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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagcatttattcttcccacctggagtttttgtgtgccagcacaattctcttacacgtgcaatgctaacttcgtctctcgtggcttttgtagGATGCTTGTGTACGAGTACGTGGACAATGGGAATCTGGAGCAGTGGCTACATGGACCTCTGTCACAAACAAACACACTTCCATGGGAAGCTCGCATGCGG

Basic information

species Physcomitrella patens
transcript PP1S568_2V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os05g36050.1 (Oryza sativa), 3'ss of exon 2
-----------------------------------gtgaagcatttattcttcccacctg--gagtttttgtgtgccagcacaattct-cttacacgtgcaatgctaacttcgtctctcgtggcttttgtagGATGCTTGTGTACGAGTACGTGGACAATGGGAATCTGGAGCAGTGGCTACATGGACCTCTGTCACAAACAAACACACTTCCATGGGAAGCTCGCATGCGG
                                   |       ||| ||||| ||   |   |  | ||    | ||||  || | || | |||     |    |  ||    |||  | ||   | |  ||||| |||||||| ||||||||||||||||| ||  ||||||||||||| |||||     |   ||     | | | ||  | |||||     | |||   
gtacactacacacaccacgcaattgccaaatcgccgccttcttttttttctttcctttttttggctgttctcttaccagatcattcctacctacctactccgatcctaccatttcttgcctgtgatct-cagGATACTTGTGTATGAGTACGTGGACAATGGCAACTTGGAGCAGTGGCTTCATGGCGACGTTGGACCGGTTAGCCCTCTGTCTTGGGACATCAGGATGAAC

upper sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os02g34430.1 (Oryza sativa), 3'ss of exon 2
---gtgaagcatttattcttcccacctggagtttttgtgtgccagcacaattctcttacacgtgcaatgctaacttcgtctctcgtggcttttgt-agGATGCTTGTGTACGAGTACGTGGACAATGGGAATCTGGAGCAGTGGCTACATGGACCTCTGTCACAAACAAACACACTTCCATGGGAAGCTCGCATGCGG
    |        | | |     |  |||     ||||      ||| |||          |   ||||  ||    || | | |||||| |    |||||||||||||| ||||| || ||||| ||||| || ||||||||||| |||||     |   ||    || | | ||| | |||||  |  |  ||  |
gtattttcttgcatgtgcacattatttggtaaccttgttgaattgcaaaatcaaaaggtttg-ataatgtaaatggtgtttat-gtggctctgaccagGATGCTTGTGTATGAGTATGTCGACAACGGGAACCTAGAGCAGTGGCTCCATGGGGAAGTTGGACCTGTAAGCCCTCTTTCGTGGGATTCCAGGGTGAAG

upper sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G014366_T03 (Zea mays), 3'ss of exon 2
-------------gtga-agcatttattcttcccacctggagtttttgtgtgccagcacaattctcttacacgtgcaatgctaacttc-gtctctcgtg-----gcttttgtagGATGCTTGTGTACGAGTACGTGGACAATGGGAATCTGGAGCAGTGGCTACATGGACCTCTGTCACAAACAAACACACTTCCATGGGAAGCTCGCATGCGG
              ||  | |  || ||| | |   | || |        |  |||      |     | |  || ||  || | | | ||| ||   |     ||||    |||||||||||||||||||| ||||||||||| ||||| || |||||||| |||||   | |   | ||  || | ||||  ||||||| |   | |||   
gtatgatggcatattgctatctcttcttcattcggtccggtgacacctactctcagtttggattctcaata-atggaagcctgattcctgtcactgtcgtctatgcttgaacagGATGCTTGTGTACGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCATGGTGATGTTGGAGAAGTAAGCCCACTAACATGGGACGTCAGGATGAAC

upper sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G147051_T03 (Zea mays), 3'ss of exon 1
--------gtgaagcatttattcttcccacctgg-----agtttttgt--gtgc-cagcacaattctcttacacgtgcaatgctaacttcgtctctcgtggcttttg----tagGATGCTTGTGTACGAGTACGTGGACAATGGGAATCTGGAGCAGTGGCTACATGGACCTCTGTCACAAACAAACACACTTCCATGGGAAGCTCGCATGCGG
        ||| |  |||  | ||||   | | |     | |||||||  |||| | || ||     | |  ||| ||  | |  |       |   || |||| ||     ||||| ||||||||||||||||||||||| || || || ||||||||||| || ||     |      |   | | | ||  | ||||| |  || |||   
gtacagaagtgcattattattgcttcttgctttgtggtaaatttttgttcgtgcgctgcgcatcgtacctctacg-gctctacctaacctaaatgcggttgcttgtgatcccagGATACTTGTGTACGAGTACGTGGACAACGGCAACCTCGAGCAGTGGCTGCACGGCGACGTCGGGGCAGTGAGCCCGCTCACCTGGGACGTCCGGATGAAC

upper sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G026301_T01 (Zea mays), 3'ss of exon 3
----gtgaagcatttattcttcccacctggagtttttgtgtgcca-gcacaattctcttacacgtgc-aatgctaacttcgtctctcgtggcttttgtagGATGCTTGTGTACGAGTACGTGGACAATGGGAATCTGGAGCAGTGGCTACATGGACCTCTGTCACAAACAAACACACTTCCATGGGAAGCTCGCATGCGG
    || ||    |||   |    | ||  |  |||  |    ||   |   || | | |    |   | || |  | |  ||         |  |  |||||||||||||| ||||||||| ||||||| ||| | || |||||||| |||||  |  ||   ||          ||| | |||||||| || |||   
agtggttaatatattaccatggaaatctatatgtttcatacatcatatattgttttttaatctatttgagtgttctcattatcatatcctcttactccagGATGCTTGTGTATGAGTACGTGAACAATGGAAATTTAGAACAGTGGCTTCATGGTGCCATGCGTCAGCATGGTGTTCTTACTTGGGAAGCCCGGATGAAA

upper sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G317938_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------gtgaagcatttattcttcccacctggagtttttgtgtgccagcacaattctcttacacgtgcaatgctaacttcgtctctcgtggcttttgtagGATGCTTGTGTACGAGTACGTGGACAATGGGAATCTGGAGCAGTGGCTACATGGACCTCTGTCACAAACAAACACACTTCCATGGGAAGCTCGCATGCGG
                                             |  |   | ||  |  || ||  |   | || |   ||   | |   | ||  |  |  | || | |||   | |||| |    ||||    |||||||| ||||| ||||| ||||||||||| ||||| || |||||||| |||||   | |     ||   | | ||||  |||||||     | |||   
gtatgtgtgttggcaggcacattgcaatctcttcttcgttcggtggacacctagttgcttctctcaatttagggttctcaatgatggaagcttgcttctgtatat-cactacta---tggtctat----gcttgaacagGATGCTCGTGTATGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCATGGTGATGTTGGCGAAGTGAGCCCACTGACATGGGACATCAGGATGAAC

upper sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA11G05830.1 (Glycine max), 3'ss of exon 2
-----------------gtgaagcattta---ttcttcccacctggagtttttgt-gtgccagcacaattctcttacacgtgcaatgctaacttcgtctctcgtggctt---ttgtagGATGCTTGTGTACGAGTACGTGGACAATGGGAATCTGGAGCAGTGGCTACATGGACCTCTGTCACAAACAAACACACTTCCATGGGAAGCTCGCATGCGG
                  | ||  ||  |   ||  | |    |    ||||||| ||      |  |   | | |   |   |    |   ||    | |  |   |     || || |||||||| || ||||||||||||||||| ||| | ||||||||||| |||||   | |    |     |   | ||  | ||||||  ||| |||   
gtattcttactttcttctttaattatccaaaattgcttcttttttttttttttgtagtatagatatgaacttttgaactgatgaggtttttttttaattattattattcacgctgcagAATGCTTGTTTATGAGTACGTGGACAATGGTAATTTAGAGCAGTGGCTGCATGGGGATGTTGGGCCTTGCAGTCCTCTAACTTGGGAAATTCGAATGAAC

upper sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA07G07250.1 (Glycine max), 3'ss of exon 3
gtgaagcatttattcttcccacc--tggagtt-------tttgtgtgccagcacaattctcttacacgtgcaatgctaacttcgtctctcgtggcttttgtagGATGCTTGTGTACGAGTACGTGGACAATGGGAATCTGGAGCAGTGGCTACATGGACCTCTGTCACAAACAAACACACTTCCATGGGAAGCTCGCATGCGG
||  |   ||| || ||   | |  || || |       ||||| ||     |  | | |   |   |  |  ||     |   |      |   | ||| |||||||||||||| || || || |||||||||||||| || |||||||| |||||   | |   ||    || | || |  |||||||    || |||   
gtatatttttttttgttttgaacattgaagctaaaagagtttgtttggtttaaagaatgtaagatttgaactttgaaggatgtattcaatattcatattgcagGATGCTTGTGTATGAATATGTTGACAATGGGAATCTAGAACAGTGGCTGCATGGGGATGTTGGACCTGTAAGCCCAATGACATGGGATATCCGAATGAAC

upper sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA09G39160.1 (Glycine max), 3'ss of exon 2
---gtga-agcatttattcttcccacctg----------gagtttttgtg-tgccagcacaattctcttacacgtgcaatgctaacttc-gtctctcgtggcttttgtagGATGCTTGTGTACGAGTACGTGGACAATGGGAATCTGGAGCAGTGGCTACATGGACCTCTGTCACAAACAAACACACTTCCATGGGAAGCTCGCATGCGG
    ||| | | | |  ||||   | ||            |   ||  || |  ||      ||   ||  || ||   ||  | ||   || |      | |||   |||||||||||||| ||||| || |||||||| ||||| ||||| ||||| |||||     |   |     || | |  |  ||||| |    || |||   
gtattgatatcttcttctcttaaaaactaaatagaaaaaaaaaattgatgctatcaattttgtttggtttgacatgatgtgagatctgaagtgtggtactgttttcacagGATGCTTGTGTATGAGTATGTAGACAATGGCAATCTAGAGCAATGGCTGCATGGGGACGTTGGAGCTGTAAGCCCTTTGACATGGAACATACGGATGAAC

upper sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA01G39420.1 (Glycine max), 3'ss of exon 3
gtgaagcatttattcttcccacctggagtttttgtgtg-ccagcacaattctcttacacgtgcaatgctaacttcgtctctcgtggcttttgtagGATGCTTGTGTACGAGTACGTGGACAATGGGAATCTGGAGCAGTGGCTACATGGACCTCTGTCACAAACAAACACACTTCCATGGGAAGCTCGCATGCGG
          || |||||    ||    ||  | | |    | |  || |  ||| |   |    |  |  ||| |  | |  | | |  || || |||||||| || |||||||| |||||||| ||| | ||||||||||| |||||   | |    |     |   | ||  | ||||||  ||| |||   
---------gtactcttcatttcttactttcctctttaattaaccaaaattgcttcctttt----ttttttctttgattattattggtcctgcagAATGCTTGTTTATGAGTACGTTGACAATGGTAATTTAGAGCAGTGGCTGCATGGGGATGTTGGGCCTTGCAGTCCTCTAACTTGGGAAATTCGAATGAAC

upper sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv15s0046g02030.t01 (Vitis vinifera), 3'ss of exon 2
--------gtgaagcatttattc--ttcccacctggagtttttgtgtgccagcacaattctcttacacgtgcaatgctaacttcgtctctcgtggcttttgtagGATGCTTGTGTACGAGTACGTGGACAATGGGAATCTGGAGCAGTGGCTACATGGACCTCTGTCACAAACAAACACACTTCCATGGGAAGCTCGCATGCGG
            | | | |  |   | |  ||   | |||||  || |    || ||  ||   |    | ||    | | ||  | | |      || | ||||||||||||||| ||||| ||||||||||| ||| |||| |||||||| |||||   | |     ||   | | | ||  |||||||   ||| ||    
gtattgctacccatcttctgctaaatcctgacactgggttttcttgaggatccaaaaaactaacattttttcatctttcatttgttttttt----tttgtctagGATGCTTGTGTATGAGTATGTGGACAATGGTAATTTGGACCAGTGGCTTCATGGGGATGTAGGGGAAGTCAGCCCTCTGACATGGGATATTCGGATTAAC

upper sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv07s0031g00480.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------------------------------------------------------------------------------gtgaagcatttattcttcccacctggagtttttgtgtgccagca-caattctcttacacgtgcaatgctaacttcgtctctcgtggcttttgtagGATGCTTGTGTACGAGTACGTGGACAATGGGAATCTGGAGCAGTGGCTACATGGACCTCTGTCACAAACAAACACACTTCCATGGGAAGCTCGCATGCGG
                                                                                                ||    |||| || ||||   ||||   || |   ||  | |  |||      | |   ||   | ||| | | || ||      || |||||||||||||||||| ||||| ||  | ||||||||| ||||||||||||| |||||   | |    |    ||   | ||| | |||||   ||| |||   
gtactttgttattgtctattgcttaatcctgcttgattgtatttgaactgcaaacaagaatatcttattaattccccattgaaaatgattttgtgttgtttaatttttttttcctggctggc-cttatacatgatatcttcaacagatatgctgatgatgtcctatccttgtttca---atctgttgtagGATGCTTGTGTATGAGTATGTAAATAATGGGAATTTGGAGCAGTGGCTTCATGGTGATGTAGGGCCTCGAAGTCCTCTTACTTGGGAGATTCGAATGAAT

upper sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ27863 (Selaginella moellendorffii), 3'ss of exon 3
gtgaagcatttattcttcccacctggagtttttgtgtgccagcacaattctcttacacgtgcaatgctaacttcgtctctcgtggcttttgtagGATGCTTGTGTACGAGTACGTGGACAATGGGAATCTGGAGCAGTGGCTACATGGACCTCTGTCACAAACAAACACACTTCCATGGGAAGCTCGCATGCGG
                                 ||  | |     ||||||| |  | | |   |  | |||| |  |  ||   ||| |  |||||||| || || |||||||| |||||||| ||||||||||||||||| || || ||    ||       ||| | |   ||||||| | | | |||   
---------------------------------gtacgtcg----aattctcatgaaagagt--ttttcactttggatgacg-aacttctacagGATGCTGGTATATGAGTACGTAGACAATGGTAATCTGGAGCAGTGGCTTCACGGCCCAGCCTCCATTCTCAACTCTCCAACATGGGAGGTTAGGATGAAA

upper sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ16857 (Selaginella moellendorffii), 3'ss of exon 3
gtgaagcatttattcttcccacctggagtttttgtgtgccagcacaattctcttacacgtgcaatgctaacttcgtctctcgtggcttttgtagGATGCTTGTGTACGAGTACGTGGACAATGGGAATCTGGAGCAGTGGCTACATGGACCTCTGTCACAAACAAACACACTTCCATGGGAAGCTCGCATGCGG
                                         |    ||  | || |   || | |  || ||  | || |    ||| |   |||||||| || ||||||||||| |||||||||||||||||||| ||||| || || ||  | ||    |||||  |  |  | ||||| ||  | |||   
-----------------------------------------gtgagatagttttccgattggacttttagct--gactttga--gctctgcaagGATGCTGGTTTACGAGTACGTAGACAATGGGAATCTGGAGCAATGGCTCCACGGGCCAATTTCGAGGACAAAGTCGTTGACGTGGGAGGCAAGGATGAAA

upper sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ36811 (Selaginella moellendorffii), 3'ss of exon 3
gtgaagcatttattcttcccacctggagtttttgtgtgccagcacaattctcttacacgtgcaatgctaacttcgtctctcgtggcttttgtagGATGCTTGTGTACGAGTACGTGGACAATGGGAATCTGGAGCAGTGGCTACATGGACCTCTGTCACAAACAAACACACTTCCATGGGAAGCTCGCATGCGG
                                 ||  | |     ||||||| |  | |     |  | |||| |  |  ||   ||| |  |||||||| || || |||||||| |||||||| ||||||||||||||||| || || ||    ||       ||| | |   ||||||||| ||| |||   
---------------------------------gtacgtcg----aattctcgtgaaagatt--ttttcactttggatgacg-aacttctacagGATGCTGGTATATGAGTACGTAGACAATGGTAATCTGGAGCAGTGGCTTCACGGCCCAGCCTCCATTCTCAACTCTCCAACATGGGAAGTTCGGATGAAA

upper sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ32138 (Selaginella moellendorffii), 3'ss of exon 3
gtgaagcatttattcttcccacctggagtttttgtgtgccagcacaattctcttacacgtgcaatgctaacttcgtctctcgtggcttttgtagGATGCTTGTGTACGAGTACGTGGACAATGGGAATCTGGAGCAGTGGCTACATGGACCTCTGTCACAAACAAACACACTTCCATGGGAAGCTCGCATGCGG
                                         |    ||  | || |   || | |  || ||  | || |    ||| |   |||||||| || ||||||||||| |||||||||||||||||||| ||||| || || ||  | ||    |||||  |  |  | ||||| ||  | |||   
-----------------------------------------gtgagatagttttccgattggacttttagct--gactttga--gctctgcaagGATGCTGGTTTACGAGTACGTAGACAATGGGAATCTGGAGCAATGGCTCCACGGGCCAATCTCGAGGACAAAGTCGTTGACGTGGGAGGCAAGGATGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagcacaattctcttacacgtgcaatgctaacttcgtctctcgtggcttttgtagGATGCTTGTGTACGAGTACGTGGACAATGGGAATCTGGAGCAGTGGCTACATGGACCTCTGTCACAAACAAACACACTTCCATGGGAAGCTCGCATGCGG
                         tgctaac  putative branch site (score: 1)
                                              cttttgt  putative PPT
                                               ttttgta  TA-rich tract