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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattttagcctcaaactcttgctgaatttttgtaagattagcgctgccgattagcttttcctttagttctttttgaccgcttacaagtgccagtcgccctactattttctttctgcatgaatgcctttcttttgagcctctaatcttcttctttttaatctcttttgtccctacgttctccgcagATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGATATATGTAGATCGACAGCTGCAAAATAGACAG

Basic information

species Physcomitrella patens
transcript PP1S100_117V6.1
intron # 10
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|208395424|gb|DC924478.1|DC924478
EST:     CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACG                         ATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
genomic: CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACGgtaattttag ... ttctccgcagATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
EST: gi|162269043|gb|FC445535.1|FC445535
EST:     CCGTANAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACG                         ATATTACCCATCCCATTCCC
genomic: CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACGgtaattttag ... ttctccgcagATATTACCCATCCCATTCCC
EST: gi|37837091|gb|BJ595099.1|BJ595099
EST:     CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACG                         ATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
genomic: CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACGgtaattttag ... ttctccgcagATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
EST: gi|162153494|gb|FC329380.1|FC329380
EST:     AACTATGCCCAACGACG                         ATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
genomic: AACTATGCCCAACGACGgtaattttag ... ttctccgcagATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
EST: gi|162278566|gb|FC454028.1|FC454028
EST:     CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACG                         ATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
genomic: CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACGgtaattttag ... ttctccgcagATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
EST: gi|162230898|gb|FC406737.1|FC406737
EST:     CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACG                         ATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
genomic: CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACGgtaattttag ... ttctccgcagATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
EST: gi|67698241|gb|BJ958474.1|BJ958474
EST:     GTAAAGGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGGACG                         ATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAG
genomic: GTAAA-GGATCTATTACTCAGATCCCAATTTTAACTATGCCCAAC-GACGgtaattttag ... ttctccgcagATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAG
EST: gi|162209307|gb|FC385227.1|FC385227
EST:     CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACG                         ATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
genomic: CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACGgtaattttag ... ttctccgcagATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
EST: gi|162153495|gb|FC329381.1|FC329381
EST:     CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACG                         ATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
genomic: CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACGgtaattttag ... ttctccgcagATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
EST: gi|162232324|gb|FC408667.1|FC408667
EST:     CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACG                         ATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA
genomic: CCGTAAAGGATCTATTACTCAGATCCCAATTTTAACTATGCCCAACGACGgtaattttag ... ttctccgcagATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgagcctctaatcttcttctttttaatctcttttgtccctacgttctccgcagATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGATATATGTAGATCGACAGCTGCAAAATAGACAG
                      ttttaat  putative branch site (score: 3)
             tcttcttctttttaat  CT-rich tract
                     tttttaatctctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattttagcctcaaactcttgctgaatttttgtaagattagcgctgccgattagcttttcctttagttctttttgaccgcttacaagtgccagtcgccctactattttctttctgcatgaatgcctttcttttgagcctctaatcttcttctttttaatctcttttgtccctacgttctccgcagATATTACCCATCCCATTCCCGATCTCACAGGATACATCACCGAAGGTCAGATATATGTAGATCGACAGCTGCAAAATAGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC