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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaattatacttcagcacaatttgtgaagtggttttgtttgttttctgctacttatctggttgcttccagtaatattctttatcttgcatcagtaaatatatcaagacaatcctgtttaacagttggtgaacttctccagGTCTTCCTTGAGTATTCAGATATTGCCGGTGCTTCGAAAGCGAAGGCTTCGCTGCATGGGCGAAGATTCGATGAAAACTTGGTAGTTGCTGTGTACTACC

Basic information

species Physcomitrella patens
transcript PP1S88_42V6.1
intron # 18
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|162187392|gb|FC363550.1|FC363550
EST:     GTGTTATTCCGAGACCTAGAAGTGGTGAAAATGTTCCTGGGTTAGGCAAG                         GTCTTCCTTGAGTATTCAGATATTGCCGGTGCTTCGAAAGCGAAGGCTTCG
genomic: GTGTTATTCCGAGACCTAGAAGTGGTGAAAATGTTCCTGGGTTAGGCAAGgtaaaaatta ... acttctccagGTCTTCCTTGAGTATTCAGATATTGCCGGTGCTTCGAAAGCGAAGGCTTCG
EST: gi|162247006|gb|FC423948.1|FC423948
EST:     GTGTTATTCCGAGACCTAGAAGTGGTGAAAATGTCCCTGGGT-AGGCA-G                         GTCTTCCTTGAGTATTCAGATATTGCCGGTGCTTCGAAAGC
genomic: GTGTTATTCCGAGACCTAGAAGTGGTGAAAATGTTCCTGGGTTAGGCAAGgtaaaaatta ... acttctccagGTCTTCCTTGAGTATTCAGATATTGCCGGTGCTTCGAAAGC
EST: gi|162247005|gb|FC423947.1|FC423947
EST:     GTGTTATTCCGAGACCTAGAAGTGGTGAAAATGTTCCTGGGTTAGGCAAG                         GTCTTCCTTGAGTATTCAGATATTGCCGGTGCTTCGAAAGCGAAGGCTTCG
genomic: GTGTTATTCCGAGACCTAGAAGTGGTGAAAATGTTCCTGGGTTAGGCAAGgtaaaaatta ... acttctccagGTCTTCCTTGAGTATTCAGATATTGCCGGTGCTTCGAAAGCGAAGGCTTCG
EST: gi|67692592|gb|BJ952825.1|BJ952825
EST:     GTGTTATTCCGAGACCTAGAAGTGGTGAAAATGTTCCTGGGTTAGGCAAG                         GTCTTCCTTGAGTATTCAGATATTGCCGGTGCTTCGAAAGCGAAGGCTTCG
genomic: GTGTTATTCCGAGACCTAGAAGTGGTGAAAATGTTCCTGGGTTAGGCAAGgtaaaaatta ... acttctccagGTCTTCCTTGAGTATTCAGATATTGCCGGTGCTTCGAAAGCGAAGGCTTCG
EST: gi|67569333|gb|BJ942157.1|BJ942157
EST:     GTGTTATTCCGAGACCTAGAAGTGGTGAAAATGTTCCTGGGTTAGGCAAG                         GTCTTCCTTGAGTATTCAGATATTGCCGGTGCTTCGAAAGCGAAGGCTTCG
genomic: GTGTTATTCCGAGACCTAGAAGTGGTGAAAATGTTCCTGGGTTAGGCAAGgtaaaaatta ... acttctccagGTCTTCCTTGAGTATTCAGATATTGCCGGTGCTTCGAAAGCGAAGGCTTCG
EST: gi|162232204|gb|FC407754.1|FC407754
EST:     GTGTTATTCCGAGACCTAGAAGTGGTGAAAATGTTCCTGGGTTAGGCAAG                         GTCTTCCTTGAGTATTCAGATATTGCCGGTGCTTCGAAAGCGAAGGCTTCG
genomic: GTGTTATTCCGAGACCTAGAAGTGGTGAAAATGTTCCTGGGTTAGGCAAGgtaaaaatta ... acttctccagGTCTTCCTTGAGTATTCAGATATTGCCGGTGCTTCGAAAGCGAAGGCTTCG
EST: gi|162190373|gb|FC365387.1|FC365387
EST:     GTGTTATTCCGAGACCTAGAAGTGGTGAAAATGTTCCTGGGTTAGGCAAG                         GTCTTCCTTGAGTATTCAGATATTGCCGGTGCTTCGAAAGCGAAGGCTTCG
genomic: GTGTTATTCCGAGACCTAGAAGTGGTGAAAATGTTCCTGGGTTAGGCAAGgtaaaaatta ... acttctccagGTCTTCCTTGAGTATTCAGATATTGCCGGTGCTTCGAAAGCGAAGGCTTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatcagtaaatatatcaagacaatcctgtttaacagttggtgaacttctccagGTCTTCCTTGAGTATTCAGATATTGCCGGTGCTTCGAAAGCGAAGGCTTCGCTGCATGGGCGAAGATTCGATGAAAACTTGGTAGTTGCTGTGTACTACC
                             gtttaac  putative branch site (score: 3)
                                              cttctcc  putative PPT
      agtaaatatatcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaattatacttcagcacaatttgtgaagtggttttgtttgttttctgctacttatctggttgcttccagtaatattctttatcttgcatcagtaaatatatcaagacaatcctgtttaacagttggtgaacttctccagGTCTTCCTTGAGTATTCAGATATTGCCGGTGCTTCGAAAGCGAAGGCTTCGCTGCATGGGCGAAGATTCGATGAAAACTTGGTAGTTGCTGTGTACTACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA