Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgtaatatgtagcatatcgcatttcaacgtcttgctacctccgtgtggatgccacattataagtctgacagtttcgtctaaattgtgattgtttgtagATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTTGAGTGCGGAAACTACTCGGGTGCATCCGACTACCTGTATGAGTATCGCG

Basic information

species Physcomitrella patens
transcript PP1S363_21V6.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S363_21V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os07g32040.1 (Oryza sativa), 3'ss of exon 1
--attgtaatatgtagcatatcgcatttcaacgtct-tgctacctccgtgtggatg---ccacattataagtctgacagtttcgtc---taaattgtgatt--gtttgtagATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTTGAGTGCGGAAACTACTCGGGTGCATCCGACTACCTGTATGAGTATCGCG
   || |  |  |     ||      |||  ||||| |   | | || ||   ||    ||| | ||  | ||  |    ||| |    ||| |   |||    | || |||| ||| |||| || ||||||||||||||||||||||||||||| ||||| || ||||| |||||| | | |||  | ||  || || ||   || || |
gttttctcttccgctagctagatttgttcttcgtctatataatcgccatgattatatatccatagtaataatcgtatgcgttcttggggtaattaacgatgtgatatgcagATTGGTCCTGATCAGATCGAGGCTCTGTATCAGTATGCCAAGTTTCAGTTCGACTGCGGGAACTACCCAGATGCTGCTGAAAACTTGCATCGATACCGTG

upper sequence: PP1S363_21V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os07g12110.1 (Oryza sativa), 3'ss of exon 1
attgtaatatgtagcatatcgcatttcaacgtcttgctacctccgtgt-ggatgccacattataagtctgacagtttcgtctaaattgtgattgtt-tgtagATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTTGAGTGCGGAAACTACTCGGGTGCATCCGACTACCTGTATGAGTATCGCG
 |||| |     |   | |   | |       | ||||   | | | | | |||      |   |  |  ||    |  || || |  || |  |  || |||| ||| ||||||| || ||| |||||||||||| ||||||||| |||||||| ||||| || ||||| | |||  | | |||| ||||| | || || |
gttgttaccatgattttgtta-agtcggttagcatgctgtatacttattgcatgtttttgtgcga-cccaactaaataatcaaactcctgttaatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTTGACTGCGGTAATTACTCAGATGCTGCTGTCTACTTGTATCAATACCGTG

upper sequence: PP1S363_21V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G107893_T01 (Zea mays), 3'ss of exon 4
attgtaat--atgtagcatatcgcatttcaacgtcttgctacctccgtgtggatgccacattataagtctgacagtttcgtctaaattgtgattgtt--tgtagATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTTGAGTGCGGAAACTACTCGGGTGCATCCGACTACCTGTATGAGTATCGCG
 |   |||  |  | | |  | | |  |   | | ||  ||   |  |  |  ||     | |||| |   |  |  | |   ||    || ||     || |||||||| |||| || || || |||||||||||||||||||| || ||||||||||| || |||||||| || ||  | || ||||| ||  ||||| | |
-tcaaaattcagatggaacgttgaagctgtgcatttt--tattgctata-gcttgttttgtgataattgctaatgaattgatcaatccttgtttaccaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATGGTG

upper sequence: PP1S363_21V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G151549_T02 (Zea mays), 3'ss of exon 1
attgtaat--atgtagcatatcgcatttcaacgtcttgctacctccgtgtggatgccacattataagtctgacagtttcgtctaaattgtgattgtt--tgtagATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTTGAGTGCGGAAACTACTCGGGTGCATCCGACTACCTGTATGAGTATCGCG
     |||  |  |   |  | | |  |   | | ||  ||   |  |  |  ||     | |||| |   |  |  | |   ||    || ||     || |||||||| |||| || || || |||||||||||||||||||| || ||||||||||| || |||||||| || ||  | || ||||| ||  ||||||| |
--caaaattcagatgaaacgttgaagctgtgcatttt-ttattgctata-gcttgttttgtgataaatgctaatgaattgatcaatccttgtttaccaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATCGTG

upper sequence: PP1S363_21V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G132144_T01 (Zea mays), 3'ss of exon 5
attgtaatatgtagcatatcgcatttcaacgtcttgctacctccgtgtggatgccacattataagtctgacagtttcgtctaaattgtgattgtt--tgtagATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTTGAGTGCGGAAACTACTCGGGTGCATCCGACTACCTGTATGAGTATCGCG
 |   |||    |  | |        |  ||  ||  ||   |  |  |  ||     | |||| |   |  |  | |   ||    || ||     || |||||||| |||| || || || |||||||||||||||||||| || ||||||||||| || |||||||| || ||  | || ||||| ||  ||||||| |
-tcaaaattcagatgaaacgttgaagctgcgcatttttattgctata-gcttgttttgtgataaatgctaatgaattgatcaatccttgtttaccaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATCGTG

upper sequence: PP1S363_21V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G038028_T01 (Zea mays), 3'ss of exon 6
attgtaatatgtagcatatcgcatttcaacgtcttgctacctccgtgtggatgccacattataagtctgacagtttcgtctaaattgtgattgtt--tgtagATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTTGAGTGCGGAAACTACTCGGGTGCATCCGACTACCTGTATGAGTATCGCG
 |   |||    |  | |        |   |  ||  ||   |  |  |  ||     | |||| |   |  |  | |   ||    || ||     || |||||||| |||| || || || |||||||||||||||||||| || ||||||||||| || |||||||| || ||  | || ||||| ||  ||||| | |
-tcaaaattcagatgaaacgttgaagctgtgcatttttattgctata-gcttgttttgtgataaatgctaatgaattgatcaatccttgtttaccaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATGGTG

upper sequence: PP1S363_21V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G105461_T01 (Zea mays), 3'ss of exon 2
attgtaatatgtagcatatcgcatttcaacgtcttgctacctccgtgtggatgccacattataagtctgacagtttcgtctaaattgtgat-tgtttgtagATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTTGAGTGCGGAAACTACTCGGGTGCATCCGACTACCTGTATGAGTATCGCG---------------
            ||    || ||| |||  |||         |  |  | ||    |    |  ||      ||||  ||||  || | || |  || || |      |        | || |||||||||||||||||||| || ||||||||||| || |||||||| || ||  | || ||||| ||  ||||| | |               
-------ggcacagatagtctcatctcatagtcagatccagcctctccgaatctggccaggtgtgttc--tggtttgctctatttttttatatacttatataatatagcC-------TTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATGGTGCTTTGTGCACAAACA

upper sequence: PP1S363_21V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G038313_T01 (Zea mays), 3'ss of exon 1
attgtaatatgtagcatatcgcatttcaacgtcttgctacctccgtgtggatgccacattataagtctgacagtttcgt-ctaaattgtgattg---tttgtagATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTTGAGTGCGGAAACTACTCGGGTGCATCCGACTACCTGTATGAGTATCGCG
     |  |     || || | || |  | |   |||    |   |||    ||| | || |  |    |   |  ||  ||||||  |  ||      || |||| ||| |||| || || || |||||||||||||||||||| || ||||||||||| || ||||||||  | ||  | || ||||||||  ||||||| |
---agatcaaaattcagatggaatgttgaagctgtgcacttttattgttatagcctc-ttctgtgctaaatgctaacgaactaaatccttgtttaacaatgcagATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCCTGGGCTGCTGAGTACCTGTACCAGTATCGTG

upper sequence: PP1S363_21V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G094083_T01 (Zea mays), 3'ss of exon 8
attgtaatatgtagcatatcgcatttcaacgtcttgctacctccgtgtggatgccacattataagtctgacagtttcgtctaaattgtgattgtt--tgtagATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTTGAGTGCGGAAACTACTCGGGTGCATCCGACTACCTGTATGAGTATCGCG
 |   |||    |  | |        |   |  ||  ||   |  |  |  ||     | |||| |   |  |  | |   ||    || ||     || ||||||||  ||| || || || |||||||||||||||||| | || ||||||||||| || |||||||| || ||  | || ||||| ||  ||||| | |
-tcaaaattcagatgaaacgttgaagctgtgcatttttattgctata-gcttgttttgtgataaatgctaatgaattgatcaatccttgtttaccaatgcagATCGGTCTTGACCAGATTGAAGCTCTGTATCAGTATGCCCAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATGGTG

upper sequence: PP1S363_21V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G156333_T01 (Zea mays), 3'ss of exon 4
attgtaatatgtagcatatcgcatttcaacgtcttgctacctccgtgtggatgccacattataagtctgacagtttcgtctaaattgtgattgtt--tgtagATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTTGAGTGCGGAAACTACTCGGGTGCATCCGACTACCTGTATGAGTATCGCG
 |   |||    |  | |        |   |  ||  ||   |  |  |  ||     | |||| |   |  |  | |   ||    || ||     || |||| | | |||| || || || | | |||||||||||||||| || ||||||||||| || |||||||| || ||    || ||||| ||  ||||||| |
-tcaaaattcagatgaaacgttgaagctgtgcatttttattgctata-gcttgttttgtgataaatgctaatgaattgatcaatccttgtttaccaatgcagATAGTTCCTGACCAGATTGAAGTTGTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGTTGATTACCTTTACCAGTATCGTG

upper sequence: PP1S363_21V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA10G16090.1 (Glycine max), 3'ss of exon 2
--attgtaatatgtagcatatcgcatttcaacgtcttgctacctccgtgtggatgccacattataagtctgacagtttcgtctaaattgtgattgttt----gtagATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTTGAGTGCGGAAACTACTCGGGTGCATCCGACTACCTGTATGAGTATCGCG
   || || |   |   | |      ||| || | |||  |     || || ||       ||| ||||           | ||||   ||||| |        |||| ||| |||  || || || ||  |||| || |||||||| |||||||||||||| ||||||||||| |||||  | ||||| || ||| ||||  | |
ctgttttagtggttttaaaagaattattctac-ttttggaa-----gtttgaattttgtggtatgagtcctgtctgactatgtaaacaatgattctgctgaaacagATTGGTCCTGCACAGATAGAAGCGTTGTACCAATATGCCAAATTCCAGTTTGAGTGTGGAAACTACTCTGGTGCTGCTGACTATCTTTATCAGTACAGAG

upper sequence: PP1S363_21V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA02G33770.1 (Glycine max), 3'ss of exon 2
attgtaatatgtagcatatcgcatttcaacgtcttgctacctccgtgtggatgccacattataa-gtctgacagtttcgtctaaattgtgattgt----ttgtagATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTTGAGTGCGGAAACTACTCGGGTGCATCCGACTACCTGTATGAGTATCGCG
  ||   ||| |   |  |   |    ||  || | |||  |  | |  | ||  |  || |    | |||       || |||||   |||| |    |   |||| ||| |||  || ||||| ||  |||| || ||| |||| |||||||||||||| ||||||||||| |||||  | ||||| || ||| | ||  | |
--tgctgtattttagaggttttaaaagaa--tcatcctagttttgagaagttga-attttgtggtatttgagttcactgtgtaaatgaggattctgctgtaacagATTGGTCCTGCACAGATCGAAGCATTGTACCAATATTCCAAATTCCAGTTTGAGTGTGGAAACTACTCTGGTGCTGCTGACTATCTTTATCAATACAGAG

upper sequence: PP1S363_21V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv00s0252g00070.t01 (Vitis vinifera), 3'ss of exon 2
attgtaatatgtagcatatcgcatt-tcaacgtcttgctacctccgtgtggatgccacattataagtctgacagtttcgtctaaattgtgattgttt---gtagATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTTGAGTGCGGAAACTACTCGGGTGCATCCGACTACCTGTATGAGTATCGCG
    |  | | |    | | | ||| |       |||  |      |  |  |       |||  | || |||   |  | |   || |   | ||      |||| ||    ||||| || |||||  | |||||||||||||| || |||||||| || ||||||||||| |||||  | || ||||||||| ||||  | |
----tcctgtttttgttgttgtattgttgctaatttgacagaattctaggtttttgggtctatttggcttacaaaattatatcccttttttcttttctgaccagATTGGCCAGGAGCAGATAGAGGCATTATATCAGTATGCCAAATTTCAGTTTGAATGTGGAAACTACTCTGGTGCTGCTGATTACCTGTATCAGTACAGGG

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|100384564|gb|BY987423.1|BY987423
EST:     TACGGTCTGATAAGCAGTACAACCTCCAAATGTTGCAAGAACGGTACCAG                         ATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTT
genomic: TACGGTCTGATAAGCAGTACAACCTCCAAATGTTGCAAGAACGGTACCAGgttagctatt ... ttgtttgtagATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTT
EST: gi|100375987|gb|BY968260.1|BY968260
EST:     CGGTCTGATAAGCAGTACAACCTCCAAAAATGT-GCA-GAACGGTACCAG                         ATNCG-TTCTGAGNCAA-TCGAGGCTCTGTATCAGTATGC-AAGTTCCAGT
genomic: CGGTCTGATAAGCAGTACAACCTCCAAA--TGTTGCAAGAACGGTACCAGgttagctatt ... ttgtttgtagAT-CGGTTCTGAG-CAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGT
EST: gi|18358262|gb|BJ190321.1|BJ190321
EST:     TACGGTCTGATAAGCAGTACAACCTCCAAATGTTGCAAGAACGGTACCAG                         ATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTT
genomic: TACGGTCTGATAAGCAGTACAACCTCCAAATGTTGCAAGAACGGTACCAGgttagctatt ... ttgtttgtagATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTT
EST: gi|100389405|gb|BY988883.1|BY988883
EST:     TACGGTCTGATAAGCAGTACAACCTCCAAATGTTGCAAGAACGGTACCAG                         ATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTT
genomic: TACGGTCTGATAAGCAGTACAACCTCCAAATGTTGCAAGAACGGTACCAGgttagctatt ... ttgtttgtagATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTT
EST: gi|18329284|gb|BJ161290.1|BJ161290
EST:     TACGGTCTGATAAGCAGTACAACCTCCAAATGTTGCAAGAACGGTACCAG                         ATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGT
genomic: TACGGTCTGATAAGCAGTACAACCTCCAAATGTTGCAAGAACGGTACCAGgttagctatt ... ttgtttgtagATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGT
EST: gi|19781185|gb|BQ039664.1|BQ039664
EST:     TACGGTCTGATAAGCAGTACAACCTCCAAATGTTGCAAGAACGGTACCAG                         ATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTT
genomic: TACGGTCTGATAAGCAGTACAACCTCCAAATGTTGCAAGAACGGTACCAGgttagctatt ... ttgtttgtagATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTT
EST: gi|67568984|gb|BJ941808.1|BJ941808
EST:     TACGGTCTGATAAGCAGTACAACCTCCAAATGTTGCAAGAACGGTACCAG                         ATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTT
genomic: TACGGTCTGATAAGCAGTACAACCTCCAAATGTTGCAAGAACGGTACCAGgttagctatt ... ttgtttgtagATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTT
EST: gi|100404357|gb|BY973536.1|BY973536
EST:     TACGGTCTGATAAGCAGTACAACCTCCAAATGTTGCAAGAACGGTACCAG                         ATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTT
genomic: TACGGTCTGATAAGCAGTACAACCTCCAAATGTTGCAAGAACGGTACCAGgttagctatt ... ttgtttgtagATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTT
EST: gi|67709902|gb|BJ965718.1|BJ965718
EST:     TACGGTCTGATAAGCAGTACAACCTCCAAATGTTGCAAGAACGGTACCAG                         ATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTT
genomic: TACGGTCTGATAAGCAGTACAACCTCCAAATGTTGCAAGAACGGTACCAGgttagctatt ... ttgtttgtagATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtggatgccacattataagtctgacagtttcgtctaaattgtgattgtttgtagATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTTGAGTGCGGAAACTACTCGGGTGCATCCGACTACCTGTATGAGTATCGCG
                                gtctaaa  putative branch site (score: 3)
          acattataa  TA-rich tract