Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattttgctcatttttatcttttccttctctctctctctcgtttttgttttgttttgttttgtttatttacttaactctttatttttgctatgggtgcagATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAATCGAGCGGATACTCTTGACCCCGCTTTACTGCGACCTGGACGACTCGATC

Basic information

species Physcomitrella patens
transcript PP1S79_171V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S79_171V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 3
--aattttgctcatttttatcttttccttctctctctctctcgtttttgt-tttgttttgttttgtttatttacttaactctttatttttgctat-gggtgcagATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAATCGAGCGGATACTCTTGACCCCGCTTTACTGCGACCTGGACGACTCGATC
     ||| | ||     || || ||        | | |    ||  | |  |||     |   || | | |    |  | ||| |||    | | |  ||||||||||||| || ||||||||||| ||||| ||||| || ||||| |||||  | |||||||| || ||||| ||| |  | || || ||  || | ||  
agggatttacacag----atattgtcgagaatattttatgaaattcctatgcttgaaggttgaagtatttctcaccatgtgtttttttaaaatgtcgaatgcagATGGATGGATTTGATCAAACAGTGAATGTGAAGGTTATAATGGCGACCAACAGGGCGGATACCCTAGACCCTGCTCTGTTACGTCCAGGTAGATTGGACA

upper sequence: PP1S79_171V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G090904_T01 (Zea mays), 3'ss of exon 3
aattttgctcatttttatcttt---tccttctctctctctctcgtttttgttttgt-tttgttttgtttatttacttaactctttatttttgctatgggtgcagATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAATCGAGCGGATACTCTTGACCCCGCTTTACTGCGACCTGGACGACTCGATC
    |  || |    || ||||      | || |   |  || | || |  ||  |  | ||||| |||||||  |        | |  ||  |   | ||||||||||||| || ||||||||||| ||||| ||||| || ||||| || ||||| || || ||||| || || |||||  |||| |||||  |||| ||  
----tctctaaaagctaactttgggaattcctatagtttcctagattataattcctactagttttttttatttcttattagtaatgtggttatttatgttgcagATGGATGGGTTTGATCAAACAGTCAATGTGAAGGTTATAATGGCAACTAATCGGGCAGACACTCTAGATCCTGCTTTGTTGCGTCCTGGTAGACTTGACA

upper sequence: PP1S79_171V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------------------------------aattttgctcatttttatcttttccttct-ctctctctctcgtttttgttttgttttg-ttttgtttatttacttaactctttattt------ttgctatggg-tgcagATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAATCGAGCGGATACTCTTGACCCCGCTTTACTGCGACCTGGACGACTCGATC
                                                                                      | || | |  | ||| ||||  |||    || | |   | |  |    ||   | || ||||   ||||| || || | ||  |||       || | |    | |||||||||||||| || |||||||||||||| || || |||||||| || ||  |||| || ||| | ||||| ||| |  |||| |||||| | || ||||
gtatctatgaaatgatatttatgttaggtgctgtgagtaggttgttactactattagtagttactaatttctgatgggctgctgtgaattagtttttgtttctcttaacctctagctatttggttgggctacacttccctatgattttagatattttctgaagtgttggtttaattacctgttcttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAACAGAGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATC

upper sequence: PP1S79_171V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 3
------------------------------------------------------------------------------------aattttgctcatttttatctttt-ccttct--ctctctctctcgtttttgttttgttttg-ttttgtttatttacttaactctttattt------ttgctatggg-tgcagATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAATCGAGCGGATACTCTTGACCCCGCTTTACTGCGACCTGGACGACTCGATC
                                                                                       || | |  | ||||||| || || |||  || | |   | |  |    ||   | || ||||   ||||  || || | ||  |||       || | |    | |||||||||||||| || |||||||||||||| || || |||||||| || ||  |||| || ||| | ||||| ||| |  |||| |||||| | || ||||
gtatctatgaaatgatatttctattaggtgctgtgagtatgttgttactactattagtagttactaatttctgctggctgctgtgtattagtttttgtttatctcttaccctctagctatttggttggactacacttctctatgattttagatattctctgaagtgttggtttaattacctgttcttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAACAGAGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATC

upper sequence: PP1S79_171V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ38338 (Selaginella moellendorffii), 3'ss of exon 3
aattttgctcatttttatcttttccttctctctctctctcgtttttgttttgttttgttttgtttatttacttaactctttatttttgctatgggtg-cagATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAATCGAGCGGATACTCTTGACCCCGCTTTACTGCGACCTGGACGACTCGATC
                                                     |           | |    |||  |  |    |   | ||  |  ||||||||||||||||||||||| || ||||| ||||| || ||||| || || || ||||| ||| | || |||||  |  |||| || ||| |||| ||  
----------------------------------------------------gtaaaaggaaccgagtagagtaagccgctgacgtccttgtgcttctcagATGGATGGTTTCGATCAAACCGTGAATGTGAAGGTTATCATGGCTACAAACCGTGCGGACACTTTGGATCCCGCGCTCTTGCGTCCGGGAAGACTTGACA

upper sequence: PP1S79_171V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ04233 (Selaginella moellendorffii), 3'ss of exon 3
aattttgctcatttttatcttttccttctctctctctctcgtttttgttttgttttgttttgtttatttacttaactctttatttttgctatgggtg-cagATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAATCGAGCGGATACTCTTGACCCCGCTTTACTGCGACCTGGACGACTCGATC
                                                     |           | |    |||  |  |    |   | ||  |  ||||||||||||||||||||||| || ||||| ||||| || ||||| || || || ||||| ||| | || |||||  |  |||| || ||| |||| ||  
----------------------------------------------------gtaaaaggaaccaagtagagtaagccgctgacgtccttgtgcttctcagATGGATGGTTTCGATCAAACCGTGAATGTGAAGGTTATCATGGCTACAAACCGTGCGGACACTTTGGATCCCGCGCTCTTGCGTCCGGGAAGACTTGACA

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|18339313|gb|BJ171340.1|BJ171340
EST:     CCGGAGCAGATAGGGAGGTTCAGCGTATCTTGATGGAGCTCTTGAACCAG                         ATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAAT
genomic: CCGGAGCAGATAGGGAGGTTCAGCGTATCTTGATGGAGCTCTTGAACCAGgtttgagaat ... atgggtgcagATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAAT
EST: gi|162254098|gb|FC429622.1|FC429622
EST:     CCGGAGCAGATAGGGAGGTTCAGCGTATCTTGATGGAGCTCTTGAACCAG                         ATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAAT
genomic: CCGGAGCAGATAGGGAGGTTCAGCGTATCTTGATGGAGCTCTTGAACCAGgtttgagaat ... atgggtgcagATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAAT
EST: gi|208380173|gb|DC927452.1|DC927452
EST:     CCGGAGCAGATAGGGAGGTTCAGCGTATCTTGATGGAGCTCTTGAACCAG                         ATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAAT
genomic: CCGGAGCAGATAGGGAGGTTCAGCGTATCTTGATGGAGCTCTTGAACCAGgtttgagaat ... atgggtgcagATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAAT
EST: gi|208383487|gb|DC923639.1|DC923639
EST:     CCGGAGCAGATAGGGAGGTTCAGCGTATCTTGATGGAGCTCCTGAACCAG                         ATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAAT
genomic: CCGGAGCAGATAGGGAGGTTCAGCGTATCTTGATGGAGCTCTTGAACCAGgtttgagaat ... atgggtgcagATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAAT
EST: gi|37838326|gb|BJ596334.1|BJ596334
EST:     CCGGAGCAGATAGGGAGGTTCAGCGTATCTTGATGGAGCTCTTGAACCAG                         ATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAAT
genomic: CCGGAGCAGATAGGGAGGTTCAGCGTATCTTGATGGAGCTCTTGAACCAGgtttgagaat ... atgggtgcagATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAAT
EST: gi|208385418|gb|DC953065.1|DC953065
EST:     CCGGAGCAGATANGGAGGTTCAGCGTATCTTGATGGAGCTCTTGANCCAG                         ATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAAT
genomic: CCGGAGCAGATAGGGAGGTTCAGCGTATCTTGATGGAGCTCTTGAACCAGgtttgagaat ... atgggtgcagATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAAT
EST: gi|18360609|gb|BJ192672.1|BJ192672
EST:     CGGAGCAGATAGGGGAGGTTCAGCGTATCTTGATGGAGCTCTTGAACCAG                         ATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAAT
genomic: CGGAGCAGATAGGG-AGGTTCAGCGTATCTTGATGGAGCTCTTGAACCAGgtttgagaat ... atgggtgcagATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAAT
EST: gi|37850846|gb|BJ608854.1|BJ608854
EST:     CCGGAGCAGATAGGGAGGTTCAGCGTATCTTGATGGAGCTCTTGAACCAG                         ATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAAT
genomic: CCGGAGCAGATAGGGAGGTTCAGCGTATCTTGATGGAGCTCTTGAACCAGgtttgagaat ... atgggtgcagATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAAT
EST: gi|208396378|gb|DC920058.1|DC920058
EST:     CCGGAGCAGATAGGGAGGTTCAGCGTATCTTGATGGAGCTCTTGAACCAG                         ATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAAT
genomic: CCGGAGCAGATAGGGAGGTTCAGCGTATCTTGATGGAGCTCTTGAACCAGgtttgagaat ... atgggtgcagATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAAT
EST: gi|18369533|gb|BJ201620.1|BJ201620
EST:     CCGGAGCAGATAGGGAGGTTCAGCGTATCTTGATGGAGCTCTTGAACCAG                         ATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAAT
genomic: CCGGAGCAGATAGGGAGGTTCAGCGTATCTTGATGGAGCTCTTGAACCAGgtttgagaat ... atgggtgcagATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAAT
EST: gi|67578343|gb|BJ950510.1|BJ950510
EST:     CCGGAGCAGATAGGGAGGTTCAGCGTATCTTGATGGAGCTCTTGAACCAG                         ATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAAT
genomic: CCGGAGCAGATAGGGAGGTTCAGCGTATCTTGATGGAGCTCTTGAACCAGgtttgagaat ... atgggtgcagATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAAT
EST: gi|37828181|gb|BJ586193.1|BJ586193
EST:     CCGGAGCAGATAGGGAGGTTCAGCGTATCTTGATGGAGCTCTTGAACCAG                         ATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAAT
genomic: CCGGAGCAGATAGGGAGGTTCAGCGTATCTTGATGGAGCTCTTGAACCAGgtttgagaat ... atgggtgcagATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAAT

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: 33 (upstream exon), 22 (downstream exon)
Score: 6

CTTCATTGATGAGATTGATGCAATTGCGACAGCTCGTTTTGATGCTCAAACCGGAGCAGATAGGGAGGTTCAGCGTATCTTGATGGAGCTCTTGAACCAGgtttgagaat ... atgggtgcagATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAATCGAGCGGATACTCTTGACCCCGCTTTACTGCGACCTGGACGACTCGATC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttgttttgttttgtttatttacttaactctttatttttgctatgggtgcagATGGATGGTTTCGATCAAACAGTTAATGTAAAGGTAATTATGGCCACCAATCGAGCGGATACTCTTGACCCCGCTTTACTGCGACCTGGACGACTCGATC
                        acttaac  putative branch site (score: 6)
       ttttgttttgtttatt  TA-rich tract