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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgccttagtgaaaacgattattctgtgtccttggattgctacgtggagaaccaatttgatcatatttcaatttctcttcatttttgctttgagtttgcagGATTGGCTGCGCTTCAGTGTTGCATTCTGGCATACTTTTCGTGGAGATGGTGGGGATCCCTTTGGATCTCCCACCAAGAGATGGCCTTGGGATGACGGCA

Basic information

species Physcomitrella patens
transcript PP1S180_53V6.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S180_53V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G081682_T02 (Zea mays), 3'ss of exon 4
---tgccttagtgaaaacgattattctgtgtccttggattgctacgtggagaaccaatttgatcatatttcaatttctcttcatttttgctt--tgagtttgc----agGATTGGCTGCGCTTCAGTGTTGCATTCTGGCATACTTTTCGTGGAGATGGTGGGGATCCCTTTGGATCTCCCACCAAGAGATGGCCTTGGGATGACGGCA
   |   | ||||||  |   | | |||  ||  |  |   |  | |  | |  || | |||   ||  ||||   || | ||| | |||||  |   |||||    |||||||| ||||||||||||||||||||||||| || || |||||   ||| |  ||||| || ||  |||| || ||||  ||||||||||| |||||||
gtatcgatcagtgaatccccatctgctgcttcactataccccctcttttacactcactgtgaa-gtacgtcaacc-ctttgcatctatgcttatttgctttgctattagGATTGGATGCGCTTCAGTGTTGCATTCTGGCACACGTTCCGTGGTACTGGCGCTGATCCTTTCGGTGCTCCTACAAAGACTTGGCCTTGGGAGGACGGCA

upper sequence: PP1S180_53V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G313536_T01 (Zea mays), 3'ss of exon 3
tgccttagtgaaaacgattattctgtgtccttgga-----ttgctacgtggagaaccaatttgatcatatttcaatttctcttcatttttgctttgagtttgcagGATTGGCTGCGCTTCAGTGTTGCATTCTGGCATACTTTTCGTGGAGATGGTGGGGATCCCTTTGGATCTCCCACCAAGAGATGGCCTTGGGATGACGGCA
     | |||||  |   | | | |  ||  |  |     |   |||    |     || |  ||||    |     ||| | | | |||||||||   ||  |||||||| |||||||||||||||| |||||||| || ||  ||||   | | |  ||||| || ||  |||| || | ||  ||||||||||| || ||||
---tctggtgaacccccatctgccgcttcactataccccctctttacactcactgtgaagtacatcaaccctttgcatctatgcttatttgctttgctatt--agGATTGGATGCGCTTCAGTGTTGCCTTCTGGCACACGTTCTGTGGTACTAGCGCTGATCCTTTCGGTGCTCCTACAATGACTTGGCCTTGGGAGGATGGCA

upper sequence: PP1S180_53V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G335948_T01 (Zea mays), 3'ss of exon 2
tgccttagtgaaaacgattattctgtgtccttgga-----ttgctacgtggagaaccaatttgatcatatttcaatttctcttcatttttgctttgagtttgcagGATTGGCTGCGCTTCAGTGTTGCATTCTGGCATACTTTTCGTGGAGATGGTGGGGATCCCTTTGGATCTCCCACCAAGAGATGGCCTTGGGATGACGGCA
     | |||||  |   | | | |  ||  |  |     |   |||    |     || |  ||||    |     ||| | | | |||||||||   ||  |||||||| |||||||||||||||| |||||||| || ||  ||||   | | |  ||||| || ||  |||| || | ||  ||||||||||| || ||||
---tctggtgaacccccatctgccgcttcactataccccctctttacactcactgtgaagtacatcaaccctttgcatctatgcttatttgctttgctatt--agGATTGGATGCGCTTCAGTGTTGCCTTCTGGCACACGTTCTGTGGTACTAGCGCCGATCCTTTCGGTGCTCCTACAATGACTTGGCCTTGGGAGGATGGCA

upper sequence: PP1S180_53V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ07726 (Selaginella moellendorffii), 3'ss of exon 3
tgccttagtgaaaacgattattctgtgtccttggattgctacgtggagaaccaatttgatcatatttcaatttctcttcatttttgctttgagtttgcagGATTGGCTGCGCTTCAGTGTTGCATTCTGGCATACTTTTCGTGGAGATGGTGGGGATCCCTTTGGATCTCCCACCAAGAGATGGCCTTGGGATGACGGCA
                               | ||   |          | | ||  | ||  |    || | || ||   |||  ||||   | || |||| |||||| | |||||||| || ||||||||||| || || || |||||| | ||||| ||||||||||| || |||   |||||||||||||| || |
------------------------------gtagaagccacttcattccatccatgcgctcg-acaaaaaatcctttttgctttc-ctttatctgtgtagGACTGGCTGAGGTTCAGTGTCGCCTTCTGGCATACATTCCGAGGGGATGGTAGTGATCCTTTTGGATCTCCGACGAAGCAGTGGCCTTGGGATGATGGAA

upper sequence: PP1S180_53V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ07670 (Selaginella moellendorffii), 3'ss of exon 3
tgccttagtgaaaacgattattctgtgtccttggattgctacgtggagaaccaatttgatcatatttcaatttctcttcatttttgctttgagtttgcagGATTGGCTGCGCTTCAGTGTTGCATTCTGGCATACTTTTCGTGGAGATGGTGGGGATCCCTTTGGATCTCCCACCAAGAGATGGCCTTGGGATGACGGCA
                               | ||  || ||    |   |     ||  |       || ||| |||  | ||| ||||   | || |||| |||||| | |||||||| || ||||||||||| || || || |||||  | ||||| ||||||||||| || |||   |||||||||||||| || |
------------------------------gtagaa-gccaccatcattccatccatgcgctcgacaaaaattccctttttctttcctttatctgtgtagGACTGGCTGAGGTTCAGTGTCGCCTTCTGGCATACATTCCGAGGCGATGGAAGTGATCCTTTTGGATCTCCGACGAAGCAGTGGCCTTGGGATGATGGAA

