Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGgtatatacattcctcgtgttgtatcttttctaagttaacacgctctacgcttttatgtcggtccaatgtgtactagaagcgtaaaatatttaaacctggc...

Basic information

species Physcomitrella patens
transcript PP1S189_118V6.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: LOC_Os03g16980.5 (Oryza sativa), 5'ss of exon 8
GAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGgtatatacattcctcgtgttgtatcttttctaagttaacacgctctacgcttttatgtcggtccaatgtgtactagaagcgtaaaatatttaaacctggc
|||| || || |||||||||||||| |||||||| || || || || ||||||||||| || |||||||||||| ||||||   | |||  | || |  || ||||| |   ||   | |  ||  | || ||  ||     |||  ||| |         |  | | ||        
GAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgta---atatttttagt-tcatacctttt-tgtcttgtgatgtactg-gattgtagttctccttaataagtattttccaatctatctctgtag-------

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 8
GAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGgtatatacatt-cctcgtgttgtatcttttcta--agttaacacgctctacgcttttatgtcggtccaatgtgtactagaagcgt---aaaatattta-aacctggc-------
|||| || ||||| ||||| ||||| |||||||| || ||||| || ||||| ||||| || |||||||||||| |||||| |||| |   || |   |  | || |  ||  || | | |  |       || | ||      | | |  ||  |   |        |||||||| || ||          
GAGTCAGGAGCTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgta-atacttcatcttgcacttaaactgtaatattagctcatagccctctttattgtgtgataactctaggcttatgatttgtcctcagcaatatttataatctatgtctgtag

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GRMZM2G300412_T01 (Zea mays), 5'ss of exon 14
GAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGgtatatacattcctcgtgttgtatcttttctaagttaacacgctctacgcttttatgtcggtccaatgtgtactagaagcgtaaaatatttaaacctggc------------------------
| || || || || ||||| ||||| |||||||| ||||||||  | ||||||||||| || | |||||||||| |||||| | || ||| || |    |     ||| |  |||  |     ||  | | | |||   |   ||    |||    || ||  || |||   | |  |                        
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTGgta-acac-ttcatctttcacttaaacttcaatattagtagctcatagtcctctttgtta-tgtgata---actctgggcttatgattttttttcttaacagtgtttatcatctatgtctgtag

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 7
GAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGgta------tatacattcctcgtgttgtatcttttctaagttaacacgctctacgctttt-----atgtcggtccaatg----tgtactagaagcgtaaaatatttaaacctggc-
| || || || || ||||| ||||| |||||||| || ||||| || ||||| ||||| || |||||||||||| ||||||       ||   |  ||     |  |   ||  ||  | |   | ||||  | | |      |    || |  |||    | || ||  ||  |  |  || ||   |||   
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgtgataactctgggcttatgattttttattaacagtatttatcatctatgtctgtag

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GLYMA11G15010.1 (Glycine max), 5'ss of exon 8
GAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGgtatatacattcctcgtgttgtatcttttctaagttaacacgctctacgcttttatgtcg-gtccaatgtgtactagaagc----gtaaaatatttaaacctggc-----------------------------------
||||  | || || ||||| ||||| ||||||||||| || ||| | |||||||| || ||||||||||||||  | ||||  | | |  ||    || |  |||||||   |    ||     |    || | | |     || |      |     |    || || || | |    |  |                                   
GAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCGgtaattccttatctttattttttccttttctccttggcaacatctcattgattgagggcacaaacagtacacgttttgcactgctgttaactaataagcaataactcaatgtgatgcttattttcatatttttctctcag

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GLYMA11G15020.1 (Glycine max), 5'ss of exon 8
GAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGgta---tatacattcctcgtgtt-gtatcttttctaagttaacacgctctacgcttttatgtcggtccaatgtgtactagaagcg-taaaatatttaaacctggc-----------------------------------
||||  | || |||||||| ||||| || ||||| ||||| ||| | |||||||| || ||||||||||||||  | ||||   | | |  | ||  | ||  ||  | || |   ||       | | |    |  |     |    |   |  || |   | || || ||||     ||                                     
GAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATAGgtaatttctgctcttcttttcttcatagttgttgttgattgttgttgttttcttcatagttgtcttttgttccttgttatagctggtagaaaattttcttttgtaagttaactgagttttttatatttctttcaacatag

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GLYMA15G04500.2 (Glycine max), 5'ss of exon 9
GAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGgta-tatacattcctcgtgttgt----atcttttctaagttaac--acgctctacgcttttatgtcggtccaatgtgtactagaagcgtaaaatatttaaacctggc----------
||||  | || |||||||| ||||| || || || ||||||||  | |||||||| |||||||||||||||||  |||||| | ||   || |  | |  |    || | ||||   ||     | |   ||  |  |   |    | |  ||| |  ||    | | |  | |||| |  |             
GAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGTTTGATTACCATAGGCAGCATGGAATTGgtaatttattgtctttttttccttataatttcttctcgttttgtttaaggcatatccaatagagatttttctttgttttttaactccttgaggtgtttatatatcctttcaacatag

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GLYMA12G06990.1 (Glycine max), 5'ss of exon 8
GAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGgtatatacattcctcgtgttgtatcttttctaagttaacacgctctacgcttttatgtcgg---tccaatgtgtactagaagcgtaaaatatttaaacctggc-------
||||  | || |||||||| ||||| || ||||| ||||| ||| | |||||||| || ||||||||||||||  | ||||  | | |  ||  | || | |   |  |    |    | |  |    |     || |    |    | |||| |  ||  |     | | ||   ||  |       
GAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATAGgtaatttcttctcttcttttttcttcatagttgtctgttgctccttgttataactggtagaaatttttctctgtaatttaactgagttttctatatttctttcaacatag

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: AT2G28760.1 (Arabidopsis thaliana), 5'ss of exon 6
GAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGgtatatacattcctcgtgttgtatcttttctaagttaacacgctctacgcttttatgtcggtccaatgtgtactagaagcgtaaaatatttaaacctggc
| || |||||||| ||||| || ||||| |||||||| ||||||||||||||||| ||||||||||| |||||  |||||| |   | ||    | ||     |||  | |   |    | | || |||| |  |  | |    | | ||||   |  ||       ||  |      
GTGTTAGAAGCTGTTATGATGAAGGAAAACGTGTTGCCGAGACTCTTATGTTTGATTACCATAGGCAACATGGGATTGgtaaaattaatcactcttttaccattttcttgaaa-actttgatttaagcttattggctgattagttat-tacttctattgtctggccattgtag-----

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 5'ss of exon 7
GAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGgta---tatacattc-----ctcgtgttgtatcttttctaagttaacacgctctacgcttttatgtcggtccaatgtgtactagaagcgtaaaatatttaaacctggc--
| || || ||||| ||||| || || |||||||||||||||||  | |||||||||||||| ||||| |||||  ||||||   |  |  |||     |||  | |  | ||||       |||   ||   |   | || |    ||||  | | | ||  ||  ||    | |||   | | |   
GTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTGgtaagttgcattttctcaggctctcgcttcaactttctccctgtaatttgcatcaacatattctcattgtcctttat-tccttaaattgtttt-tgtttcttctttgtag

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 5'ss of exon 8
GAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGgtatatacattcctcgtgttgtatcttttctaagttaacacgctctacgcttttatgtcggtccaatgtgtactagaagcgtaaaatatttaaacctggc
| ||  | ||||||||||| ||||| |||||||| ||||||||| | |||||||| || |||||||| |||||  | ||||  |       | ||||| | | ||||     | ||||  ||  |      ||||  | |  ||| |||| |           ||||||    | |  
GTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAGgtaact------tttgtgtttttttttttaatcctgaacaaacttca-atgaatatgaagttttaatatgta-tgttgtttctttatattttggacag--

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: Vv13s0019g00840.t01 (Vitis vinifera), 5'ss of exon 8
GAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGgtata--tacattcctcgtgttgtatcttttc------taagttaacacgctc-tacgcttttatgtcggtccaatgtgtactagaa-gcgtaaaat-atttaaacctggc---------------------------------------------------------------------------
|||| || || |||||||| ||||||||||| || ||||| ||||| |||||||| || || |||||||||||  | |||| |  |    |||   | |   |||  | |       |     |||| | |  ||      |  |     || |   |  | | | | |||||||  || |  ||   |                                                                           
GAGTCAGGAGTTGCTATGATGAGGGAAAGCGAGTGGCTGAAACTCTGATGTTTGATTATCACAGGCAGCATGGAATAGgtaaaattgggctccctctctctgatccatacacccaacacacagacacccccacacctacacacattcactcagtcactgatgggatgtgtaaaattgttcactcccttcccctccctctctctatctgaaactctactttccaatgcactctcactttattttgaaatggtgatcctataacag

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|208390897|gb|DC945914.1|DC945914
EST:     GCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTG                         AAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCG
genomic: GCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGgtatatacat ... gtggtggcagAAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCG
EST: gi|37850860|gb|BJ608868.1|BJ608868
EST:     GCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTG                         AAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCG
genomic: GCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGgtatatacat ... gtggtggcagAAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCG
EST: gi|67692844|gb|BJ953077.1|BJ953077
EST:     GCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTG                         AAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCG
genomic: GCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGgtatatacat ... gtggtggcagAAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCG
EST: gi|208360291|gb|DC943021.1|DC943021
EST:     GCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTG                         AAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCG
genomic: GCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGgtatatacat ... gtggtggcagAAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCG
EST: gi|67697660|gb|BJ957893.1|BJ957893
EST:     CTACCATAGGCAGCATGGNCGTTGA                         AAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATC
genomic: CTACCATAGGCAGCATGG-CGTTG-gtatatacat ... gtggtggcagAAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATC
EST: gi|67697660|gb|BJ957893.1|BJ957893
EST:     CTACCATAGGCAGCATGGNCGTTGA                         AAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATC
genomic: CTACCATAGGCAGCATGG-CGTTG-gtatatacat ... gtggtggcagAAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATC
EST: gi|208385608|gb|DC948967.1|DC948967
EST:     GCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTG                         AAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCG
genomic: GCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGgtatatacat ... gtggtggcagAAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCG
EST: gi|37843082|gb|BJ601090.1|BJ601090
EST:     GCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTG                         AAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCG
genomic: GCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGgtatatacat ... gtggtggcagAAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCG
EST: gi|208385977|gb|DC956493.1|DC956493
EST:     GCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTG                         AAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCG
genomic: GCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGgtatatacat ... gtggtggcagAAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCG
EST: gi|208371231|gb|DC956009.1|DC956009
EST:     GCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTG                         AAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCG
genomic: GCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGgtatatacat ... gtggtggcagAAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCG

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), 31 (downstream exon)
Score: 4

GAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGgtatatacat ... gtggtggcagAAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAG




<











<


<