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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgaacgatattcaccagaactctgcatcaccttaagttgacttctttttgatttaaaacttgtcttctttcctgagtaaaacgtcgatgcttgtgtagCTTCTGGATTTGGATCGAAGTACCAGTACCTGTTTGGCAAAATTGGGATGAGCATGAAGCTGGTTCCCGGAAACTCTGCTGGCACTGTGACAGCGTATTA

Basic information

species Physcomitrella patens
transcript PP1S309_38V6.2
intron # 2
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|208394669|gb|DC928829.1|DC928829
EST:     -TTGCTCAACAGT-GTCAACAAGTGCAGCTAGTGCTTGATGAATATTCAG                         CTTCTGGATTTGGATCGAAGTACCAGTACCTGTTTGGCAAAATTGGGATGA
genomic: TTTGCTCAACAGTGGTCAACAAGTGCAGCTAGTGCTTGATGAATATTCAGgtactccgca ... gcttgtgtagCTTCTGGATTTGGATCGAAGTACCAGTACCTGTTTGGCAAAATTGGGATGA
EST: gi|208360178|gb|DC939189.1|DC939189
EST:     TTGCTCAACAGTGGTCAACAAGTGCAGCTAGTGCT-GNATGAATATTCAG                         CTTCTGGATT-GGATCGAANTACNAGTACCTGNTTGGCAAA
genomic: TTGCTCAACAGTGGTCAACAAGTGCAGCTAGTGCTTG-ATGAATATTCAGgtactccgca ... gcttgtgtagCTTCTGGATTTGGATCGAAGTACCAGTACCTGTTTGGCAAA
EST: gi|208364079|gb|DC943391.1|DC943391
EST:     TTTGCTCAACAGTGGTCAACAAGTGCAGCTAGTGCTTGATGAATATTCAG                         CTTCTGGATTTGGATCGAAGTACCAGTACCTGTTTGGCAAAATTGGGATGA
genomic: TTTGCTCAACAGTGGTCAACAAGTGCAGCTAGTGCTTGATGAATATTCAGgtactccgca ... gcttgtgtagCTTCTGGATTTGGATCGAAGTACCAGTACCTGTTTGGCAAAATTGGGATGA
EST: gi|208387990|gb|DC933124.1|DC933124
EST:     TTTGCTCAACAGTGGTCAACAAGTGCAGCTAGTGCTTGATGAATATTCAG                         CTTCTGGATTTGGATCGAAGTACNAGTACCTGTTTGGCAAA-TTGG-ANGA
genomic: TTTGCTCAACAGTGGTCAACAAGTGCAGCTAGTGCTTGATGAATATTCAGgtactccgca ... gcttgtgtagCTTCTGGATTTGGATCGAAGTACCAGTACCTGTTTGGCAAAATTGGGATGA
EST: gi|208391828|gb|DC942348.1|DC942348
EST:     TTTGCTCAACAGTGGTCAACAAGTGCAGCTAGTGCTTGATGAATATTCAG                         CTTTCTGGATTGGGATCGAAGTACCAGTACCTGTTTGGCAAA-TTGGGATG
genomic: TTTGCTCAACAGTGGTCAACAAGTGCAGCTAGTGCTTGATGAATATTCAGgtactccgca ... gcttgtgtagCTT-CTGGATTTGGATCGAAGTACCAGTACCTGTTTGGCAAAATTGGGATG
EST: gi|208379673|gb|DC903728.1|DC903728
EST:     TTTGCTCAACAGTGGTCAACAAGTGCAGCTAGTGCTTGATGAATATTCAG                         CTTCTGGATT-GGATCGAAGTACCAGTACCTGTTTGGCAAA-TTGGGATGA
genomic: TTTGCTCAACAGTGGTCAACAAGTGCAGCTAGTGCTTGATGAATATTCAGgtactccgca ... gcttgtgtagCTTCTGGATTTGGATCGAAGTACCAGTACCTGTTTGGCAAAATTGGGATGA
EST: gi|208392256|gb|DC929503.1|DC929503
EST:     TTTGCTCAACAGTGGTCAACAAGTGCAGCTAGTGCTTGATGAATATTCAG                         CTTCTGGATTTGGATCGAAGTACCAGTACCTGTTTGGCAAAATTGGGATGA
genomic: TTTGCTCAACAGTGGTCAACAAGTGCAGCTAGTGCTTGATGAATATTCAGgtactccgca ... gcttgtgtagCTTCTGGATTTGGATCGAAGTACCAGTACCTGTTTGGCAAAATTGGGATGA
EST: gi|208392015|gb|DC941863.1|DC941863
EST:     TTTGCTCAACAGTGGTCAACAAGTGCAGCTAGTGCTTGATGAATATTCAG                         CTTCTGGATTTGGATCGAAGTACCAGTACCTGTTTGGCAAA-TTGGGATGA
genomic: TTTGCTCAACAGTGGTCAACAAGTGCAGCTAGTGCTTGATGAATATTCAGgtactccgca ... gcttgtgtagCTTCTGGATTTGGATCGAAGTACCAGTACCTGTTTGGCAAAATTGGGATGA
EST: gi|208384465|gb|DC911551.1|DC911551
EST:     TTTGCTCAACAGTGGTCAACAAGTGCAGCTAGTGCTTGATGAATATTCAG                         CTTCTGGATTTGGATCGAAGTACCAGTACCTGTTTGGCAAANT-GGGATGA
genomic: TTTGCTCAACAGTGGTCAACAAGTGCAGCTAGTGCTTGATGAATATTCAGgtactccgca ... gcttgtgtagCTTCTGGATTTGGATCGAAGTACCAGTACCTGTTTGGCAAAATTGGGATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttttgatttaaaacttgtcttctttcctgagtaaaacgtcgatgcttgtgtagCTTCTGGATTTGGATCGAAGTACCAGTACCTGTTTGGCAAAATTGGGATGAGCATGAAGCTGGTTCCCGGAAACTCTGCTGGCACTGTGACAGCGTATTA
  ttttgat  putative branch site (score: 4)
       atttaaaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgaacgatattcaccagaactctgcatcaccttaagttgacttctttttgatttaaaacttgtcttctttcctgagtaaaacgtcgatgcttgtgtagCTTCTGGATTTGGATCGAAGTACCAGTACCTGTTTGGCAAAATTGGGATGAGCATGAAGCTGGTTCCCGGAAACTCTGCTGGCACTGTGACAGCGTATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG