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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatatttttctgtgatttctatcttatttctattttttattttatgtttgtttattttttttagtttttttctgactgtccaatttgatgctggtgaagCTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGCTCGGCATCGTGGCGCCAAGTGTATGCTGTCGTTCTGGATAATAATCTAA

Basic information

species Physcomitrella patens
transcript PP1S98_84V6.3
intron # 1
splice site 3'
intron type U2

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|18348368|gb|BJ180416.1|BJ180416
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAG                         CTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... gctggtgaagCTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
EST: gi|100443881|gb|BY982109.1|BY982109
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAG                         CTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... gctggtgaagCTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
EST: gi|67704222|gb|BJ964455.1|BJ964455
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAG                         CTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... gctggtgaagCTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
EST: gi|7148073|gb|AW509995.1|AW509995
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCTAG                         CTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... gctggtgaagCTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
EST: gi|208378757|gb|DC914731.1|DC914731
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAG                         CTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... gctggtgaagCTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
EST: gi|67571140|gb|BJ943964.1|BJ943964
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTC--G                         ---AGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... gctggtgaagCTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
EST: gi|18328498|gb|BJ160503.1|BJ160503
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAG                         CTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... gctggtgaagCTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
EST: gi|162229735|gb|FC404019.1|FC404019
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAG                         CTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... gctggtgaagCTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
EST: gi|100372576|gb|BY985666.1|BY985666
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAG                         CTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... gctggtgaagCTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
EST: gi|208368426|gb|DC935991.1|DC935991
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAG                         CTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... gctggtgaagCTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
EST: gi|100398110|gb|BY954093.1|BY954093
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAG                         CTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... gctggtgaagCTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
EST: gi|67569229|gb|BJ942053.1|BJ942053
EST:     AGTTTTGCCACATTTCGTTGCTCGTCTGAGGAGAATCGGGCGGATTCGAG                         CTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
genomic: AG-TTTGCCACATTTCGTTG-TCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... gctggtgaagCTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
EST: gi|100418392|gb|BY957396.1|BY957396
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAG                         CTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... gctggtgaagCTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
EST: gi|18371783|gb|BJ203385.1|BJ203385
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAT                         CTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... gctggtgaagCTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
EST: gi|162225034|gb|FC401450.1|FC401450
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTC--G                         ---AGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... gctggtgaagCTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
EST: gi|100416857|gb|BY993124.1|BY993124
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAG                         CTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... gctggtgaagCTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
EST: gi|208353978|gb|DC930118.1|DC930118
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAG                         CTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... gctggtgaagCTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
EST: gi|100442029|gb|BY962922.1|BY962922
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTC--G                         ---AGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... gctggtgaagCTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
EST: gi|100452996|gb|CJ975548.1|CJ975548
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAG                         CTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... gctggtgaagCTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
EST: gi|208400107|gb|DC904755.1|DC904755
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAG                         CTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... gctggtgaagCTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
EST: gi|208377991|gb|DC914368.1|DC914368
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTC--G                         ---AGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... gctggtgaagCTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttgtttattttttttagtttttttctgactgtccaatttgatgctggtgaagCTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGCTCGGCATCGTGGCGCCAAGTGTATGCTGTCGTTCTGGATAATAATCTAA
      tttattttttttagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatatttttctgtgatttctatcttatttctattttttattttatgtttgtttattttttttagtttttttctgactgtccaatttgatgctggtgaagCTAAGGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGCTCGGCATCGTGGCGCCAAGTGTATGCTGTCGTTCTGGATAATAATCTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG