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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAGGTTTGCAAAACTATTGCTTGGTGAAGATATGTCAGGTGGGGGCAAAGGGGTTTGCACAGCGTTGGCTATATCGAATGCAATCACAAATTTGTCAGgtgaaaatcaaagctattaccgtaatggcaatagattgtttgttttcatgttgaaagcaagaatgattttcgcgttgtaaatattaatgtccagatttttgttcacag

Basic information

species Physcomitrella patens
transcript PP1S58_274V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S58_274V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA18G03610.1 (Glycine max), 5'ss of exon 1
GAGAGGTTTGCAAAACTATTGCTTGGTGAAGATATGTCAGGTGGGGGCAAAGGGGTTTGCACAGCGTTGGCTATATCGAATGCAATCACAAATTTGTCAGgtgaaaa-------tcaaagctattaccgtaa--tggcaat---------agattgtttgtttt---catgttgaaagcaagaatga-ttttcgcgttgtaaatattaatgtccagatttttgttcacag---------------------------------
||||||||||||||| | ||||||||||||||||||||||||   || |||||||||||||| || ||||| || || ||||| || || ||| |||  |||            |   ||  | |  | ||   |  | ||         | | |||||  |||    ||||||  |   ||    | |||| |  || |   |  |  | |  |  ||    || | |                                  
GAGAGGTTTGCAAAATTGTTGCTTGGTGAAGATATGTCAGGTTCTGGAAAAGGGGTTTGCACTGCTTTGGCCATCTCTAATGCCATTACTAATCTGTGCGgtatggtttctctcttgcaggcactgacataggctcacgatgtaattgagaaactgtttagtttgtctatgttggcaattagttcaaatttttgaattttctgttctggttttaaatttgagttttataacttattcaaatttggattatttgcaacgtgtag

upper sequence: PP1S58_274V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA11G34690.1 (Glycine max), 5'ss of exon 1
GAGAGGTTTGCAAAACTATTGCTTGGTGAAGATATGTCAGGTGGGGGCAAAGGGGTTTGCACAGCGTTGGCTATATCGAATGCAATCACAAATTTGTCAGgtg--------aaaatcaaagctattac-------cgtaatgg---caatagattgtttgtttt-catgttgaaagcaagaatgattttcgcgttgtaaatattaatgtccagatttttgttcacag-----------------------------------------
||||||||||||||| | ||||||||||||||||||||||||   || |||||||||||||| || ||||| || || ||||| || || ||| | |  |||         |   |  || |  || |       | | |||      | |   |||||  ||    |||  |       ||  | ||     || | ||| ||  ||| | | ||||   |   ||                                         
GAGAGGTTTGCAAAATTGTTGCTTGGTGAAGATATGTCAGGTTCTGGAAAAGGGGTTTGCACTGCTTTGGCCATTTCTAATGCCATTACTAATCTCTGCGgtatgctttccatcttgcaaacacttgcataggctcattatgtaattgagaagctgtttacttagtttgtctatgttggcaaatagttcaaaattttgaattttc-tgttctggttttaaatttgagttttataacttattcaagtttggattatttgcaacttgtag

upper sequence: PP1S58_274V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA01G26010.1 (Glycine max), 5'ss of exon 1
GAGAGGTTTGCAAAACTATTGCTTGGTGAAGATATGTCAGGTGGGGGCAAAGGGGTTTGCACAGCGTTGGCTATATCGAATGCAATCACAAATTTGTCAGgtgaaaatcaa--agctattaccgtaatggcaatagattgtttgttttcatgttgaaagcaagaatgattttcgcgttgtaaatattaatgtccagatttttgttcacag------------------
||||||||||||||| | || ||||| |||||||||||||||   || || || ||     |||| ||| || |||| ||||| ||||| ||| | |  ||||   | | |  |   | |  | | |||     || ||   | |  | |  || ||    |     ||| | || |  | |||  | |||| | |||| || |  | |                   
GAGAGGTTTGCAAAATTGTTACTTGGAGAAGATATGTCAGGTTCTGGAAATGGAGTCCCTGCAGCCTTGACTGTATCCAATGCCATCACTAATCTATGTGgtgtgtacccatgaaacagtttcttgatg----caggtttcatttagtgaattttaa--ttactgcaattcttgc-tcctgaat-ctgatgttctgattgttatcgaaacatttttctgaatctgtag

upper sequence: PP1S58_274V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA02G41980.1 (Glycine max), 5'ss of exon 2
GAGAGGTTTGCAAAACTATTGCTTGGTGAAGATATGTCAGGTGGGGGCAAAGGGGTTTGCACAGCGTTGGCTATATCGAATGCAATCACAAATTTGTCAGgtgaaaatcaaagctattac-cgtaatggcaatagattgtttgttttcatgttga-aagcaagaatgattttc-----gcgttgtaaatattaatgtc--cagatttttgttcacag-----------------------
|| |||||||||||| || ||||||| ||||||||||||||    || ||||| || ||||  || ||||| || || ||||| ||||| ||| | |  |||     |      ||  |   ||  ||  ||     |   | |||     |||  ||      |  ||||||       | ||| ||| |||||||    | | |  ||||   |                        
GAAAGGTTTGCAAAATTACTGCTTGGGGAAGATATGTCAGGATCTGGGAAAGGAGTGTGCAGTGCTTTGGCCATCTCTAATGCTATCACTAATCTCTGTGgtatgctttctttgtaacatatgttttgagaaagtggtacctttttctggattggcaaatttttaaaattttcctattatggtgtgaattttaatgtttttataataatgtttctaatttgaatttcatgcaacatgtag

upper sequence: PP1S58_274V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA07G16790.1 (Glycine max), 5'ss of exon 2
GAGAGGTTTGCAAAACTATTGCTTGGTGAAGATATGTCAGGTGGGGGCAAAGGGGTTTGCACAGCGTTGGCTATATCGAATGCAATCACAAATTTGTCAGgtg----------aaaatcaaagctattaccgtaatggcaatagattgtttgttttcat-gttgaaagcaagaatgattttcgcgttgtaaatattaatgtccagatttttgttcacag---------------------------
||||||||||||||| | || ||||| ||||||||||||||| | || || |||||    |||||  ||||||| || ||||| || || ||| | |  |||           | |||  ||||  |||| ||  |   | | | || ||| |||| ||   |    |||||  || || | | |   |  | | |  | | |     | || |                                
GAGAGGTTTGCAAAATTGTTACTTGGAGAAGATATGTCAGGTTGCGGAAATGGGGTCACTACAGCCCTGGCTATTTCAAATGCCATAACCAATCTATGTGgtatgcaaaatgcacaattgaagcagttactgtgtttttatttggttttttctttttattaattggtgcaagt-tggttgtggtgaattttagagtgctattcttgcctgtgattgtgatggctctttcctttgctgaatatgtag

upper sequence: PP1S58_274V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA18G41330.1 (Glycine max), 5'ss of exon 2
GAGAGGTTTGCAAAACTATTGCTTGGTGAAGATATGTCAGGTGGGGGCAAAGGGGTTTGCACAGCGTTGGCTATATCGAATGCAATCACAAATTTGTCAGgtg---aaaat-------caaagctattaccgtaatggcaata--gattgtttgttttcatg--ttgaaagcaagaatgattttcgcgttgtaaatattaatgtccagatttttg-----ttcacag
||||||||||||||| | || ||||| ||||||||||||||| | || || |||||    ||||| |||||||| || ||||| || || ||| | |  |||    |||||         ||||  |||| ||  |   | |    |||  ||| | |  ||  ||  |  ||      ||| | |  || | | | ||  ||| ||  | ||||     ||  |||
GAGAGGTTTGCAAAATTGTTACTTGGAGAAGATATGTCAGGTTGTGGAAATGGGGTCGCTACAGCCTTGGCTATCTCAAATGCCATAACCAATCTATGTGgtatgcaaaatgcacacttgaagcagttactgtgtttttattttttattaattggtgtggtgaattttattcatttgctattcttgactt-tgattgttgttgttcatttctttgctgaatttgcag

upper sequence: PP1S58_274V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv13s0019g02710.t01 (Vitis vinifera), 5'ss of exon 2
GAGAGGTTTGCAAAACTATTGCTTGGTGAAGATATGTCAGGTGGGGGCAAAGGGGTTTGCACAGCGTTGGCTATATCGAATGCAATCACAAATTTGTCAGgtgaaaatcaaagctattaccgtaa-----tggcaatagattgtttg---ttttcatgttgaaagcaagaatgattttcgcgttgtaaatattaatgtccagatttttgttcacag
||||||||| | ||||| |||||||||||||| ||||||||    || ||||||||||| ||||| ||||| || || ||||| ||||| ||| | |  ||||    |     || | |   |||     ||    |   ||  ||    ||||  | |||        | ||   |||   |  |    |||| |  |||   | |  |  | ||
GAGAGGTTTTCGAAACTGTTGCTTGGTGAAGACATGTCAGGGTCTGGAAAAGGGGTTTGTACAGCTTTGGCCATTTCAAATGCTATCACCAATCTTTGCGgtgtgttttctctctctcattctaaggctttgtttttcagttaattagtcttttttttttggctttttaattgcaattcatttcatttccattatt--cca---tgtcatctatag

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|162161816|gb|FC337931.1|FC337931
EST:     AGGGGTTTGCACAGCGTTGGCTATATCGAATGCAATCACAAATTTGTCAG                         CGTCAGTGTTTGGAGAGCTATGGAGGCTAGAACCACTCCCTATGAAGCGGC
genomic: AGGGGTTTGCACAGCGTTGGCTATATCGAATGCAATCACAAATTTGTCAGgtgaaaatca ... ttgttcacagCGTCAGTGTTTGGAGAGCTATGGAGGCTAGAACCACTCCCTATGAAGCGGC




















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: 28 (upstream exon), 13 (downstream exon)
Score: 2

GAGAGGTTTGCAAAACTATTGCTTGGTGAAGATATGTCAGGTGGGGGCAAAGGGGTTTGCACAGCGTTGGCTATATCGAATGCAATCACAAATTTGTCAGgtgaaaatca ... ttgttcacagCGTCAGTGTTTGGAGAGCTATGGAGGCTAGAACCACTCCCTATGAAGCGGCAGACCATGTGGAGACGAGAGATGGAGTGGATGCTTTCAGTTACTGACCA




<











<


<