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|18324844|gb|BJ156839.1|BJ156839
EST:     CTTATAAATACTATAATGCTGAGGAACTGATTTTTGGCAAGAAGATGAAG                         GATTGGCTGCGCTTCAGTGTTGCATTCTGGCATACTTTTCGTGGAGATGGT
genomic: CTTATAAATACTATAATGCTGAGGAACTGATTTTTGGCAAGAAGATGAAGgtgaggtttt ... gagtttgcagGATTGGCTGCGCTTCAGTGTTGCATTCTGGCATACTTTTCGTGGAGATGGT
EST: gi|208374343|gb|DC941156.1|DC941156
EST:     CTTATAAATACTATAATGCTGAGGAACTGATTTTTGGCAAGAAGATGAAG                         GATTGGCTGCGCTTCAGTGTTGCATTCTGGCATACTTTTCGTGGAGATGGT
genomic: CTTATAAATACTATAATGCTGAGGAACTGATTTTTGGCAAGAAGATGAAGgtgaggtttt ... gagtttgcagGATTGGCTGCGCTTCAGTGTTGCATTCTGGCATACTTTTCGTGGAGATGGT
EST: gi|100392407|gb|BY953347.1|BY953347
EST:     CTTATAAATACTATAATGCTGAGGAACTGATTTTTGGCAAGAAGATGAAG                         GATTGGCTGCGCTTCAGTGTTGCATTCTGGCATACTTTTCGTGGAGATGGT
genomic: CTTATAAATACTATAATGCTGAGGAACTGATTTTTGGCAAGAAGATGAAGgtgaggtttt ... gagtttgcagGATTGGCTGCGCTTCAGTGTTGCATTCTGGCATACTTTTCGTGGAGATGGT
EST: gi|100358061|gb|BY965452.1|BY965452
EST:     CTTATAAATACTATAATGCTGAGGAACTGATTTTTGGCAAGAAGATGAAG                         GATTGGCTGCGCTTCAGTGTTGCATTCTGGCATACTTTTCGTGGAGATGGT
genomic: CTTATAAATACTATAATGCTGAGGAACTGATTTTTGGCAAGAAGATGAAGgtgaggtttt ... gagtttgcagGATTGGCTGCGCTTCAGTGTTGCATTCTGGCATACTTTTCGTGGAGATGGT
EST: gi|100404244|gb|BY955328.1|BY955328
EST:     CTTATAAATACTATAATGCTGAGGAACTGATTTTTGGCAAGAAGATGAAG                         GATTGGCTGCGCTTCAGTGTTGCATTCTGGCATACTTTTCGTGGAGATGGT
genomic: CTTATAAATACTATAATGCTGAGGAACTGATTTTTGGCAAGAAGATGAAGgtgaggtttt ... gagtttgcagGATTGGCTGCGCTTCAGTGTTGCATTCTGGCATACTTTTCGTGGAGATGGT
EST: gi|208376225|gb|DC914510.1|DC914510
EST:     CTTATAAATACTATAATGCTGAGGAACTGATTTTTGGCAAGAAGATGAAG                         GATTGGCTGCGCTTCAGTGTTGCATTCTGGCATACTTTTCGTGGAGAT
genomic: CTTATAAATACTATAATGCTGAGGAACTGATTTTTGGCAAGAAGATGAAGgtgaggtttt ... gagtttgcagGATTGGCTGCGCTTCAGTGTTGCATTCTGGCATACTTTTCGTGGAGAT
EST: gi|100398077|gb|BY954076.1|BY954076
EST:     CTTATAAATACTATAATGCTGAGGAACTGATTTTTGGCAAGAAGATGAAG                         GATTGGCTGCGCTTCAGTGTTGCATTCTGGCATACTTTTCGTGGAGATGGT
genomic: CTTATAAATACTATAATGCTGAGGAACTGATTTTTGGCAAGAAGATGAAGgtgaggtttt ... gagtttgcagGATTGGCTGCGCTTCAGTGTTGCATTCTGGCATACTTTTCGTGGAGATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagaaccaatttgatcatatttcaatttctcttcatttttgctttgagtttgcagGATTGGCTGCGCTTCAGTGTTGCATTCTGGCATACTTTTCGTGGAGATGGTGGGGATCCCTTTGGATCTCCCACCAAGAGATGGCCTTGGGATGACGGCA
        atttgat  putative branch site (score: 5)
                         tttctcttcatttttg  putative PPT
       aatttgatcatatttc  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgccttagtgaaaacgattattctgtgtccttggattgctacgtggagaaccaatttgatcatatttcaatttctcttcatttttgctttgagtttgcagGATTGGCTGCGCTTCAGTGTTGCATTCTGGCATACTTTTCGTGGAGATGGTGGGGATCCCTTTGGATCTCCCACCAAGAGATGGCCTTGGGATGACGGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG