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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaccttcatcttcatgccttaagcatcgagatcagtaatcatttttaatgtatgttgtggtgtggcattagtgccaatttcggcgaactggattggaattaatttaactcctcttgaattttaatgtgaaagaatcagtacatcggctgccttaccgttgggtttttgttatgtggcaagtgcagGATAGAGAAAGTTATTGGAAAATGATGCACAAGTACATAGGTTCTGACATTACTTCAATGGTGACACTTCCAGTCATCATATTTGAGCCCATGACTACGC

Basic information

species Physcomitrella patens
transcript PP1S148_87V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S148_87V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 2
gtgaccttcatcttcatgccttaagcatcgagatcagtaatcatttttaatgtatgttgtggtgtggcattagtgccaatttcggcgaactggattggaattaatttaactcctcttgaattttaatgtgaaagaatcagtacatcggctgccttaccgttgggtttttgttatgtggcaagtgcagGATAGAGAAAGTTATTGGAAAATGATGCACAAGTACATAGGTTCTGACATTACTTCAATGGTGACACTTCCAGTCATCATATTTGAGCCCATGACTACGC
                                                                                      || ||   | |    | |||  |   |  ||| |||| |     | ||  |       |      | | |   |    ||    ||       |  |||||||| | || ||||||||||| ||||||||||||||||||||  | ||  |||| ||| | ||||||||||| |||||||| |||||||| ||||| | ||
--------------------------------------------------------------------------------------gatctttctagaggatgattggaacacctttgtatttcagctgcacagtgttctcgtgtatatcccttcat-atgctcttgacattccaattaatctgcagGATCGTGATAGTTATTGGAAGATGATGCACAAGTACATAGGGGCAGATGTTACATCACTTGTGACACTTCCGGTCATCATTTTTGAGCCAATGACAATGC

upper sequence: PP1S148_87V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G114126_T02 (Zea mays), 3'ss of exon 2
gtgaccttcatcttcatgccttaagcatcgagatcagtaatcatttttaatgtatgttgtggtgtggcattagtgccaatttcggcgaactggattggaattaatttaactcctcttgaattttaatgtgaaagaatcagtacatcggctgccttaccgttgggtttttgttatgtggcaagtgcagGATAGAGAAAGTTATTGGAAAATGATGCACAAGTACATAGGTTCTGACATTACTTCAATGGTGACACTTCCAGTCATCATATTTGAGCCCATGACTACGC
                                                              | |||  |||  | ||   | |    ||  ||| | |  || || || | ||       | | ||     || |||| ||  |   |  ||||          | | ||||  |      |||||||| | || || |||||||| |||||||||||||||||||| || ||  |||| ||| | ||||||||||||||||| || |||||||| ||||| | ||
------------------------------------------------------------tctatggttttaaggtcatagtagttttac--gatcgta--tacttgaagttct-----ggtctgattc---aggatcactattttaacaaccttg---------tgtggttaatt------tgcagGATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC

upper sequence: PP1S148_87V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 2
gtgaccttcatcttcatgccttaagcatcgagatcagtaatcatttttaatgtatgttgtggtgtggcattagtgccaatttcggcgaactggattggaattaatttaactcctcttgaattttaatgtgaaagaatcagtacatcggctgccttaccgttgggtttttgttatgtggcaagt--gcagGATAGAGAAAGTTATTGGAAAATGATGCACAAGTACATAGGTTCTGACATTACTTCAATGGTGACACTTCCAGTCATCATATTTGAGCCCATGACTACGC
                                                                                        |  | | | |   | ||  ||||  |    |   |  |  || |    | |    ||       |      ||      |  |  |||||  | |  ||||||  | || || || ||||| ||||||||||| |||||||| || ||  |||| ||| | ||||||||||||||||| || |||||||| ||||| | ||
----------------------------------------------------------------------------------------atcgtagtagttatgatccaactatttactatcctacacttggagttctgacctgattcaggatcacgatctttaacaatcat-gtgtggttaatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC

upper sequence: PP1S148_87V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA07G15930.3 (Glycine max), 3'ss of exon 2
gtgaccttcatcttcatgccttaagcatcgagatcagtaatcatttttaatgtatgttgtggtgtggcattagtgccaatttcggcgaactggattggaattaatttaactcctcttgaattttaatgtgaaagaatcagtacatcggctgccttaccgttgggtttttgttatgtggcaagtgcagGATAGAGAAAGTTATTGGAAAATGATGCACAAGTACATAGGTTCTGACATTACTTCAATGGTGACACTTCCAGTCATCATATTTGAGCCCATGACTACGC
                                                                      || |     |   || | |||   ||||||  ||||    ||||||  | || ||||||      |||| |   || ||    |||        |||   |||  |      | |||||  |||| ||||| |||||||||||||| |||||  | || ||||| || || |||||||||||||||||||| ||||| ||||| || ||||| | ||
------------------------------------------------------------------tttctattttatctcatggtggact---ttggaaa-aattattttcctctatatttataatgt------atcatt---tctgcatgttta--------tttcctttacttacactttacagGAGCGAGATAGTTACTGGAAAATGATGCAAAAGTATGTTGGCTCTGATATCACATCAATGGTGACACTTCCAGTTATCATTTTTGAACCAATGACAATGC

upper sequence: PP1S148_87V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA18G39880.1 (Glycine max), 3'ss of exon 2
gtgaccttcatcttcatgccttaagcatcgagatcagtaatcatttttaatgtatgttgtggtgtggcattagtgccaatttcggcgaactggattggaattaatttaactcctcttgaattttaatgtgaaagaatcagtacatcggctgccttaccgttgggtttttgttatgtggcaagtgcagGATAGAGAAAGTTATTGGAAAATGATGCACAAGTACATAGGTTCTGACATTACTTCAATGGTGACACTTCCAGTCATCATATTTGAGCCCATGACTACGC
                                                                     ||| |     |   || |||||   |||||   |||||  ||  || |  || || ||   || | |||| |   || ||    |||        |||   |||  |         ||||  ||||  |||| |||||||||||||| |||||  | || ||||| || || ||||||||||||||||| || ||||| |||||||| ||||| |   
-----------------------------------------------------------------atttttattttatctcatggtgaact---ttggag--aattt--cttttcctccatatttat---aatgtatcaat---tctgcatgttta--------tttcctttacttacacttaataGGAGCGAGATGGTTACTGGAAAATGATGCAAAAGTATGTTGGCTCTGATATCACATCAATGGTGACACTTCCGGTTATCATTTTTGAGCCAATGACAATA-

upper sequence: PP1S148_87V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgaccttcatcttcatgccttaagcatcgagatcagtaatcatttttaatgtatgttgtggtgtggcattagtgccaatttcggcgaactggattggaattaatttaactcctcttgaattttaatgtgaaagaatcagtacatcggctgccttaccgttgggtttttgttatgtggcaagtg-cagGATAGAGAAAGTTATTGGAAAATGATGCACAAGTACATAGGTTCTGACATTACTTCAATGGTGACACTTCCAGTCATCATATTTGAGCCCATGACTACGC
                                                                                              |    | |  |  |     ||||  ||  |  |    ||    |  ||  |       ||||||    |    || |  | | | |  |   ||||  |||| ||||| ||||| |||||||| || || |||||||| || ||||| ||||||||||| ||||| ||  | ||||||||||| ||||||| ||
---------------------------------------------------------------------------------------------gtaactaatcgtcgatggtgtctttgatacttcttcttaaattcctctatgtttctctacttacccgaagaaacttatgtttttgtatttaatagGAACGAGATAGTTACTGGAAGATGATGCAGAAATATATAGGTTCGGATATTACGTCAATGGTGACTCTTCCTGTTGTTATATTTGAGCCTATGACTATGC

upper sequence: PP1S148_87V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT3G09300.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgaccttcatcttcatgccttaagcatcgagatcagtaatcatttttaatgtatgttgtggtgtggcattagtgccaatttcggcgaactggattggaattaatttaactcctcttgaattttaatgtgaaagaatcagtacatcggctgccttaccgttgggtttttgttatgtggcaagtgcagGATAGAGAAAGTTATTGGAAAATGATGCACAAGTACATAGGTTCTGACATTACTTCAATGGTGACACTTCCAGTCATCATATTTGAGCCCATGACTACGC
                                                                                                    |  || ||  || || |  | | |    ||      |    | | | | ||   ||   |    |      |||     |     ||||| ||||  | |||||||| |||||||| ||||||||||| |||||  |||| ||||||||||| ||||| || || || ||||| || ||||| | ||
---------------------------------------------------------------------------------------------------gtatatatacttcttcctttactat----tgttgttgttgacataactgttgatcta--atcatctgagaaatatacacaattcttagGATCGAGATGGCTATTGGAAGATGATGCAGAAGTACATAGGATCTGATGTTACATCAATGGTGACCCTTCCTGTGATTATTTTTGAACCAATGACAATGC

upper sequence: PP1S148_87V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv08s0007g00480.t01 (Vitis vinifera), 3'ss of exon 2
gtgaccttcatcttcatgccttaagcatcgagatcagtaatcatttttaatgtatgttgtggtgtggcattagtgccaatttcggcgaactggattggaattaatttaactcctct-tgaattttaatgtgaaagaatcagtacatcggctgccttaccgttgggtttttgttatgtggcaagtgcagGATAGAGAAAGTTATTGGAAAATGATGCACAAGTACATAGGTTCTGACATTACTTCAATGGTGACACTTCCAGTCATCATATTTGAGCCCATGACTACGC
                                                                |||    ||||  || || || |||   ||   |||         || |||| |  ||||| |  |      ||   | | ||   |   ||   |||   ||||| ||          | |||||  | || ||||| ||||| |||||||||||||| ||||| |||||  | || ||||||||||||||||| || || || ||||||||  ||||||  |
---------------------------------------------------------------atgg----agtgataaattgggggaaaaagaaaagaa-------ggcttctctgtatatttttacatatggttattgatgc-tcattt---tttgggttaattttttttt----------tccagGACCGGGACAGTTACTGGAAGATGATGCACAAGTATATAGGCTCTGATGTCACATCAATGGTGACACTTCCTGTTATGATTTTTGAGCCGTTGACTATAC

upper sequence: PP1S148_87V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 2
gtgaccttcatcttcatgccttaagcatcgagatcagtaatcatttttaatgtatgttgtggtgtggcattagtgccaatttcggcgaactggattggaattaatttaactcctcttgaattttaatgtgaaagaatcagtacatcggctgccttaccgttgggtttttgttatgtggcaagtgcagGATAGAGAAAGTTATTGGAAAATGATGCACAAGTACATAGGTTCTGACATTACTTCAATGGTGACACTTCCAGTCATCATATTTGAGCCCATGACTACGC
                                                                                       | || |  | ||||||    |  |    |   ||||||       |   |   |   |    ||   |    ||  |   ||||| |||      || |||| || || ||||| ||||| |||||||| ||||| |||||||| ||  | || ||||||||||||||||||||  | || |||||||| ||||| | ||
--------------------------------------------------------------------------------------aatcttgtcttgaattacccgatatgaaatcatattttagcaatttatcctgtattttttatttgtgctgatattttgagcttgttctgttttct-tgtagGAAAGGGACAGTTACTGGAAGATGATGCAAAAGTATATAGGTTCAGATGTCACCTCAATGGTGACACTTCCAGTTCTGATTTTTGAGCCAATGACAATGC

upper sequence: PP1S148_87V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ08612 (Selaginella moellendorffii), 3'ss of exon 2
gtgaccttcatcttcatgccttaagcatcgagatcagtaatcatttttaatgtatgttgtggtgtggcattagtgccaatttcggcgaactggattggaattaatttaactcctcttgaattttaatgtgaaagaatcagtacatcggctgccttaccgttgggtttttgttatgtggcaagtgcagGATAGAGAAAGTTATTGGAAAATGATGCACAAGTACATAGGTTCTGACATTACTTCAATGGTGACACTTCCAGTCATCATATTTGAGCCCATGACTACGC
                                                                                               |     |    |   || | ||   || |  | | ||    |   |   |  | | ||| ||  || ||| |||   ||    | |    ||||| | || || || |||||||||||||||||||| || || || ||| | ||||| ||||||||||| |||||  | || |||||||||||||| | ||
----------------------------------------------------------------------------------------------gtaagtcttcccttgttctttttc--ttgttctttcaatacttgtttttgtttgtttcctcactctttggtctttacgat----cga---tagGATCGTGAGAGCTACTGGAAAATGATGCACAAGTATATTGGATCGGACGTCACTTCCATGGTGACACTGCCAGTTTTGATTTTTGAGCCCATGACGATGC

upper sequence: PP1S148_87V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ19778 (Selaginella moellendorffii), 3'ss of exon 2
gtgaccttcatcttcatgccttaagcatcgagatcagtaatcatttttaatgtatgttgtggtgtggcattagtgccaatttcggcgaactggattggaattaatttaactcctcttgaattttaatgtgaaagaatcagtacatcggctgccttaccgttgggtttttgttatgtggcaagtgcagGATAGAGAAAGTTATTGGAAAATGATGCACAAGTACATAGGTTCTGACATTACTTCAATGGTGACACTTCCAGTCATCATATTTGAGCCCATGACTACGC
                                                                                               |     |    |   || | ||   || |  | | ||    |   |   |  | | ||| ||  || ||| |||   ||    | |    ||||| | || || || |||||||||||||||||||| || || || ||| | ||||| ||||||||||| |||||  | || |||||||||||||| | ||
----------------------------------------------------------------------------------------------gtaagtcttcccttgttctttttc--ttgttcttttaatacttgtttttgtttgtttcctcactctttggtctttacgat----cga---tagGATCGTGAGAGCTACTGGAAAATGATGCACAAGTATATTGGATCGGACGTCACTTCCATGGTGACACTGCCAGTTTTGATTTTTGAGCCCATGACGATGC

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: 34

TTTACTGGGACATGAGGGCTTGGAGGTAGTCAACCCTGAAGGAGGGCAGGAAGATGTTGAGGAAGAGGCGATCCGCGGCAGGTTCAAGCAAGAGgtgaccttca ... gcaagtgcagGATAGAGAAAGTTATTGGAAAATGATGCACAAGTACATAGGTTCTGACATTACTTCAATGGTGACACTTCCAGTCATCATATTTGAGCCCATGACTACGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaatcagtacatcggctgccttaccgttgggtttttgttatgtggcaagtgcagGATAGAGAAAGTTATTGGAAAATGATGCACAAGTACATAGGTTCTGACATTACTTCAATGGTGACACTTCCAGTCATCATATTTGAGCCCATGACTACGC
                  gccttac  putative branch site (score: 34)
                                tttttgttat  TA-rich tract