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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caggaaaggtttctgttttaattattttttctagattaaaaatttggagatatgtctatgagcttggttgaatgtattactgaatcggtgcactatgcagGTAGCGCTAGCACATACAATTGGTCATGTGGCAGCGACAGTGAGCATGTCGAAGGTTGCAGTATCTTTCACACACATCATCAAAAGTTCTGAACCTGCAT

Basic information

species Physcomitrella patens
transcript PP1S241_24V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S241_24V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os08g08840.2 (Oryza sativa), 3'ss of exon 2
-caggaaaggtttctgttttaattattttttctagattaaaaatttggagatatgtctatgagcttggttgaatgtattactgaatcggtgcactatgcagGTAGCGCTAGCACATACAATTGGTCATGTGGCAGCGACAGTGAGCATGTCGAAGGTTGCAGTATCTTTCACACACATCATCAAAAGTTCTGAACCTGCAT
    |     | | | | ||    ||| ||| || |||       ||    |   |     ||| || |||| |       ||  |   | |  | || |||| ||  | || ||||||||||| ||||| || ||||||||||| ||||| || || ||||| || ||||||||||| ||||||||| | || |||||||
gtgagtggaatctttttcttggcaattatttgtatatttg----ctgtgcctgcttgggcaagcatgattgatt------ttggctattttccttttgaagGTTGCTGTGGCTCATACAATTGGGCATGTTGCTGCGACAGTGAGTATGTCAAAAGTAGCAGTGTCATTCACACACATTATCAAAAGTGCAGAGCCTGCAT

upper sequence: PP1S241_24V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G431314_T01 (Zea mays), 3'ss of exon 2
caggaaaggtttctgttttaattattttttctagattaaaaatttggagatatgtctatgagcttggttgaatgtattactgaatc----ggtgcact-atgcagGTAGCGCTAGCACATACAATTGGTCATGTGGCAGCGACAGTGAGCATGTCGAAGGTTGCAGTATCTTTCACACACATCATCAAAAGTTCTGAACCTGCAT
             ||  ||  ||||||  |     | |    | |     | | | ||    | |||   | ||||  |||||||     | |  ||| ||| |||| ||  | |||||||||||||| ||||| || ||||||||||||||||| ||||| ||||| || ||||||||||| || |||||| | ||||||||||
------------gtgagttgcttatttcgtgccagtaactcttcttttattttatataccttcctggaaaagtgta--actgaatttggtgattaactgatgaagGTTGCTGTGGCACATACAATTGGCCATGTTGCTGCGACAGTGAGCATGTCTAAGGTGGCAGTGTCATTCACACACATAATTAAAAGTGCAGAACCTGCAT

upper sequence: PP1S241_24V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 2
caggaaaggtttctgttttaattattttttctagattaaaaatttggagatatgtctatgagcttggttgaatgtattactgaatc----ggtgcact-atgcagGTAGCGCTAGCACATACAATTGGTCATGTGGCAGCGACAGTGAGCATGTCGAAGGTTGCAGTATCTTTCACACACATCATCAAAAGTTCTGAACCTGCAT
             ||  || |||||||| |     |  ||  | |     | | | ||   || |||   | ||||  |||||||     | |  ||| ||| |||| ||  | || ||||||||||| ||||| || || |||||||||||||| ||||| ||||| || ||||||||||| || |||||  | ||||||||||
------------gtgagttgattattttgtgccagt--aacttcttttattttatttacctgcctggaaaagtgta--actgaatttggtgattaactgatgaagGTTGCTGTGGCGCATACAATTGGCCATGTTGCTGCTACAGTGAGCATGTCTAAGGTGGCAGTGTCATTCACACACATAATTAAAAGCGCAGAACCTGCAT

upper sequence: PP1S241_24V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA02G25290.1 (Glycine max), 3'ss of exon 2
------caggaaaggtttctgttttaattattttttctagattaaaaatttggagatatgtctatgagcttggttgaatgtattactgaatcggtgcactatgcagGTAGCGCTAGCACATACAATTGGTCATGTGGCAGCGACAGTGAGCATGTCGAAGGTTGCAGTATCTTTCACACACATCATCAAAAGTTCTGAACCTGCAT
          ||| |||  || |  | |||    ||||   || |  ||      |||| | |    |  || | || | || |  |   |   |      | ||||| ||  | |||||||||||||| ||||| || || ||||| |||||||| || ||||| ||||| ||||||||||| ||||| |||  ||||||||| |
gttgtttcaaaaaagttattgatcaatttagccattctccttttattatc-----atatttttgaatggatgat-gactttagttttcgttttatttctccttcagGTTGCTGTTGCACATACAATTGGACATGTAGCGGCAACAGTTAGCATGTCAAAAGTTGCGGTATCATTCACACACATTATCAAGAGTGGTGAACCTGCTT

upper sequence: PP1S241_24V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA07G38830.1 (Glycine max), 3'ss of exon 1
caggaaaggtttctgttttaattattttttctag--attaaaaatttggagatatgtctatgagcttg-gttgaatgtattactgaatcggtgcactatgcagGTAGCGCTAGCACATACAATTGGTCATGTGGCAGCGACAGTGAGCATGTCGAAGGTTGCAGTATCTTTCACACACATCATCAAAAGTTCTGAACCTGCAT
   |  |   |  |      ||||     |  |   | | | |||    |   ||   | | |  | |   | ||||    | |  |    |      ||||||| ||| |   |||||||||||| ||||| ||||| || ||||| ||||| || |||||||| || || || ||||||||||| ||| | ||||||||||
---ggcaaaatagtaaagagattagggggtaaaagaaatcataatcgtcaagcattaatgtcaattagtactcaatggggaatttgaaactttgggagtgcagGTCGCGGTGTTACATACAATTGGGCATGTTGCAGCTACGGTGAGTATGTCCAAAGTTGCAGTTTCATTTACCCACATCATCAAGAGTGCAGAACCTGCAT

upper sequence: PP1S241_24V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA13G27680.1 (Glycine max), 3'ss of exon 1
caggaaaggtttctgttttaatta--ttttttctagattaaaaatttggagatat--gtctatgagcttggttgaatgtattactgaatcggtgcactatgcagGTAGCGCTAGCACATACAATTGGTCATGTGGCAGCGACAGTGAGCATGTCGAAGGTTGCAGTATCTTTCACACACATCATCAAAAGTTCTGAACCTGCAT
 | | || |  | | |  |  | |  |  |   |   ||  || |  ||| |  |   | ||  ||        || | | |    |||   |    | ||||||| ||| | ||||| |||||||| ||||| || || || ||||||||||| |||||||| || || ||||| ||||||||||| |||   || || || |
-aagtaacgcgtttatggtggtcaaatggtgggtgagtttgaagtaaggaaaggttgatttagtagtactcactaaagaaatttcaaattttt---ttgtgcagGTTGCGGTGGCACACACAATTGGGCATGTTGCTGCAACTGTGAGCATGTCCAAGGTTGCTGTTTCATTCACTCACATCATCAAGAGTGGAGAGCCAGCTT

upper sequence: PP1S241_24V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA15G11270.1 (Glycine max), 3'ss of exon 1
caggaaaggtttctgtt--ttaattattttttctagattaaaaatttggagatatgtctatgagcttggttgaatgtattactgaatcggtgcactatgcagGTAGCGCTAGCACATACAATTGGTCATGTGGCAGCGACAGTGAGCATGTCGAAGGTTGCAGTATCTTTCACACACATCATCAAAAGTTCTGAACCTGCAT
    |    ||| || |  | || |  | |   |   ||  || |  ||| |  |   | ||||      | | |  |  | |       |  | | ||||||| ||| | ||||| |||||||| ||||| || || || ||||||||||| |||||||| || || ||||| ||||||||||| |||   || || || |
-gcaatgcatttatggtggtcaaatggtgtgagtgagtttgaagtaaggaaaggttgat-tgagtagtactcacttgagaaatttcaaattttattgtgcagGTTGCGGTGGCACACACAATTGGGCATGTTGCTGCAACTGTGAGCATGTCCAAGGTTGCTGTTTCATTCACTCACATCATCAAGAGTGGAGAGCCAGCTT

upper sequence: PP1S241_24V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA17G01890.1 (Glycine max), 3'ss of exon 1
caggaaaggtttctgttttaattattttttctagatta-aaaatttggagatatgtctatgagcttggttgaatgtattactgaatcggtgcactatgcagGTAGCGCTAGCACATACAATTGGTCATGTGGCAGCGACAGTGAGCATGTCGAAGGTTGCAGTATCTTTCACACACATCATCAAAAGTTCTGAACCTGCAT
 |  |||   |   |   | |     |     | |||| || | |   | ||   |||       |  ||    | |    ||||    ||     ||||||| ||| |   |||||||||||| ||||| ||||| || ||||| ||||| || |||||||| || || || ||||||||||| ||| | || |||||||
tacaaaatagtgaagagattagggggtaaaagaaattataatagtcaaacattaatctcaattaatacttattgggaaatttgaaattttggga-gtgcagGTTGCGGTGTTACATACAATTGGGCATGTTGCAGCTACCGTGAGTATGTCCAAAGTTGCAGTTTCATTTACCCACATCATCAAGAGTGCAGAGCCTGCAT

upper sequence: PP1S241_24V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT5G54800.1 (Arabidopsis thaliana), 3'ss of exon 1
-caggaaaggtttctgttttaattattttttctagattaaaaatttggagatatgtctatgagcttg-gttgaatgtattactgaatcggtgcactatgcagGTAGCGCTAGCACATACAATTGGTCATGTGGCAGCGACAGTGAGCATGTCGAAGGTTGCAGTATCTTTCACACACATCATCAAAAGTTCTGAACCTGCAT
   |  |   | |   || || |  ||  |||||| |||||   ||| |  | |   |||    |||   |||| ||  |  |   | |     | ||  |||| ||  | ||||| ||||||||||||||||| || || ||||| ||||| |||||||| || |||||||| ||||||||||| |||  ||||||||| |
cttgtcattatatagcttctagtatttcattctagtttaaagtattgaactttttgatattttgttgtactgaaagtggt-ttatgttgaattgc-atatagGTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCAAAGGTTGCTGTTTCTTTCACTCACATCATCAAGAGTGGTGAACCTGCGT

upper sequence: PP1S241_24V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT1G61800.1 (Arabidopsis thaliana), 3'ss of exon 1
caggaaaggtttctgttttaattattt-tttctagattaaaaatttggagatatgtctatgagcttggttgaatgtattactgaatcggtgcactatgcagGTAGCGCTAGCACATACAATTGGTCATGTGGCAGCGACAGTGAGCATGTCGAAGGTTGCAGTATCTTTCACACACATCATCAAAAGTTCTGAACCTGCAT
      | |||  || || |   |||| |   |   ||     | ||   ||       || | || | |  ||||     |   |   |   ||    |||| ||  ||||||| || || || || || ||||| |||||||| ||||| || || ||||| || |||||||||||||| ||||||  |||||| || |
ttcatgatgttgttgcttgatggatttataattttgtttgttgtctgataatgaaagagtgtgttttgatcgatgttcccgttttttcttattcttca-agGTCGCTGTAGCACACACGATAGGACACGTTGCAGCAACAGTGAGTATGTCAAAAGTAGCAGTTTCCTTCACACACATCATTAAAAGTGGTGAACCAGCTT

upper sequence: PP1S241_24V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv10s0116g00760.t01 (Vitis vinifera), 3'ss of exon 1
---caggaaaggtttctgttttaattattttttctagattaaaaatttggagatatgtctatgagcttggttgaatgtattactgaatcggtgc-actatgcagGTAGCGCTAGCACATACAATTGGTCATGTGGCAGCGACAGTGAGCATGTCGAAGGTTGCAGTATCTTTCACACACATCATCAAAAGTTCTGAACCTGCAT
   | ||    |  |   ||| || |  || |  |       || |||      |     |  |    | || | | || |  ||||| | |     | || |||| ||  |||| ||||||||||||||||| ||||| || || |||||||| || |||||||| || ||||| ||||||||||| |||  ||| ||||| |
gttctggttttgcctaaatttaaaattcttgtctttttcctgaagtttttccgcagacaaacaaa---gctttagtttaat-ttgaatggcttttgttgtgtagGTTGCAGTAGCTCATACAATTGGTCATGTAGCAGCAACTGTTAGCATGTCAAAAGTTGCAGTTTCCTTCACCCACATCATCAAGAGTGGTGAGCCTGCTT

upper sequence: PP1S241_24V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv19s0177g00300.t01 (Vitis vinifera), 3'ss of exon 1
-caggaaaggtttctgttttaattattttttctagattaaaaatttggagatatgtctatgagcttggttg--aatgtattactgaatcggt---gcactatgcagGTAGCGCTAGCACATACAATTGGTCATGTGGCAGCGACAGTGAGCATGTCGAAGGTTGCAGTATCTTTCACACACATCATCAAAAGTTCTGAACCTGCAT
  |      ||| || ||  |||   ||    ||| ||     | | |  |       | ||||| | |||  ||| ||| |   |   | |       | || |||| ||  | || ||||||||||| |||||||| || |||||||| ||||| |||||||| || ||||| || ||||| ||||| |||  ||| |||||||
taaattggagttgcttttaaaatggattcccttagttt-----tctcggcagccaaaca-gagctggattgtgaatttataatcaatctgattttatgttttgtagGTTGCTGTGGCTCATACAATTGGGCATGTGGCTGCAACAGTGAGTATGTCCAAGGTTGCGGTGTCTTTTACTCACATAATCAAGAGTGGTGAGCCTGCAT

upper sequence: PP1S241_24V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ15098 (Selaginella moellendorffii), 3'ss of exon 1
caggaaaggtttctgttttaattattttttctagattaaaaatttggagatatgtctatgagcttggttgaatgtattactgaatcggtgcactatgcagGTAGCGCTAGCACATACAATTGGTCATGTGGCAGCGACAGTGAGCATGTCGAAGGTTGCAGTATCTTTCACACACATCATCAAAAGTTCTGAACCTGCAT
                                    |||    | |   ||   |   | | |  |    ||   ||  ||     | |   || | ||||||||  | || ||||| |||||||| || |||||||| ||||||||||| ||||| || || || ||||| ||||| ||||| || || ||||| ||||
-----------------------------------gtaagctctcgctcatgcttggctaaacgagaaataaca-atctctattgtgttctcctgtacagGTAGCCTTGGCCCATACCATTGGTCACGTAGCAGCGACGGTGAGCATGTCCAAGGTGGCTGTCTCCTTCACGCACATTATCAAGAGCTCGGAACCGGCAT

upper sequence: PP1S241_24V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ37591 (Selaginella moellendorffii), 3'ss of exon 1
caggaaaggtttctgttttaattattttttctagattaaaaatttggagatatgtctatgagcttggttgaatgtattactgaatcggtgcac-tatgcagGTAGCGCTAGCACATACAATTGGTCATGTGGCAGCGACAGTGAGCATGTCGAAGGTTGCAGTATCTTTCACACACATCATCAAAAGTTCTGAACCTGCAT
                                       ||  |       |||  ||       |    |    | |    | |  |||| | | | ||||||||  | || ||||| |||||||| || |||||||| ||||||||||| ||||| || || || ||||| ||||| ||||| || || ||||| ||||
-------------------------------------gtaagctctcgctcatgcttagctaaacgagaaataacaatctctattgtgtgctcctgtacagGTAGCTTTGGCCCATACCATTGGTCACGTAGCAGCGACGGTGAGCATGTCCAAGGTGGCTGTCTCCTTCACGCACATTATCAAGAGCTCGGAACCGGCAT

upper sequence: PP1S241_24V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ37594 (Selaginella moellendorffii), 3'ss of exon 1
caggaaaggtttctgttttaattattttttctagattaaaaatttggagatatgtctatgagcttggttgaatgtattactgaatcggtgcactatgcagGTAGCGCTAGCACATACAATTGGTCATGTGGCAGCGACAGTGAGCATGTCGAAGGTTGCAGTATCTTTCACACACATCATCAAAAGTTCTGAACCTGCAT
                                           |  |   |    ||  |||||   |||| | |    || || |   | ||     |||| ||||| || ||||| |||||||| || || || || ||||||||||| |||||||| || || ||||| ||||||||||| ||  | || || || |
------------------------------------------gtaagtcctccacctgcgagctc--ttgacttt-ccgctaaaaccacgaac-----agGTTGCGCTGGCTCATACCATTGGTCACGTTGCCGCCACGGTGAGCATGTCCAAGGTTGCCGTCTCCTTCACTCACATCATCAAGAGCGCGGAGCCAGCCT

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|162156508|gb|FC332116.1|FC332116
EST:     TTGTGGATCCACCTGAGGTGGATGCAGACTTCTGGAAGAGCCTTGCCCCG                         GTAGCGCTAGCACATACAATTGGTCATGTGGCAGCGACAGTGAGCATGTCG
genomic: TTGTGGATCCACCTGAGGTGGATGCAGACTTCTGGAAGAGCCTTGCCCCGgtatgcgcta ... cactatgcagGTAGCGCTAGCACATACAATTGGTCATGTGGCAGCGACAGTGAGCATGTCG
EST: gi|162187919|gb|FC364909.1|FC364909
EST:     TTGTGGATCCACCTGAGGTGGATGCAGACTTCTGGAAGAGCCTTGCCCCG                         GTAGCGCTAGCACATACAATTGGTCATGTGGCAGCGACAGTGAGCATGTCG
genomic: TTGTGGATCCACCTGAGGTGGATGCAGACTTCTGGAAGAGCCTTGCCCCGgtatgcgcta ... cactatgcagGTAGCGCTAGCACATACAATTGGTCATGTGGCAGCGACAGTGAGCATGTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagatatgtctatgagcttggttgaatgtattactgaatcggtgcactatgcagGTAGCGCTAGCACATACAATTGGTCATGTGGCAGCGACAGTGAGCATGTCGAAGGTTGCAGTATCTTTCACACACATCATCAAAAGTTCTGAACCTGCAT
                         aatgtatta  TA-rich tract