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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataagcctagcgtgaataaccagcttgaagatgtcactcgaatttaagccagtaaggtgtgaatttggtatgccctctttttgcttgatgttttgaagcgtagttggatcatgaagttggtactcacctgtgcagGCCCTGGACACATTTAACACGGCAATTGTTTCTCCTATATATTACGTCATGTTCACATCATTGACCATCCTGGCGAGTGCTATCATGTTCAAG

Basic information

species Physcomitrella patens
transcript PP1S49_181V6.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S49_181V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G120175_T03 (Zea mays), 3'ss of exon 6
gtaataagcctagcgtgaataaccagcttgaagatgtcactcgaatttaagccagtaaggtgtgaatttggtatgccctctttttgcttgatgttttgaagcgtagttggatcatgaagttggtactcacctgtgcagGCCCTGGACACATTTAACACGGCAATTGTTTCTCCTATATATTACGTCATGTTCACATCATTGACCATCCTGGCGAGTGCTATCATGTTCAAG
                  | |||   ||  |   ||| ||| || ||    |||  ||  | | ||  |  |  |  |   || ||||| |||   | |   || |||           ||  |  |  |   || |||| || ||||| || |||||||||||||| ||||| |||||||| || ||||||||| |  | || || || || || |  || |||||||||
------------------acaacgcactgaagtgtgttactagagtt---accacaaa--tattaagctactg-gttcctgttctgctttatggagtaagtagtggtt-----------tttttttttgc---tgtagGCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAG

upper sequence: PP1S49_181V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA04G00690.1 (Glycine max), 3'ss of exon 5
gtaataagcctagcgtgaataaccagcttgaagatgtcactcgaatttaagccagtaaggtgtgaatttggtatgccctctttttgcttgatgttttgaagcgtagttggatcatgaagttggtactcacctgtgcagGCCCTGGACACATTTAACACGGCAATTGTTTCTCCTATATATTACGTCATGTTCACATCATTGACCATCCTGGCGAGTGCTATCATGTTCAAG
                          | | |    |    ||  ||   ||    |||||  | |  || || | || |  | |||       | ||||| | |  | | |  ||| |  |  |  |        ||||| ||||| ||||||||||| |||||||| |||||  ||||||| |||||||||||| |  |||||||  | || ||||  || ||||| |||
--------------------------cctaatatggcttttcctatcagagatc-taaggcct-atcttagttt-ccttgatcttgtaactaatcttgaa-cattttggcactatggaacta-tgttt-------cagGCACTGGATACATTTAACACCGCAATTGTCTCTCCCGTATATTATGTCATGTTCACAACTCTGACCATTATTGCTAGTGTGATAATGTTTAAG

upper sequence: PP1S49_181V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA06G00730.1 (Glycine max), 3'ss of exon 5
gtaataagcctagcgtgaataaccagcttgaagatgtcactcgaatttaagccag-taaggtgtgaatttggtatgccctctttttgcttgatgttttgaagcgtagttggatcatgaagttggtactcacctgtgcagGCCCTGGACACATTTAACACGGCAATTGTTTCTCCTATATATTACGTCATGTTCACATCATTGACCATCCTGGCGAGTGCTATCATGTTCAAG-------
                              || ||| |  | |  | | |||||  |||||| ||   || || | || || | |||       | ||||| | |  ||| |  ||| |  |  |  |        ||||| ||||| ||||| ||||| |||||||| |||||  ||||||| |||||||||||| |  |||||||  | || || |  || ||||| |||       
---------------------------cctaatatgac-tttgcctatcagccatctaaggtctgt-cttagttt-ccttcatcttgtaactaatcttgaa-catttttgcactatggaacta-tgttt-------cagGCACTGGATACATTCAACACAGCAATTGTCTCTCCCGTATATTATGTCATGTTCACAACTCTGACCATTATTGCTAGCGTGATAATGTTTAAGGTATCAT

upper sequence: PP1S49_181V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA02G44980.2 (Glycine max), 3'ss of exon 5
gtaataagcctagcgtgaataaccagcttgaagatgtcactcgaatttaagccagta-aggtgtgaatttggtatgccctctttttgcttgatgttttgaagcgtagttggatcatgaagttggtactcacctgtgcagGCCCTGGACACATTTAACACGGCAATTGTTTCTCCTATATATTACGTCATGTTCACATCATTGACCATCCTGGCGAGTGCTATCATGTTCAAG
                        || ||     ||| | |  |    |||    || |  | |||| ||  |  |  |  ||  |  ||  | ||      | |  ||| ||  | |         | |  |   ||||| || ||||| || ||||| |||||||| ||||||||||| || |||||||||||| || | || || || || ||||  || ||||| |||
------------------------agattttctgtgt-attatatacaaagttcttatatatatgaaatt--ttggatcaattactaattactcttcactgacatgattgtattgtaa---------ttattt---cagGCTCTTGACACCTTCAACACAGCAATTGTATCTCCTATATACTATGTCATGTTCACAACACTTACAATACTAGCCAGTGTAATAATGTTTAAG

upper sequence: PP1S49_181V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA14G03790.1 (Glycine max), 3'ss of exon 6
gtaataagcctagcgtgaataaccagcttgaagatgtcactcgaatttaagccagtaaggtgtgaatttggtatgccctctttttgcttgatgttttgaagcgtagttggatcatgaagttggtactcacctgtgcagGCCCTGGACACATTTAACACGGCAATTGTTTCTCCTATATATTACGTCATGTTCACATCATTGACCATCCTGGCGAGTGCTATCATGTTCAAG
                                    ||    ||||| |      |    |||| |||   ||     |  || |   |||  ||||| | |     |   |||   |  || |    |  | | ||||| || ||||| || ||||| |||||||| ||||||||||| || |||||||||||| || | || || || || ||||  || ||||| |||
-----------------------------------ttctagagaattcagatt--ttctctgtgcattatatacaaagttcttatatatgaaattttggatcaattattcttcactgacatgattgcaatattt-cagGCTCTTGACACCTTCAACACAGCAATTGTATCTCCTATATACTATGTCATGTTCACAACACTTACAATACTAGCCAGTGTAATAATGTTTAAG

upper sequence: PP1S49_181V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA16G00560.1 (Glycine max), 3'ss of exon 6
gtaataagcctagcgtgaataaccagcttgaagatgtcactcgaatttaagccagtaaggtgtgaatttggtatgccctctttttgcttgatgttttgaagcgtagttggatcatgaagttggtactcacctgtgcagGCCCTGGACACATTTAACACGGCAATTGTTTCTCCTATATATTACGTCATGTTCACATCATTGACCATCCTGGCGAGTGCTATCATGTTCAAG
                           |  |   ||||||    |||||      |  | | |||   ||  | |  |  | |||  || ||  ||       || |      ||    ||   | |        ||||| ||||| || ||||| |||||| | || |||||||||||||| || ||||||||| |||| |||||  |||| |||| ||| ||||| |||
--------------------------ttacatattgtcacctccatttatatttttgggat-tga---tgaaaagttccttcttt--tttataattcatgtgataat------atatttttttcatttttgcaatcagGCACTGGATACTTTTAATACGGCAGTGGTATCTCCTATATATTATGTTATGTTCACAACATTTACCATTGTGGCTAGTGTTATTATGTTTAAG

upper sequence: PP1S49_181V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT1G34470.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaataagcctagcgtgaataaccagcttgaagatgtcactcgaatttaagccagtaaggtgtgaatttggtat-gccctctttttgcttgatgttttgaagcgtagttggatcatgaagttggtactcacctgtgcagGCCCTGGACACATTTAACACGGCAATTGTTTCTCCTATATATTACGTCATGTTCACATCATTGACCATCCTGGCGAGTGCTATCATGTTCAAG
                                               ||     |||  |  | | |||  | | |   ||| ||  |   || |  ||||   |  || |         || ||  ||     | ||||| || ||||| || ||||||||  | ||||| |||||||| || || ||||||||||||||||||||||| || ||||  |||||||| |||
----------------------------------------------gtatagaggta--gcatcagtttcatgttgatatctgttaac---atatcatgaaatttcattcggcttctctttttgttttcttgattacagGCGCTTGACACTTTCAACACGGCTGTAGTTTCACCTATATACTATGTTATGTTCACATCATTGACCATCCTAGCTAGTGTCATCATGTTTAAG

upper sequence: PP1S49_181V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT4G38730.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaataagcctagcgtgaataaccagcttgaagatgtcactcgaatttaagccagtaag-gtgtgaatttggtatgccctctttttgcttgatgttttgaagcgtagttggatcatgaagttggtactcacctgtgcagGCCCTGGACACATTTAACACGGCAATTGTTTCTCCTATATATTACGTCATGTTCACATCATTGACCATCCTGGCGAGTGCTATCATGTTCAAG
                                   || |   |||  |  ||  ||    ||||||  | |   ||  | |  ||||    ||| ||  ||  |||||   ||          ||  |    ||| ||||| ||||||||||| ||| | |||||||||||||| || ||||| || ||||||||| || | || ||  | || ||||| ||||||||||||
-----------------------------------gtaagaagaacctgtgcatgtgtctgtgtgatgtagtgttgagcacactttggccaatggtt--aatagtagtcatat----------gttttgttttgt-cagGCGCTGGACACATTCAACGCAGCAATTGTTTCTCCAATCTATTATGTGATGTTCACAACACTCACAATTGTCGCTAGTGCAATCATGTTCAAG

upper sequence: PP1S49_181V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv03s0038g01940.t01 (Vitis vinifera), 3'ss of exon 6
gtaataagcctagcgtgaataaccagcttgaagatgtcactcgaatttaagccagtaaggtgtgaatttggtatgccctctttttgcttgatgttttgaagcgta-gttggatcatgaagttggtactcacctgtgcagGCCCTGGACACATTTAACACGGCAATTGTTTCTCCTATATATTACGTCATGTTCACATCATTGACCATCCTGGCGAGTGCTATCATGTTCAAG
                                    |    | ||||   |   || || | |    |   | |    |   |   |  | | ||   |  |    ||||| | |||    | |   ||     | ||||| ||||| ||||||||  | |||||||||||||| || ||||| |||||||||||| |  |||| ||    || ||||| || |||||||||
------------------------------------ttctcctaatt--ggtttgttagctatttggtgaatgtagtttaagtgaacaggctcttgcaattctcgtgttggctgatgtttatagc-ttctttgttccagGCGCTGGATACATTTAATGCAGCAATTGTTTCTCCAATTTATTATGTCATGTTCACAACTCTGACTATAAGTGCAAGTGCAATAATGTTCAAG

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|208383507|gb|DC923659.1|DC923659
EST:     CGATGGTAGTCCTTATTTGCATACTGACACAAATGAATTACCTCAATAAG                         GCCCTGGACACATTTAACACGGCAATTGTTTCTCCTATATATTACGTCATG
genomic: CGATGGTAGTCCTTATTTGCATACTGACACAAATGAATTACCTCAATAAGgtaataagcc ... acctgtgcagGCCCTGGACACATTTAACACGGCAATTGTTTCTCCTATATATTACGTCATG
EST: gi|7067027|gb|AW496882.1|AW496882
EST:     CGATGGTAGTCCTTATTTGCATACTGACACAAATGAATTACCTCAATAAG                         GCCCTGGACACATTTAACACGGCAATTGTTTCTCCTATATATTACGTCATG
genomic: CGATGGTAGTCCTTATTTGCATACTGACACAAATGAATTACCTCAATAAGgtaataagcc ... acctgtgcagGCCCTGGACACATTTAACACGGCAATTGTTTCTCCTATATATTACGTCATG

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: 34 (upstream exon), 34 (downstream exon)
Score: 4

GACTTTGCAAGGGCAGAATCAATTGATCTATCCTCAGACGTCGGTGTTTGCGATGGTAGTCCTTATTTGCATACTGACACAAATGAATTACCTCAATAAGgtaataagcc ... acctgtgcagGCCCTGGACACATTTAACACGGCAATTGTTTCTCCTATATATTACGTCATGTTCACATCATTGACCATCCTGGCGAGTGCTATCATGTTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcttgatgttttgaagcgtagttggatcatgaagttggtactcacctgtgcagGCCCTGGACACATTTAACACGGCAATTGTTTCTCCTATATATTACGTCATGTTCACATCATTGACCATCCTGGCGAGTGCTATCATGTTCAAG
                                        tactcac  putative branch site (score: 4)
                                          ctcacct  CT-rich tract
       atgtttt  TA-rich tract