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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gccaccactgtgtcactgttgggaaagtgagacgatgtgcagtgaatcattttgtacagttgtgaaaccgcgttccttgactacgatgttgttggcgcagGCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTATGGGTGTCATGCGACCTGAGCTAGTGATGAAGTCCATCGTCCCAGTGGT

Basic information

species Physcomitrella patens
transcript PP1S2_120V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S2_120V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os05g01560.1 (Oryza sativa), 3'ss of exon 1
gccaccactgtgtcactgttgggaaagtgagacgatgtgcagtgaatcattttgtacagttgtgaaaccgcgttccttgactacgatgttgttggcgca------------gGCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTATGGGTGTCATGCGACCTGAGCTAGTGATGAAGTCCATCGTCCCAGTGGT
                                   |  ||    |||| |    | || ||         |    ||   ||  ||||  |||| | ||            ||||||||||| ||||| || || ||||| || || || || ||||| || ||||| || ||||| || || || |||||||||||||||||||| || ||
----------------------------------gtaagctcccaatcttccccttcactttctcggggccagatctgatctgagatgaggttgacacacgacgcatgcaagGCATGGGCGCCGCCTACGGCACCGCCAAGAGCGGCGTGGGCGTGGCGTCCATGGGGGTGATGCGCCCGGAACTGGTGATGAAGTCCATCGTCCCCGTCGT

upper sequence: PP1S2_120V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G101020_T01 (Zea mays), 3'ss of exon 1
gccaccact-gtgtcactgttgggaaagtgagacgatgtgcagtgaatcattttgta--cagttgtgaaaccgcgttccttgactacgatgttgttggcgcagGCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTATGGGTGTCATGCGACCTGAGCTAGTGATGAAGTCCATCGTCCCAGTGGT
|  |  | | | ||         |    || ||||       | |||   ||| ||    | |      | | |  ||  ||  |  | ||| | |  |||||||||||| || || || || || ||||| ||||| || || ||||| || |||||||||||||| || ||||| || |||||||||||||| || |||||
gagagaatttgggttggatccatgtggctgggacgtgtgagggcgaaatttttggtggtgaatgacatgatctccctctgtgtatgtg-tgtggct--cgcagGCATGGGGGCGGCGTACGGGACAGCCAAGAGTGGCGTCGGCGTGGCGTCCATGGGTGTCATGCGCCCAGAGCTCGTCATGAAGTCCATCGTGCCCGTGGT

upper sequence: PP1S2_120V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM5G893252_T01 (Zea mays), 3'ss of exon 1
----gccaccactgtgtcactgttgggaaagtgagacgatgtgcagtgaatcattttg-tacagttgtgaaaccgcgttccttgactacgatgttgttggcgcagGCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTATGGGTGTCATGCGACCTGAGCTAGTGATGAAGTCCATCGTCCCAGTGGT
    ||  |||     || |  |        |    |  |||    |  | ||    | | ||    |  |  |      |    |  |   | || || |  |||||||||||| ||||| || |||||||| || || || || || || || ||||| |||||||| || ||||| || ||||||||||||||||| || ||
gtaagcacccatcagatctccctccctccctt----ctctgtctctttcaccagccggatccaaccatccattcctcactcccatcacctcggctggtgcc-tagGCATGGGCGCCGCCTACGGGACGGCCAAGAGCGGCGTCGGCGTCGCCTCCATGGGCGTCATGCGCCCCGAGCTCGTCATGAAGTCCATCGTCCCCGTCGT

upper sequence: PP1S2_120V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G177005_T01 (Zea mays), 3'ss of exon 1
---gccaccactgtgtcactgttgggaaagtgagacgatgtgcagtgaatcattttgtacagttgtgaaaccgcgttccttgactacgatgttgttggcgcagGCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTATGGGTGTCATGCGACCTGAGCTAGTGATGAAGTCCATCGTCCCAGTGGT
    ||      |||||| | |   | |    |||    |    |    |    | |  ||||||   | |   | |  |  | |  | |      ||||||||||||||||| || || || || || || || || || || ||||| || |||||||| ||||| || ||||| || |||||||||||||| || |||||
tggtccgatcgggtgtcagtctgtcggattccagaaagcggtgggctttttcggtcgggcagttgctga-ctaggctgtt--attttgcttgatccggcgcagGCATGGGCGCCGCGTACGGGACCGCGAAGAGCGGCGTCGGCGTGGCGTCGATGGGTGTGATGCGGCCGGAGCTCGTCATGAAGTCCATCGTGCCCGTGGT

upper sequence: PP1S2_120V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA11G11760.1 (Glycine max), 3'ss of exon 1
-gccaccactgtgtcactgttgggaaagtgagacgatgtgcagtgaatcattttgtacagttgtgaaaccgcgttccttgactacgatgttgttggcgcagGCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTATGGGTGTCATGCGACCTGAGCTAGTGATGAAGTCCATCGTCCCAGTGGT
     |   | | | |     |  ||||  |  |   |     |   |   |||| |   ||     |      || || | ||| |  |  | |  | ||| ||||| ||||||||||| || || || ||||| ||||| ||||| || |||||||| ||| |||| ||||| ||||||||||| || ||||| || ||
ttatgcgtatatataaagaaagacaaagaaattcagagcttcttcgttagctttgcattttttctgtagatttatctttaa-tactaattgatggatgaagGTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTTGGCGTGGCTTCGATGGGTGTGATGAGACCAGAGCTGGTGATGAAGTCTATTGTCCCTGTTGT

upper sequence: PP1S2_120V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA04G00950.1 (Glycine max), 3'ss of exon 1
gccaccactgtgtcactgttgggaaagtgagacgatgtgcagtgaatcattt----tgtacagttgtgaaaccgcgttccttgactacgatgttgttggcgcagGCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTATGGGTGTCATGCGACCTGAGCTAGTGATGAAGTCCATCGTCCCAGTGGT
  |||   ||||  | || | |     |   |   |   |   |  |  |||    ||   |  | ||  |     ||| ||           |||||    ||| ||||| ||||||||||| || || || ||||| || || ||||| || |||||||| ||| |||||||||| ||||||||||| || ||||| || ||
--cactcatgtgaaagtgattgatcgatcgaatcttaatcttagggttgtttgaagtgataaaatctgtgaggaatttcatttgtatttgaactgttgat--agGTATGGGAGCTGCCTATGGCACAGCAAAGAGTGGTGTGGGCGTGGCTTCCATGGGTGTGATGAGACCTGAGCTGGTGATGAAGTCTATTGTCCCTGTTGT

upper sequence: PP1S2_120V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA06G00980.1 (Glycine max), 3'ss of exon 1
---gccaccactgtgtcactgttgggaaagtgagacgatgtgcagtgaatcattttgtacagttgtgaaaccgcgttccttgactacgatgttgttggcgcagGCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTATGGGTGTCATGCGACCTGAGCTAGTGATGAAGTCCATCGTCCCAGTGGT
     |||   ||||  | || | |     |   |   |   |   |  |  |||  |  | |||  |||     |     || |   || ||||||    ||| ||||| ||||||||||| || || || ||||| || || ||||| || |||||||| ||| |||||||||| ||||||||||| || || || || ||
aatttcacacgtgtgaaagtgattgatcgatcgaattttaatcttagggttgtttgtttgaattgataaaa-atttgtgaggaattttattttgttgat--agGTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCCATGGGTGTAATGAGACCTGAGCTGGTGATGAAGTCGATTGTTCCTGTTGT

upper sequence: PP1S2_120V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA12G04090.1 (Glycine max), 3'ss of exon 1
gccaccactgtgtcactgttgggaaagtgagacgatgtgcagtgaatcattttgtacagt-tgtgaaaccgcgttcc---ttgactac--gatgttgttggcgcagGCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTATGGGTGTCATGCGACCTGAGCTAGTGATGAAGTCCATCGTCCCAGTGGT
        | | | |     |  ||||  |  |   |     |  ||   |||| |   | |||  |      ||     |  | |    ||  |  | |  | ||| ||||| ||||||||||| || || || ||||| || || ||||| || |||||||| ||| |||| ||||| ||||||||||| || ||||| || ||
------tgtatataaagaaagaaaaagaaattctgagcttcttcgatagctttgcattttctgtagatttatctttaatatgaattgtttgaactgatggaggaagGTATGGGAGCTGCCTATGGCACAGCGAAGAGTGGCGTGGGCGTGGCTTCGATGGGTGTGATGAGACCGGAGCTGGTGATGAAGTCTATTGTCCCTGTTGT

upper sequence: PP1S2_120V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT4G38920.1 (Arabidopsis thaliana), 3'ss of exon 1
gccaccactgtgtcactgttgggaaagtgagacgatgtgcagtgaatcattttgtacagttgtgaaaccgcgttccttg-actacgatgttgttggcgcagGCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTATGGGTGTCATGCGACCTGAGCTAGTGATGAAGTCCATCGTCCCAGTGGT
       || | ||    |   ||| |   |  |||     ||| |     | ||    ||||||            || |      |||| ||  |  ||| ||||| ||||| || || || || || ||||| || |||||||||||||||||||| ||| | || ||| | ||||||||||| || |||||||| ||
aattatgctttttcttcatatcgaaggcatgttgattacttgtgtaaaccatagttagattgtgaccttaaagagtgtgtatctttgtgttattaaca-agGTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTATGGGTGTGATGAGGCCGGAGTTGGTGATGAAGTCTATTGTCCCAGTTGT

upper sequence: PP1S2_120V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv03s0038g00790.t01 (Vitis vinifera), 3'ss of exon 1
--gccaccactgtgtcactgttgggaaagtgagacgatgtgcagtgaatcattttgtacagttgtgaaaccgcgttccttgactacgatgttgttggcgcagGCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTATGGGTGTCATGCGACCTGAGCTAGTGATGAAGTCCATCGTCCCAGTGGT
   | |  | |   || |  |        |      |    | |   ||   | | || |  |  ||  | |  ||   ||       | |  ||   | ||| ||||| ||||| ||||||||||| || ||||| || |||||||| || ||||| || ||| | || ||||| ||||||||||| || || ||||| ||
attcgataatttcttctccttcttcttcattttctcaataaccggacatagatatatagatcttcgattctg-attgactgttgtttttataatttttg-agGTATGGGAGCTGCGTATGGAACGGCGAAGAGTGGCGTCGGAGTGGCGTCGATGGGAGTGATGAGGCCGGAGCTGGTGATGAAGTCGATTGTACCAGTTGT

upper sequence: PP1S2_120V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ33972 (Selaginella moellendorffii), 3'ss of exon 1
gccaccactgtgtcactgttgggaaagtgagacgatgtgcagtgaatcattttgtacagttgtgaaaccgcgttccttgactacgatgttgttggcgcagGCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTATGGGTGTCATGCGACCTGAGCTAGTGATGAAGTCCATCGTCCCAGTGGT
                                   |  ||   || || ||||   |  |  |  || |||  | |  ||        | | |    |||||||||| ||||||||||| || ||||| || || || || ||||| || ||||| |||||| |||| ||||| |||||||| || |||||||| |||||
----------------------------------gtaagcca-gattctttttcctctttgatctaatcgcaatgc--gatggatcaatcgat--tacagGCATGGGAGCTGCCTATGGCACTGCCAAGAGCGGCGTGGGCGTGGCGTCCATGGGCGTCATGAGACCGGAGCTCGTGATGAAATCGATCGTCCCGGTGGT

upper sequence: PP1S2_120V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 1
--------------------------------------------------------------------gccaccactgtgtcactg-ttgggaaagtgagacgatgtgcagtg-aatcattttgt-acagttgtgaaaccgcgttccttga-------------ctacgatgttgttggcgcagGCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTATGGGTGTCATGCGACCTGAGCTAGTGATGAAGTCCATCGTCCCAGTGGT
                                                                    | ||   |  || |   | |||||  |  ||  ||   | | | |  ||    |||  ||| |   || |   || |||   |              || |   || |    ||||||||||| |||||||||||||| || || ||||| |||||||||||||| ||||| || ||||| || ||||| |||||||| || ||||| ||||||||
gtaagttcttgcctctcaccgccatggctggactggatctagggttgtggtgcgtgtctcggctgcgcggcattgcaatgcctgagcttgggccatggattcgccttcctgcgcgatttccttgccacaatcccgagatttcgatcccaaaattccccattttcttatggaattttctttgcagGCATGGGAGCTGCCTATGGAACCGCAAAGAGTGGTGTTGGAGTGGCATCCATGGGCGTGATGCGGCCGGAGCTCGTGATGAAATCGATCGTGCCAGTGGT

upper sequence: PP1S2_120V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ26016 (Selaginella moellendorffii), 3'ss of exon 1
--------------------------------------------------------------------gccaccactgtgtcactg-ttgggaaagtgagacgatgtgcagtg-aatcattttgt-acagttgtgaaaccgcgttccttgact-------------acgatgttgttggcgcagGCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTATGGGTGTCATGCGACCTGAGCTAGTGATGAAGTCCATCGTCCCAGTGGT
                                                                    | ||   |  || |   | |||||  |  ||  ||   | | | |  ||    |||  ||| |   || |   || |||   | |             | |   || |    ||||||||||| |||||||||||||| || || ||||| ||||||||||| || ||||| || ||||| || ||||| |||||||| || ||||| ||||||||
gtaagttcttgcctctcaccgccatggctggactggatctagggttgtggtgcgtgtctcggctgcgcggcattgcaatgcctgagcttgggccatggattcgccttcctgcgcgatttccttgccacaatcccgatatttcgatcccaaaattccccattttctcatggaattttctttgcagGCATGGGAGCTGCCTATGGAACCGCAAAGAGTGGTGTTGGAGTGGCGTCCATGGGCGTGATGCGGCCGGAGCTCGTGATGAAATCGATCGTGCCAGTGGT

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|18361848|gb|BJ193915.1|BJ193915
EST:     CGCTCCCTTCTTCGGCTTCATCGGAGCTGCAGCTGCCCTTGTCTTTTCAT                         GCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTA
genomic: CGCTCCCTTCTTCGGCTTCATCGGAGCTGCAGCTGCCCTTGTCTTTTCATgtacgttccc ... gttggcgcagGCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTA
EST: gi|162273187|gb|FC449207.1|FC449207
EST:     CGCTCCCTTCTTCGGCTTCATCGGAGCTGCAGCTGCCCTTGTCTTTTCAT                         GCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTA
genomic: CGCTCCCTTCTTCGGCTTCATCGGAGCTGCAGCTGCCCTTGTCTTTTCATgtacgttccc ... gttggcgcagGCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTA
EST: gi|162240885|gb|FC415164.1|FC415164
EST:     CGCTCCCTTCTTCGGCTTCATCGGAGCTGCAGCTGCCCTTGTCTTTTCAT                         GCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTA
genomic: CGCTCCCTTCTTCGGCTTCATCGGAGCTGCAGCTGCCCTTGTCTTTTCATgtacgttccc ... gttggcgcagGCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTA
EST: gi|162249700|gb|FC426814.1|FC426814
EST:     CGCTCCCTTCTTCGGCTTCATCGGAGCTGCAGCTGCCCTTGTCTTTTCAT                         GCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTA
genomic: CGCTCCCTTCTTCGGCTTCATCGGAGCTGCAGCTGCCCTTGTCTTTTCATgtacgttccc ... gttggcgcagGCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTA
EST: gi|162273188|gb|FC449208.1|FC449208
EST:     CGCTCCCTTCTTCGGCTTCATCGGAGCTGCAGCTGCCCTTGTCTTTTCAT                         GCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTA
genomic: CGCTCCCTTCTTCGGCTTCATCGGAGCTGCAGCTGCCCTTGTCTTTTCATgtacgttccc ... gttggcgcagGCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTA
EST: gi|18351684|gb|BJ183736.1|BJ183736
EST:     CGCTCCCTTCTTCGGCTTCATCGGAGCTGCAGCTGCCCTTGTCTTTTCAT                         GCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTA
genomic: CGCTCCCTTCTTCGGCTTCATCGGAGCTGCAGCTGCCCTTGTCTTTTCATgtacgttccc ... gttggcgcagGCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTA
EST: gi|162268509|gb|FC444382.1|FC444382
EST:     CGCTCCCTTCTTCGGCTTCATCGGAGCTGCAGCTGCCCTTGTCTTTTCAT                         GCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTA
genomic: CGCTCCCTTCTTCGGCTTCATCGGAGCTGCAGCTGCCCTTGTCTTTTCATgtacgttccc ... gttggcgcagGCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTA
EST: gi|37845222|gb|BJ603230.1|BJ603230
EST:     GGCTTCATCGGAGCTGCAGCTGCCCTTGTCTTTTCAT                         GCATGGGCGCTGCNTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTA
genomic: GGCTTCATCGGAGCTGCAGCTGCCCTTGTCTTTTCATgtacgttccc ... gttggcgcagGCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTA
EST: gi|162255646|gb|FC431644.1|FC431644
EST:     CGCTCCCTTCTTCGGCTTCATCGGAGCTGCAGCTGCCCTTGTCTTTTCAT                         GCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTA
genomic: CGCTCCCTTCTTCGGCTTCATCGGAGCTGCAGCTGCCCTTGTCTTTTCATgtacgttccc ... gttggcgcagGCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTA
EST: gi|67702760|gb|BJ962993.1|BJ962993
EST:     CGCTCCCTTCTTCGGCTTCATCGGAGCTGCAGCTGCCCTTGTCTTTTCAT                         GCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTA
genomic: CGCTCCCTTCTTCGGCTTCATCGGAGCTGCAGCTGCCCTTGTCTTTTCATgtacgttccc ... gttggcgcagGCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTA
EST: gi|18334293|gb|BJ166310.1|BJ166310
EST:     CGCTCCCTTCTTCGGCTTCATCGGAGCTGCAGCTGCCCTTGTCTTTTCAT                         GCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTA
genomic: CGCTCCCTTCTTCGGCTTCATCGGAGCTGCAGCTGCCCTTGTCTTTTCATgtacgttccc ... gttggcgcagGCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTA

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: 29 (upstream exon), 27 (downstream exon)
Score: 14

TCTTTCTCGATCATCATGTCGACTGCCGCGGCGTTCAATGGAGATGAGGTCGCTCCCTTCTTCGGCTTCATCGGAGCTGCAGCTGCCCTTGTCTTTTCATgtacgttccc ... gttggcgcagGCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTATGGGTGTCATGCGACCTGAGCTAGTGATGAAGTCCATCGTCCCAGTGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcattttgtacagttgtgaaaccgcgttccttgactacgatgttgttggcgcagGCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTATGGGTGTCATGCGACCTGAGCTAGTGATGAAGTCCATCGTCCCAGTGGT
                             ccttgac  putative branch site (score: 14)