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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagacatcatgttctgcaccctcaaacgtactcatgtttatctagcatttatgctttaataggtcttcctttggagtgttaatgcatgatcttcgttgtattggatttgtcctggcagGTGACACTTTCCCAGTAGGATGCGCTTTTGATCCCGCCATTGTGCACACCGAG

Basic information

species Physcomitrella patens
transcript PP1S94_154V6.1
intron # 4
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|208387406|gb|DC949191.1|DC949191
EST:     AGTGTTGTTGCATCCTTTGTTCGGAGAGGAGCCTCAATATGCAGTTGTTG                         GTGACACTTTCCCAGTAGGATGCGCTTTTGATCCCGCCATTGTGCACACCG
genomic: AGTGTTGTTGCATCCTTTGTTCGGAGAGGAGCCTCAATATGCAGTTGTTGgtagacatca ... gtcctggcagGTGACACTTTCCCAGTAGGATGCGCTTTTGATCCCGCCATTGTGCACACCG
EST: gi|208374909|gb|DC956182.1|DC956182
EST:     AGTGTTGTTGCATCCTTTGTTCGGAGAGGAGCCTCAATATGCAGTTGTTG                         GTGACACTTTCCCAGTAGGATGCGCTTTTGATCCCGCCATTGTGCACACCG
genomic: AGTGTTGTTGCATCCTTTGTTCGGAGAGGAGCCTCAATATGCAGTTGTTGgtagacatca ... gtcctggcagGTGACACTTTCCCAGTAGGATGCGCTTTTGATCCCGCCATTGTGCACACCG
EST: gi|208365450|gb|DC950917.1|DC950917
EST:     AGTGTTGTTGCATCCTTTGTTCGGAGAGGAGCCTCAATATGCAGTTGTTG                         GTGACACTTTCCCAGTAGGATGCGCTTTTGATCCCGCCATTGTGCACACCG
genomic: AGTGTTGTTGCATCCTTTGTTCGGAGAGGAGCCTCAATATGCAGTTGTTGgtagacatca ... gtcctggcagGTGACACTTTCCCAGTAGGATGCGCTTTTGATCCCGCCATTGTGCACACCG
EST: gi|208354165|gb|DC957399.1|DC957399
EST:     AGTGTTGTTGCATCCTTTGTTCGGAGAGGAGCCTCAATATGCAGTTGTTG                         GTGACACTTTCCCAGTAGGATGCGCTTTTGATCCCGCCATTGTGCACACCG
genomic: AGTGTTGTTGCATCCTTTGTTCGGAGAGGAGCCTCAATATGCAGTTGTTGgtagacatca ... gtcctggcagGTGACACTTTCCCAGTAGGATGCGCTTTTGATCCCGCCATTGTGCACACCG
EST: gi|208385585|gb|DC937130.1|DC937130
EST:     AGTGTTGTTGCATCCTTTGTTCGGAGAGGAGCCTCAATATGCAGTTGTTG                         GTGACACTTTCCCAGTAGGATGCGCTTTTGATCCCGCN-TTGTGCACACCG
genomic: AGTGTTGTTGCATCCTTTGTTCGGAGAGGAGCCTCAATATGCAGTTGTTGgtagacatca ... gtcctggcagGTGACACTTTCCCAGTAGGATGCGCTTTTGATCCCGCCATTGTGCACACCG
EST: gi|208369206|gb|DC955835.1|DC955835
EST:     AGTGTTGTTGCATCCTTTGTTCGGAGAGGAGCCTCAATATGCAGTTGTTG                         GTGACACTTTCCCAGTAGGATGCGCTTTTGATCCCGCCATTGTGCACACCG
genomic: AGTGTTGTTGCATCCTTTGTTCGGAGAGGAGCCTCAATATGCAGTTGTTGgtagacatca ... gtcctggcagGTGACACTTTCCCAGTAGGATGCGCTTTTGATCCCGCCATTGTGCACACCG
EST: gi|67724374|gb|BJ974633.1|BJ974633
EST:     AGTGNTGTTGCATCC-TTGTT-NGAGAGGAGCCTCAATATGCAGTTGTTG                         GTGACACTTTCCCAGTAGGATGCGC-TTTGATCCCGCCATTGTGCACACCG
genomic: AGTGTTGTTGCATCCTTTGTTCGGAGAGGAGCCTCAATATGCAGTTGTTGgtagacatca ... gtcctggcagGTGACACTTTCCCAGTAGGATGCGCTTTTGATCCCGCCATTGTGCACACCG
EST: gi|208390700|gb|DC937856.1|DC937856
EST:     AGTGTTGTTGCATCCTTTGTTCGGAGAGGAGCCTCAATATGCAGTTGTTG                         GTGACACTTTCC-AGTANGATGCGCTTT-GATCCC
genomic: AGTGTTGTTGCATCCTTTGTTCGGAGAGGAGCCTCAATATGCAGTTGTTGgtagacatca ... gtcctggcagGTGACACTTTCCCAGTAGGATGCGCTTTTGATCCC
EST: gi|208385576|gb|DC937121.1|DC937121
EST:     AGTGTTGTTGCATCCTTTGTTCGGAGAGGAGCCTCAATATGCAGTTGTTG                         GTGACACTTTCCCAGTAGGATGCGCTTTTGATCCCGCCATTGTGCACACCG
genomic: AGTGTTGTTGCATCCTTTGTTCGGAGAGGAGCCTCAATATGCAGTTGTTGgtagacatca ... gtcctggcagGTGACACTTTCCCAGTAGGATGCGCTTTTGATCCCGCCATTGTGCACACCG
EST: gi|208354175|gb|DC957409.1|DC957409
EST:     AGTGTTGTTGCATCCTTTGTTCGGAGAGGAGCCTCAATATGCAGTTGTTG                         GTGACACTTTCCCAGTAGGATGCGCTTTTGATCCCGCCATTGTGCACACCG
genomic: AGTGTTGTTGCATCCTTTGTTCGGAGAGGAGCCTCAATATGCAGTTGTTGgtagacatca ... gtcctggcagGTGACACTTTCCCAGTAGGATGCGCTTTTGATCCCGCCATTGTGCACACCG
EST: gi|208370394|gb|DC931806.1|DC931806
EST:     AGTGTTGTTGCATCCTTTGTTCGGAGAGGAGCCTCAATATGCAGTTGTTG                         GTGACACTTTCCCAGTAGGATGCGCTTTTGATCCCGCCATTGTGCACACCG
genomic: AGTGTTGTTGCATCCTTTGTTCGGAGAGGAGCCTCAATATGCAGTTGTTGgtagacatca ... gtcctggcagGTGACACTTTCCCAGTAGGATGCGCTTTTGATCCCGCCATTGTGCACACCG
EST: gi|208365296|gb|DC950767.1|DC950767
EST:     AGTGTTGTTGCATCCTTTGTTCGGAGAGGAGCCTCAATATGCAGTTGTTG                         GTGACACTTTCCCAGTAGGATGCGCTTTTGATCCCGCCATTGTGCACACCG
genomic: AGTGTTGTTGCATCCTTTGTTCGGAGAGGAGCCTCAATATGCAGTTGTTGgtagacatca ... gtcctggcagGTGACACTTTCCCAGTAGGATGCGCTTTTGATCCCGCCATTGTGCACACCG
EST: gi|208372504|gb|DC940779.1|DC940779
EST:     AGTGTTGTTGCATCCTTTGTTCGAA-AGGAGCCTCAATATGCAGTTGTTG                         GTGACACTTTCC-AGTANGATGCGCTTTTGATCCCGC
genomic: AGTGTTGTTGCATCCTTTGTTCGGAGAGGAGCCTCAATATGCAGTTGTTGgtagacatca ... gtcctggcagGTGACACTTTCCCAGTAGGATGCGCTTTTGATCCCGC
EST: gi|208389871|gb|DC937702.1|DC937702
EST:     AGTGTTGTTGCATCCTTTGTTCGGAGAGGAGCCTCA-TATGCAGTTGTTG                         GTGACACTTTCCNAGTANGATGCGCTTTTGATCC
genomic: AGTGTTGTTGCATCCTTTGTTCGGAGAGGAGCCTCAATATGCAGTTGTTGgtagacatca ... gtcctggcagGTGACACTTTCCCAGTAGGATGCGCTTTTGATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcctttggagtgttaatgcatgatcttcgttgtattggatttgtcctggcagGTGACACTTTCCCAGTAGGATGCGCTTTTGATCCCGCCATTGTGCACACCGAG
             tgttaat  putative branch site (score: 3)
                                          tttgtcct  putative PPT
             tgttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagacatcatgttctgcaccctcaaacgtactcatgtttatctagcatttatgctttaataggtcttcctttggagtgttaatgcatgatcttcgttgtattggatttgtcctggcagGTGACACTTTCCCAGTAGGATGCGCTTTTGATCCCGCCATTGTGCACACCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG