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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_181V6.1
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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcttgatgttttgaagcgtagttggatcatgaagttggtactcacctgtgcagGCCCTGGACACATTTAACACGGCAATTGTTTCTCCTATATATTACGTCATGTTCACATCATTGACCATCCTGGCGAGTGCTATCATGTTCAAG
                                        tactcac  putative branch site (score: 1)
                                          ctcacct  CT-rich tract
       atgtttt  TA-rich tract