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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGTTGATGTGGAGTAGTCGACCTCACAGGCCTCTTCGTCACTGCTGCTTGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAGgtgcatcttcccgtcgttggtggttgttttgctgcatttgatgttctgatctttggagctggctgcaattctgctggagcaatggcagttgttgcctttg...

Basic information

species Physcomitrella patens
transcript PP1S61_236V6.2
intron # 1
splice site 5'
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|100391090|gb|BY953100.1|BY953100
EST:     TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAG                         AGGATTGTGGAGTGCGCTTGGTGAACATGGCAGCCAATGCATTCCTTGCGA
genomic: TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAGgtgcatcttc ... ttttctgtagAGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
EST: gi|162170725|gb|FC346312.1|FC346312
EST:     CATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAG                         AGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
genomic: CATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAGgtgcatcttc ... ttttctgtagAGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
EST: gi|208379062|gb|DC911587.1|DC911587
EST:     TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAG                         AGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
genomic: TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAGgtgcatcttc ... ttttctgtagAGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
EST: gi|162159310|gb|FC335137.1|FC335137
EST:     TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAG                         AGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
genomic: TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAGgtgcatcttc ... ttttctgtagAGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
EST: gi|162252429|gb|FC427823.1|FC427823
EST:     TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAG                         AGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
genomic: TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAGgtgcatcttc ... ttttctgtagAGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
EST: gi|208346318|gb|DC905265.1|DC905265
EST:     TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAG                         AGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
genomic: TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAGgtgcatcttc ... ttttctgtagAGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
EST: gi|208359372|gb|DC939125.1|DC939125
EST:     TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAG                         AGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
genomic: TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAGgtgcatcttc ... ttttctgtagAGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
EST: gi|100360090|gb|BY966020.1|BY966020
EST:     TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAG                         AGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
genomic: TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAGgtgcatcttc ... ttttctgtagAGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
EST: gi|67573350|gb|BJ946174.1|BJ946174
EST:     CTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAG                         AGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
genomic: CTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAGgtgcatcttc ... ttttctgtagAGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
EST: gi|100388863|gb|BY988739.1|BY988739
EST:     TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAG                         AGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
genomic: TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAGgtgcatcttc ... ttttctgtagAGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
EST: gi|208383415|gb|DC907590.1|DC907590
EST:     TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAG                         AGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
genomic: TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAGgtgcatcttc ... ttttctgtagAGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
EST: gi|208398083|gb|DC904388.1|DC904388
EST:     TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAG                         AGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
genomic: TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAGgtgcatcttc ... ttttctgtagAGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
EST: gi|100435354|gb|BY979201.1|BY979201
EST:     GCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAG                         AGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
genomic: GCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAGgtgcatcttc ... ttttctgtagAGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
EST: gi|100387924|gb|BY970669.1|BY970669
EST:     TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAG                         AGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
genomic: TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAGgtgcatcttc ... ttttctgtagAGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
EST: gi|19789638|gb|BQ041425.1|BQ041425
EST:     TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAG                         AGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
genomic: TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAGgtgcatcttc ... ttttctgtagAGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
EST: gi|208346250|gb|DC909542.1|DC909542
EST:     TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAN                         AGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
genomic: TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAGgtgcatcttc ... ttttctgtagAGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
EST: gi|208388898|gb|DC932926.1|DC932926
EST:     TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAG                         AGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
genomic: TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAGgtgcatcttc ... ttttctgtagAGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
EST: gi|67719140|gb|BJ969399.1|BJ969399
EST:     TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAG                         AGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
genomic: TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAGgtgcatcttc ... ttttctgtagAGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
EST: gi|162202874|gb|FC379856.1|FC379856
EST:     TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAG                         AGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
genomic: TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAGgtgcatcttc ... ttttctgtagAGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
EST: gi|162244029|gb|FC422345.1|FC422345
EST:     TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAG                         AGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
genomic: TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAGgtgcatcttc ... ttttctgtagAGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
EST: gi|18330624|gb|BJ162630.1|BJ162630
EST:     TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAG                         AGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
genomic: TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAGgtgcatcttc ... ttttctgtagAGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
EST: gi|18351259|gb|BJ183311.1|BJ183311
EST:     TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAG                         AGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA
genomic: TGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAGgtgcatcttc ... ttttctgtagAGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 34 (upstream exon), 33 (downstream exon)
Score: 9

ATTGTTGATGTGGAGTAGTCGACCTCACAGGCCTCTTCGTCACTGCTGCTTGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAGgtgcatcttc ... ttttctgtagAGGATTGTGGAGTGCGCTTGGTGGACATGGCAGCCAATGCATTCCTTGCGAACAGGTTGACGGCCGCGCCTTCACTGGCCTCGGCTTCCTGCTCACACAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGTTGATGTGGAGTAGTCGACCTCACAGGCCTCTTCGTCACTGCTGCTTGGTTTAGCATCCTTCGCTGCGCACTTGGAGTCCTTTCTCAGCCTCTGAGgtgcatcttcccgtcgttggtggttgttttgctgcatttgatgttctgatctttggagctggctgcaattctgctggagcaatggcagttgttgcctttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG