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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgattgatgatagtcaactttgtagattttttcactattctattatggacgaagcgatgtctgtcatataactagtacctcgtttctgatgatgacagGGGCCTGAAATCAGAACAGGGAATTTGGCAAGTGGAAAACCTATCCAACTGAAGCGCGGCGAGGAGATCTTGATCACCACTGACTACAGTCACTTGGGAG

Basic information

species Physcomitrella patens
transcript PP1S90_133V6.1
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|162231959|gb|FC409033.1|FC409033
EST:     TTGCTTGCGAGAACACTCAAATAATGTGTGCTGTCCTTCTGGATACTAAG                         GGGCCTGAAATCAGAACAGGGAATTTGGCAAGTGGAAAACCTATCCAACTG
genomic: TTGCTTGCGAGAACACTCAAATAATGTGTGCTGTCCTTCTGGATACTAAGgtacaaaagc ... atgatgacagGGGCCTGAAATCAGAACAGGGAATTTGGCAAGTGGAAAACCTATCCAACTG
EST: gi|67508255|gb|BJ941124.1|BJ941124
EST:     TTGCTTGCGAGAACACTCAAATAATGTGTGCTGTCCTTCTGGATACTAAG                         GGGCCTGAAATCAGAACAGGGAATTTGGCAAGTGGAAAACCTATCCAACTG
genomic: TTGCTTGCGAGAACACTCAAATAATGTGTGCTGTCCTTCTGGATACTAAGgtacaaaagc ... atgatgacagGGGCCTGAAATCAGAACAGGGAATTTGGCAAGTGGAAAACCTATCCAACTG
EST: gi|162184090|gb|FC358836.1|FC358836
EST:     TTGCTTGCGAGAACACTCAAATAATGTGTGCTGTCCTTCTGGATACTAAG                         GGGCCTGAAATCAGAACAGGGAATTTGGCAAGTGGAAAACCTATCCAACTG
genomic: TTGCTTGCGAGAACACTCAAATAATGTGTGCTGTCCTTCTGGATACTAAGgtacaaaagc ... atgatgacagGGGCCTGAAATCAGAACAGGGAATTTGGCAAGTGGAAAACCTATCCAACTG
EST: gi|162169996|gb|FC345936.1|FC345936
EST:     TTGCTTGCGAGAACACTCAAATAATGTGTGCTGTCCTTCTGGATACTAAG                         GGGCCTGAAATCAGAACAGGGAATTTGGCAAGTGGAAAACCTATCCAACTG
genomic: TTGCTTGCGAGAACACTCAAATAATGTGTGCTGTCCTTCTGGATACTAAGgtacaaaagc ... atgatgacagGGGCCTGAAATCAGAACAGGGAATTTGGCAAGTGGAAAACCTATCCAACTG
EST: gi|162217847|gb|FC393843.1|FC393843
EST:     TTGCTTGCGAGAACACTCAAATAATGTGTGCTGTCCTTCTGGATACTAAG                         GGGCCTGAAATCAGAACAGGGAATTTGGCAAGTGGAAAACCTATCCAACTG
genomic: TTGCTTGCGAGAACACTCAAATAATGTGTGCTGTCCTTCTGGATACTAAGgtacaaaagc ... atgatgacagGGGCCTGAAATCAGAACAGGGAATTTGGCAAGTGGAAAACCTATCCAACTG
EST: gi|67573146|gb|BJ945970.1|BJ945970
EST:     TTGCTTGCGAGAACACTCAAATAATGTGTGCTGTCCTTCTGGATACTAAG                         GGGCCTGAAATCAGAACAGGGAATTTGGCAAGTGGAAAACCTATCCAACTG
genomic: TTGCTTGCGAGAACACTCAAATAATGTGTGCTGTCCTTCTGGATACTAAGgtacaaaagc ... atgatgacagGGGCCTGAAATCAGAACAGGGAATTTGGCAAGTGGAAAACCTATCCAACTG
EST: gi|162201584|gb|FC377440.1|FC377440
EST:     TTGCTTGCGAGAACACTCAAATAATGTGTGCTGTCCTTCTGGATACTAAG                         GGGCCTGAAATCAGAACAGGGAATTTGGCAAGTGGAAAACCTATCCAACTG
genomic: TTGCTTGCGAGAACACTCAAATAATGTGTGCTGTCCTTCTGGATACTAAGgtacaaaagc ... atgatgacagGGGCCTGAAATCAGAACAGGGAATTTGGCAAGTGGAAAACCTATCCAACTG
EST: gi|162186070|gb|FC361274.1|FC361274
EST:     TTGCTTGCGAGAACACTCAAATAATGTGTGCTGTCCTTCTGGATACTAAG                         GGGCCTGAAATCAGAACAGGGAATTTGGCAAGTGGAAAACCTATCCAACTG
genomic: TTGCTTGCGAGAACACTCAAATAATGTGTGCTGTCCTTCTGGATACTAAGgtacaaaagc ... atgatgacagGGGCCTGAAATCAGAACAGGGAATTTGGCAAGTGGAAAACCTATCCAACTG
EST: gi|100438252|gb|BY979863.1|BY979863
EST:     TTGCTTGCGAGAACACTCAAATAATGTGTGCTGTCCTTCTGGATACTAAG                         GGGCCTGAAATCAGAACAGGGAACTTGGCAAGTTGGAAAAC-TATCCAACT
genomic: TTGCTTGCGAGAACACTCAAATAATGTGTGCTGTCCTTCTGGATACTAAGgtacaaaagc ... atgatgacagGGGCCTGAAATCAGAACAGGGAATTTGGCAAGT-GGAAAACCTATCCAACT
EST: gi|100450655|gb|CJ974372.1|CJ974372
EST:     TTGCTTGCGAGAACACTCAAATAATGTGTGCTGTCCTTCTGGATACTAAG                         GGGCCTGAAATCAGAACANGNAATTTGGCANGTGGAAAACCTATCC
genomic: TTGCTTGCGAGAACACTCAAATAATGTGTGCTGTCCTTCTGGATACTAAGgtacaaaagc ... atgatgacagGGGCCTGAAATCAGAACAGGGAATTTGGCAAGTGGAAAACCTATCC
EST: gi|162188471|gb|FC365069.1|FC365069
EST:     TTGCTTGCGAGAACACTCAAATAATGTGTGCTGTCCTTCTGGATACTAAG                         GGGCCTGAAATCAGAACAGGGAATTTGGCAAGTGGAAAACCTATCCAACTG
genomic: TTGCTTGCGAGAACACTCAAATAATGTGTGCTGTCCTTCTGGATACTAAGgtacaaaagc ... atgatgacagGGGCCTGAAATCAGAACAGGGAATTTGGCAAGTGGAAAACCTATCCAACTG
EST: gi|208358499|gb|DC930631.1|DC930631
EST:     TTGCTTGCGAGAACACTCAAATAATGTGTGCTGTCCTTCTGGATACTAAG                         GGGCCTGAAATCAGAACAGGGAATTTGGCAAGTGGAAAACCTATCCAACTG
genomic: TTGCTTGCGAGAACACTCAAATAATGTGTGCTGTCCTTCTGGATACTAAGgtacaaaagc ... atgatgacagGGGCCTGAAATCAGAACAGGGAATTTGGCAAGTGGAAAACCTATCCAACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggacgaagcgatgtctgtcatataactagtacctcgtttctgatgatgacagGGGCCTGAAATCAGAACAGGGAATTTGGCAAGTGGAAAACCTATCCAACTGAAGCGCGGCGAGGAGATCTTGATCACCACTGACTACAGTCACTTGGGAG
                                        ttctgat  putative branch site (score: 3)
                      atataacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtgattgatgatagtcaactttgtagattttttcactattctattatggacgaagcgatgtctgtcatataactagtacctcgtttctgatgatgacagGGGCCTGAAATCAGAACAGGGAATTTGGCAAGTGGAAAACCTATCCAACTGAAGCGCGGCGAGGAGATCTTGATCACCACTGACTACAGTCACTTGGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC