGTGACTGCGCTCAACCCT                         AAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
genomic: TCGCTAATGCTTGTGACTGCGCTCAACCCTgtaagttcac ... tgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
EST: gi|208373600|gb|DC952425.1|DC952425
EST:     TCGCTAATGCTTGTGACTGCGCTCAACCCT                         AAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
genomic: TCGCTAATGCTTGTGACTGCGCTCAACCCTgtaagttcac ... tgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
EST: gi|162199787|gb|FC375860.1|FC375860
EST:     TCGCTAATGCTTGTGACTGCGCTCAACCCT                         AAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
genomic: TCGCTAATGCTTGTGACTGCGCTCAACCCTgtaagttcac ... tgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
EST: gi|37839892|gb|BJ597900.1|BJ597900
EST:     TCGCTAATGCTTGTGACTGCGCTCAACCCT                         AAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
genomic: TCGCTAATGCTTGTGACTGCGCTCAACCCTgtaagttcac ... tgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
EST: gi|37844267|gb|BJ602275.1|BJ602275
EST:     TCGCTAATGCTTGTGACTGCGCTCAACCCT                         AAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA
genomic: TCGCTAATGCTTGTGACTGCGCTCAACCCTgtaagttcac ... tgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAA

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: 18 (upstream exon), 24 (downstream exon)
Score: 2

TCGCTAATGCTTGTGACTGCGCTCAACCCTgtaagttcac ... tgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtgtggacattctctccggaagtggcattgctgatttcattcttgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAG
                              tgctgat  putative branch site (score: 2)
                                    tttcattctt  CT-rich tract
                                   atttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcacttgccttctttttgtgcgtttaattaagttggacggctgctattattttgaaaggagattttattgctctatgcgtttggggttgtcttgatgagtacaattgtgtgctgagtgtggacattctctccggaagtggcattgctgatttcattcttgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG