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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGTCAAGCGGGTCGTCCTAAGACCATCACTGGCTTCCAGACACACACTACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAAgtacgttccctcagtactgcatctgattaatttcattgcatggttgtgtctggaatgaatttctgacctgcatctttgatggacattttgcag

Basic information

species Physcomitrella patens
transcript PP1S414_22V6.1
intron # 24
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|162196692|gb|FC373825.1|FC373825
EST:     ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAA                         GTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
genomic: ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAAgtacgttccc ... cattttgcagGTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
EST: gi|162181393|gb|FC358449.1|FC358449
EST:     ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAA                         GTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
genomic: ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAAgtacgttccc ... cattttgcagGTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
EST: gi|37846088|gb|BJ604096.1|BJ604096
EST:     ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAA                         GTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
genomic: ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAAgtacgttccc ... cattttgcagGTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
EST: gi|162275984|gb|FC452052.1|FC452052
EST:     ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAA                         GTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
genomic: ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAAgtacgttccc ... cattttgcagGTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
EST: gi|162255375|gb|FC432101.1|FC432101
EST:     ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAA                         GTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
genomic: ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAAgtacgttccc ... cattttgcagGTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
EST: gi|162192599|gb|FC370646.1|FC370646
EST:     ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAA                         GTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
genomic: ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAAgtacgttccc ... cattttgcagGTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
EST: gi|37828992|gb|BJ587004.1|BJ587004
EST:     ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAA                         GTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
genomic: ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAAgtacgttccc ... cattttgcagGTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
EST: gi|162196103|gb|FC372742.1|FC372742
EST:     ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAA                         GTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
genomic: ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAAgtacgttccc ... cattttgcagGTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
EST: gi|162172803|gb|FC348392.1|FC348392
EST:     ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAA                         GTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
genomic: ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAAgtacgttccc ... cattttgcagGTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
EST: gi|162192598|gb|FC370645.1|FC370645
EST:     ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAA                         GTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
genomic: ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAAgtacgttccc ... cattttgcagGTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
EST: gi|162154532|gb|FC330742.1|FC330742
EST:     ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAA                         GTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
genomic: ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAAgtacgttccc ... cattttgcagGTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
EST: gi|19790154|gb|BQ041724.1|BQ041724
EST:     ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAA                         GTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
genomic: ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAAgtacgttccc ... cattttgcagGTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
EST: gi|37827917|gb|BJ585929.1|BJ585929
EST:     ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAA                         GTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
genomic: ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAAgtacgttccc ... cattttgcagGTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
EST: gi|162175300|gb|FC351498.1|FC351498
EST:     ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAA                         GTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
genomic: ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAAgtacgttccc ... cattttgcagGTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
EST: gi|37832308|gb|BJ590320.1|BJ590320
EST:     ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAA                         GTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
genomic: ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAAgtacgttccc ... cattttgcagGTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
EST: gi|162198495|gb|FC375330.1|FC375330
EST:     ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAA                         GTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
genomic: ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAAgtacgttccc ... cattttgcagGTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
EST: gi|37848660|gb|BJ606668.1|BJ606668
EST:     ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAA                         GTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
genomic: ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAAgtacgttccc ... cattttgcagGTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
EST: gi|15327138|gb|BI487641.1|BI487641
EST:     ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAA                         GTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
genomic: ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAAgtacgttccc ... cattttgcagGTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
EST: gi|37824938|gb|BJ583004.1|BJ583004
EST:     ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAA                         GTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA
genomic: ACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAAgtacgttccc ... cattttgcagGTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAA

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: 35 (upstream exon), 30 (downstream exon)
Score: 10

TTGGTCAAGCGGGTCGTCCTAAGACCATCACTGGCTTCCAGACACACACTACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAAgtacgttccc ... cattttgcagGTACCTTCCTTTGTCATCGGTGTTAGAAGGATTTGTTATTTTGAAGCTCAACCCGGATTATGAGGATGATCATTTGAGTTAAATTTGTAGAAATTGACGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGGTCAAGCGGGTCGTCCTAAGACCATCACTGGCTTCCAGACACACACTACTCCTGTTATTTTGGCTACTGGTGACCGTGCAGAGCTGGCCACTGACAAgtacgttccctcagtactgcatctgattaatttcattgcatggttgtgtctggaatgaatttctgacctgcatctttgatggacattttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT