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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgtatgcagccggtgcattgatggtgcagtctgcagattgggatgggcctagggggggggggtatagctgtaaggtggagggtggattggcagagctgatgagggttgtgcgtggttgtaatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGAGGATTGCGAGCGCTGCCAACGCGATTGTTTGAGAGGGTAGTTTGGGAGT

Basic information

species Physcomitrella patens
transcript PP1S62_133V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S62_136V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os02g56960.1 (Oryza sativa), 3'ss of exon 3
gtgagtgtatgcagccggtgcattgatggtgcagtctgcagattgggatgggcctagggggggggggtatagctgtaaggtggagggtggattggcagagctgatgagggttgtgcgtggttgtaatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGAGGATTGCGAGCGCTGCCAACGCGATTGTTTGAGAGG-GTAGTTTGGGAGT
                  ||    | |  | |  |      | |    |    | |          | ||||||  | | |          | | | || || || |      |  |   ||  |   |||||||||||||||||||||||| ||||| ||||||||||| ||  | ||||| |||||||| || || || || ||||| || | |  |  | ||     ||  
------------------tgaccagctatttcctttcttgaaatcttgtactacaaaactaataatgcatagcttcacgat----------tagcctgaccttataaa-----tatgcacttccatgatgcagGTTCTGCCATCACTGGACCTATCGGAAAGGAGTGCGCTGATCTCTGGCCCAGGATTGCAAGTGCAGCAAATGCGATCGTCTAATCGAAGCAGCCATTGAA-

upper sequence: PP1S62_136V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os10g32920.1 (Oryza sativa), 3'ss of exon 3
gtgagtgtatgcagccggtgcattgatggtgcagtctgcagattgggatgggcctagggggggggggtatagctgtaaggtggagggtggattggcagagctgatgagggttgtgcgtggttgtaatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGAGGATTGCGAGCGCTGCCAACGCGATTGTTTGAGAGGGTAGTTTGGG-AGT
                            ||   |   | | | |   ||   || |   |    |  | |   ||||   |     |  |  |  |||     || |        |   ||  |  | | |||||||||| ||||||||||| || || ||||||||||| ||| | ||||| |||||||| ||||| || || || ||||| | ||||  |  || | | |||
----------------------------gtatggcgagaacactactatactcccatatgttatg--tgttattgtattttctctcgaagcctaccagg--caataatttactcactgtgtattcttttccagGTTCTGCTATCACTGGACCCATTGGTAAGGAGTGCGCCGACCTCTGGCCAAGGATTGCTAGCGCAGCAAATGCCATTGTCT-AGAGCTTGTTTGGAGTAGT

upper sequence: PP1S62_136V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os03g04590.3 (Oryza sativa), 3'ss of exon 3
gtgagtgtatgcagccggtgcattgatggtgcagtctgcagattgggatgggcctagggggggggggtatagctgtaaggtggagggtggattggcagagctgatgagggttgtgcgtggttgtaatgtgc----agGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGAGGATTGCGAGCGCTGCCAACGCGATTGTTTGAGAGGGTAGTTTGGGAGT
                                             | |       ||     |    | | | ||     |  |   |  |||||    | | |    | || |   ||||    |||| |    ||||||||| ||||||||||| |||||||||||||| || ||| | ||||| ||||| || || || || || || ||||| ||||   ||      | | |
---------------------------------------------gtaacaatgcagaacttgactttcttgatgctgaat--aatctaaattggacatgttaact--gattatatatggtctatatgttctatcagGTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTAGGATAGCTAGTGCAGCAAATGCTATTGTCTGAGCTTGTTTGAATGAATT

upper sequence: PP1S62_136V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G102230_T01 (Zea mays), 3'ss of exon 4
gtgagtgtatgcagccggtgcattgatggtgcagtctgcagattgggatgggcctagggggggggggtatagctgtaaggtggagggtggattggcagagctgatgagggttgtgcgtggttgtaatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGAGGATTGCGAGCGCTGCCAACGCGATTGTTTGAGAGGGTAGTTTGGGAGT
                     |||  |         || |||||    | |   |            | || |  ||  || |      |||     |   ||||  |  || | | ||    | |||  |||| ||||||||||||||||| ||||| |||||||| || ||  ||||||| |||||||| ||||| || || |||||||| |    |  |   |||   | 
---------------------atttctctaatctcttggagattctcttagcttttattataa----tctaacactacagttggaaaatgat-----gtattgatacgcatt-tccatgaccatgatg--cagGCTCTGCCATCACTGGACCCATCGGAAAGGAGTGTGCTGATCTGTGGCCTAGGATTGCCAGCGCGGCAAATGCGATTGTCTAGTGGAATCAGTTGATCGA

upper sequence: PP1S62_136V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G102230_T03 (Zea mays), 3'ss of exon 5
gtgagtgtatgcagccggtgcattgatggtgcagtctgcagattgggatgggcctagggggggggggtatagctgtaaggtggagggtggattggcagagctgatgagggttgtgcgtggttgtaatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGAGGATTGCGAGCGCTGCCAACGCGATTGTTTGAGAGGGTAGTTTGGGAGT
                     |||  |         || |||||    | |   |            | || |  ||  || |      |||     |   ||||  |  || | | ||    | |||  |||| ||||||||||||||||| ||||| |||||||| || ||  ||||||| |||||||| ||||| || || |||||||| |                   
---------------------atttctctaatctcttggagattctcttagcttttattataa----tctaacactacagttggaaaatgat-----gtattgatacgcatt-tccatgaccatgatg--cagGCTCTGCCATCACTGGACCCATCGGAAAGGAGTGTGCTGATCTGTGGCCTAGGATTGCCAGCGCGGCAAATGCGATTGTCTAG-----------------

upper sequence: PP1S62_136V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G150058_T02 (Zea mays), 3'ss of exon 1
gtgagtgtatgcagccggtgcattgatggtgcagtctgcagattgggatgggcctagggggggggggtatagctgtaaggtggagggtggattggcagagctgatgagggttgtgcgtggttgtaatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGAGGATTGCGAGCGCTGCCAACGCGATTGTTTGAGAGGGTAGTTTGGGAGT-
                                             | |||        |         ||  ||  |   | | |  |    ||   |   ||    |  |          | |    ||||||||| || ||||||||||| ||||| |||||||| || ||  | ||||| |||||||| ||||| || ||||| ||||||||||||  | ||| |    | 
---------------------------------------------gtatgaatt----gtccacaataattcctccagcattgggcctattctgtttggcatggcatgactaactatcaaatttgtcttgcagGTTCCGCTATCACTGGACCTATCGGCAAGGAGTGTGCTGATCTTTGGCCTAGGATTGCTAGCGCAGCAAACGCCATTGTTTGAGAGCTT-GTTGGAATATG

upper sequence: PP1S62_136V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G078396_T02 (Zea mays), 3'ss of exon 3
------------------------gtgagtgtatgcagccggtgca-ttgatggtgcagtctgca-gattgggatgggcctaggg-----ggggggggtatagctgtaaggtggag-ggtggattggcagagctgatgagg--gttgtgcgtggttgtaatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGAGGATTGCGAGCGCTGCCAACGCGATTGTTTGAGAGG-GTAGTTTGGGAGT
                         |   | |          | ||  |  | |||| ||  |||   |||  ||    |          |   |  || ||||| ||   |      |  |  | ||| ||  | || ||   |  |  ||  |  |    ||||||||||||||||||||| || ||||| ||||||||||| ||  | ||||| |||||||| ||||| || || ||||| || | |  |  | ||||||     
gtatagtattgaaggttctgatggtttcatatgcattattattacagctacttgtgctgtgggcatagttgaaattcatcccaaaatacagcaagctgtttagctttatcataagctagcagcctagcacagaagttggggaaataatatgtactcctgtgctgcagGTTCTGCCATCACTGGGCCCATCGGAAAGGAGTGCGCTGATCTCTGGCCCAGGATTGCTAGCGCGGCAAATGCGATCGTCTAAAGGAAGCAGTTTGTCGA-

upper sequence: PP1S62_136V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G078396_T03 (Zea mays), 3'ss of exon 4
------------------------gtgagtgtatgcagccggtgca-ttgatggtgcagtctgcagattggga--tgggcctagg----gggggggggtatagctgtaaggtggag-ggtggattggcagagctgatgaggg--ttgtgcgtggttgtaatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGAGGATTGCGAGCGCTGCCAACGCGATTGTTTGAGAGGGTAGTTTGGGAGT
                         |   | |          | ||  |  | |||| ||  ||| | | | |  |   || |       |   |  || ||||| ||   |      |  |  | ||| ||  | || ||   |  |  ||  |  |    ||||||||||||||||||||| || ||||| ||||||||||| ||  | ||||| |||||||| ||||| || || ||||| || | |                 
gtatagtattgaaggttctgatggtttcatatgcattattattacagctacttgtgctgtgggcatagttgaaattcatcccaaaatacagcaagctgtttagctttatcataagctagcagcctagcacagaagttggggaaataatatgtactcctgtgctgcagGTTCTGCCATCACTGGGCCCATCGGAAAGGAGTGCGCTGATCTCTGGCCCAGGATTGCTAGCGCGGCAAATGCGATCGTCTAA-----------------

upper sequence: PP1S62_136V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G123495_T01 (Zea mays), 3'ss of exon 3
gtgagtgtatgcagccggtgcattgatggtgcagtctgcagattgggatg-ggcctagggggggggggtatagctgtaaggtggagggtggattggcagagctgatgagggttgtgcgtggttgtaatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGAGGATTGCGAGCGCTGCCAACGCGATTGTTTGAGAGGGTAGTTTGGGAGT
                       | |  |||  | || |   |   ||||  | ||     |    | | |  ||||| |||| ||||  |     ||| |||||  |   || ||| || |  |  | |||||| ||||||||||||||||| || || ||||||||||| ||| | ||||| |||||||| || || || || || ||||| ||| |     | ||||||| 
----------------------gtaagagtgtggcctact--tcacgatgcagtctccctagttttgatctc-ctgta-ggtgcagggcag-----cagcgctgaaca---ttttgc-tgctcct--tttgcagGATCTGCCATCACTGGACCTATTGGCAAGGAGTGCGCTGACCTTTGGCCTAGGATTGCTAGTGCAGCAAATGCTATTGTCTGATACTACTGGTTGGGAGG

upper sequence: PP1S62_136V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G171181_T01 (Zea mays), 3'ss of exon 3
gtgagtgtatgcagccggtgcattgatggtgcagtctgcagattgggatgggcctagggggggggggtatagctgtaa-ggtggagggtggattggcagagctgatgagggttgtgcgtggttgtaatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGAGGATTGCGAGCGCTGCCAACGCGATTGTTTGAGAGGGTAGTTTGGGAGT-
                                             | |||   | |   | |     |  | |   |   |   || |  | ||||||  ||     | |    | |   ||     | |||||||||||| ||||||||||| ||||| |||||||| || ||| | ||||| ||||| || || || || || || || |||||||||  | ||| |   || 
---------------------------------------------gtatgatacaacctgagattcctccatcatcatcagccaagtgctgtttggcaaggcatgaaacgaacttacaatgtctctct-tgcagGTTCTGCAATCACTGGACCTATCGGCAAGGAGTGTGCTGACCTTTGGCCTAGGATCGCTAGTGCAGCAAATGCCATCGTTTGAGAGCTT-GTTGGAATGTG

upper sequence: PP1S62_136V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA19G35110.1 (Glycine max), 3'ss of exon 3
gtgagtgtatgcagccggtgcattgatggtgcagtctgcagattgggatgggcctagggggggggggtatagctgtaaggtggagggtggattggcagagctgatgag-ggttgtgcgtggttgtaatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGAGGATTGCGAGCGCTGCCAACGCGATTGTTTGAGAGGGTAGTTTGGGAGT
                              | ||| ||     || |||  |  | | |        | | | | |    |   | ||  | ||| |    || ||   | ||| | |||  |  ||  || ||||||||| |||||||| || || ||||||||||| || ||  ||||||| |||||||| || |||||||| || ||||||| ||   | | ||| |   |
------------------------------ggagtttgtg---tgagatcagagt-gtgatcttacttgttggtcttgtttcttgtgttaaatggtatgtgtggtgtttgattgggtgtgacttcaaattgtagGTTCTGCTATCACTGGTCCAATTGGGAAGGAGTGTGCTGATCTGTGGCCCAGGATTGCAAGTGCTGCCAATGCTATTGTTTAAGCTAGGATTTTAGTTTT

upper sequence: PP1S62_136V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA03G32380.1 (Glycine max), 3'ss of exon 3
gtgagtgtatgcagccggtgcattgatggtgcagtctgcagattgggatgggcctagggggggggggtatagctgtaaggtggagggtggattggcagagctgatgagggttgtgcgtggttgtaatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGAGGATTGCGAGCGCTGCCAACGCGATTGTTTGAGAGGGTAGTTTGGGAGT
                              ||| | |     || |  ||      | | | |    | | | | |    |     ||| | ||       |  ||   | |  | | | || | |  || ||||||||| |||||||| || || ||||||||||| || ||  ||||||| |||||||| || ||||| || || ||||||| ||  ||   ||| |    
----------------------------ccgcattattggtctttgtgtgaaatccgagtgtgatcttgttgattttttttcctctgtgaaatgtt-----tagtgtttgattggtgagatttttaattgtagGTTCTGCTATCACTGGTCCTATTGGGAAGGAGTGTGCTGATCTGTGGCCCAGGATTGCAAGTGCTGCAAATGCTATTGTTTAAGCTGGGTTTTTAGTTTA

upper sequence: PP1S62_136V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ36569 (Selaginella moellendorffii), 3'ss of exon 3
gtgagtgtatgcagccggtgcattgatggtgcagtctgcagattgggatgggcctagggggggggggtatagctgtaaggtggagggtggattggcagagctgatgagggttgtgcg-tggttgtaatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGAGGATTGCGAGCGCTGCCAACGCGATTGTTTGAGAGGGTAGTTTGGGAGT
                                                                         | |   ||     |    | |         ||||| |||    | | ||| |  |||  ||| |||||||||||||| || ||||| ||||| ||||| || ||||||||  | || || ||||||||||| || || ||||||         | | || |
------------------------------------------------------------------------gtatggagttcttcgcctctcgcgctttggaatgagagtttgatgcttgttct--tgtctagGATCTGCCATCACTGGCCCAATCGGCAAGGAATGCGCGGATTTGTGGCCTCGAATCGCCAGCGCTGCCAATGCCATCGTTTGATTCAAAGCCTGGAGACT

upper sequence: PP1S62_136V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ18478 (Selaginella moellendorffii), 3'ss of exon 3
gtgagtgtatgcagccggtgcattgatggtgcagtctgcagattgggatgggcctagggggggggggtatagctgtaaggtggagggtggattggcagagctgatgagggttgtgcg-tggttgtaatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGAGGATTGCGAGCGCTGCCAACGCGATTGTTTGAGAGGGTAGTTTGGGAGT
                                                                         | |   ||     |    | |         ||||| |||    | | ||| |  |||  ||| |||||||||||||| || ||||| ||||| ||||| || ||||||||  | || || ||||||||||| || || ||||||   |     | | || |
------------------------------------------------------------------------gtatggagttcttcgcctctcgcgctttggaatgagagtttgatgcttgttct--tgtttagGATCTGCCATCACTGGCCCAATCGGCAAGGAATGCGCGGATTTGTGGCCTCGAATCGCCAGCGCTGCCAATGCCATCGTTTGATTCGAAGCCTGGAGACT

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), 35 (downstream exon)
Score: 191

ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGGgtgagtgtat ... taatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGAGGATTGCGAGCGCTGCCAACGCGATTGTTTGAGAGGGTAGTTTGGGAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtggagggtggattggcagagctgatgagggttgtgcgtggttgtaatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGAGGATTGCGAGCGCTGCCAACGCGATTGTTTGAGAGGGTAGTTTGGGAGT
                    agctgat  putative branch site (score: 191)
                                          ttgtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgtatgcagccggtgcattgatggtgcagtctgcagattgggatgggcctagggggggggggtatagctgtaaggtggagggtggattggcagagctgatgagggttgtgcgtggttgtaatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGAGGATTGCGAGCGCTGCCAACGCGATTGTTTGAGAGGGTAGTTTGGGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG