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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcatgtctggaagtttctgtttttgaattaacaaatgcgacatttccggcagataatttctgtgtggtgattcattcagcaccgtatattcgtatcaaaatgaagaaatttggaaaaatgtttcgtcaaaatcattgaatcatatgattgattcgatgcagGGCCGTGAGGAGTCAGTGCAGGAGTTTGTGACTCGTAATCTGGGCCAGGAGGTCTTTGAGCGGCTGATTGAGCCTTTCTGTTCTG

Basic information

species Physcomitrella patens
transcript PP1S28_304V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S28_304V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os01g18320.1 (Oryza sativa), 3'ss of exon 2
gtaagttcatgtctggaagtttctgtttttgaattaacaaatgcgacatttccggcagataatttctgtgtggtgattcattcagcaccgtatattcgtatcaaaatgaagaaatttggaaaaatgtttcgtcaaaatcattgaatcatatgattgattcgatgcagGGCCGTGAGGAGTCAGTGCAGGAGTTTGTGACTCGTAATCTGGGCCAGGAGGTCTTTGAGCGGCTGATTGAGCCTTTCTGTTCTG
| |||||| | || | | || |||| | | | |||||| | | || | | || || || | ||| |||| ||||||||||| ||| |||| || ||| || || || ||| ||||||||||||||| || |||||||||||||| || |
---------------------------------------------------------------gtttgtgtgct------ctccccgctgtgcattcttgattcacttgtgaaattcga---------ttgtgctgagcgtt---tccggcgaaggtttc-----agGGGCGTGAGGAGTCGGTGGAGGACTTCGTGCGGCGCAACCTCGGCGCGGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAG
















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|162186656|gb|FC363628.1|FC363628
EST:     GAAAGCTTCGGGCTGGTTTTGGAGCTATGGGATTGAGGCCTGGAGCTCCA                         GGCCGTGAGGAGTCAGTGCAGGAGTTTGTGACTCGTAATCTGGGCCAGGAG
genomic: GAAAGCTTCGGGCTGGTTTTGGAGCTATGGGATTGAGGCCTGGAGCTCCAgtaagttcat ... ttcgatgcagGGCCGTGAGGAGTCAGTGCAGGAGTTTGTGACTCGTAATCTGGGCCAGGAG
EST: gi|100430853|gb|BY978430.1|BY978430
EST:     GAAAGCTTCGGGCTGGTTTTGGAGCTATGGGATTGAGGCCTGGAGCTCCA                         GGCCGTGAGGAGTCAGTGCAGGAGTTTGTGACTCGTAATCTGGGCCAGGAG
genomic: GAAAGCTTCGGGCTGGTTTTGGAGCTATGGGATTGAGGCCTGGAGCTCCAgtaagttcat ... ttcgatgcagGGCCGTGAGGAGTCAGTGCAGGAGTTTGTGACTCGTAATCTGGGCCAGGAG
EST: gi|162155602|gb|FC331540.1|FC331540
EST:     GAAAGCTTCGGGCTGGTTTTGGAGCTATGGGATTGAGGCCTGGAGCTCCA                         GGCCGTGAGGAGTCAGTGCAGGAGTTTGTGACTCGTAATCTGGGCCAGGAG
genomic: GAAAGCTTCGGGCTGGTTTTGGAGCTATGGGATTGAGGCCTGGAGCTCCAgtaagttcat ... ttcgatgcagGGCCGTGAGGAGTCAGTGCAGGAGTTTGTGACTCGTAATCTGGGCCAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttggaaaaatgtttcgtcaaaatcattgaatcatatgattgattcgatgcagGGCCGTGAGGAGTCAGTGCAGGAGTTTGTGACTCGTAATCTGGGCCAGGAGGTCTTTGAGCGGCTGATTGAGCCTTTCTGTTCTG
                                       gattgat  putative branch site (score: 4)
 aaaaatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcatgtctggaagtttctgtttttgaattaacaaatgcgacatttccggcagataatttctgtgtggtgattcattcagcaccgtatattcgtatcaaaatgaagaaatttggaaaaatgtttcgtcaaaatcattgaatcatatgattgattcgatgcagGGCCGTGAGGAGTCAGTGCAGGAGTTTGTGACTCGTAATCTGGGCCAGGAGGTCTTTGAGCGGCTGATTGAGCCTTTCTGTTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT