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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatactttacttgaactttcatatgcctctcttttgtttaattgcctaatgaaattggaatgctcagttttagggtactgggaatcagccgccatatagtcgaccttttcatgacatgaaggatgtgtgttgcagACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGG

Basic information

species Physcomitrella patens
transcript PP1S11_173V6.1
intron # 3
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|7147844|gb|AW509766.1|AW509766
EST:     CCCAAGACTAGAAAGACCATGCAATTGTTGCGCTTGAAACAG                         ACATTCGATGGGGTTCTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
genomic: CCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAGgtaagaatac ... tgtgttgcagACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
EST: gi|208365775|gb|DC951038.1|DC951038
EST:     ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAG                         ACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
genomic: ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAGgtaagaatac ... tgtgttgcagACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
EST: gi|162206553|gb|FC382922.1|FC382922
EST:     ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAG                         ACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
genomic: ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAGgtaagaatac ... tgtgttgcagACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
EST: gi|18363812|gb|BJ195884.1|BJ195884
EST:     ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAG                         ACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
genomic: ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAGgtaagaatac ... tgtgttgcagACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
EST: gi|37821482|gb|BJ579548.1|BJ579548
EST:     ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAG                         ACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
genomic: ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAGgtaagaatac ... tgtgttgcagACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
EST: gi|67694029|gb|BJ954262.1|BJ954262
EST:     ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAG                         ACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
genomic: ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAGgtaagaatac ... tgtgttgcagACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
EST: gi|162227524|gb|FC403466.1|FC403466
EST:     ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAG                         ACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
genomic: ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAGgtaagaatac ... tgtgttgcagACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
EST: gi|162209025|gb|FC385577.1|FC385577
EST:     ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAG                         ACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
genomic: ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAGgtaagaatac ... tgtgttgcagACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
EST: gi|162275286|gb|FC451262.1|FC451262
EST:     ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAG                         ACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
genomic: ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAGgtaagaatac ... tgtgttgcagACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
EST: gi|37834457|gb|BJ592469.1|BJ592469
EST:     ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAG                         ACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
genomic: ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAGgtaagaatac ... tgtgttgcagACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
EST: gi|162230791|gb|FC406422.1|FC406422
EST:     ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAG                         ACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
genomic: ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAGgtaagaatac ... tgtgttgcagACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
EST: gi|37840975|gb|BJ598983.1|BJ598983
EST:     ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAG                         ACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
genomic: ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAGgtaagaatac ... tgtgttgcagACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
EST: gi|162209026|gb|FC385578.1|FC385578
EST:     ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAG                         ACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
genomic: ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAGgtaagaatac ... tgtgttgcagACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
EST: gi|67700234|gb|BJ960467.1|BJ960467
EST:     ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAG                         ACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
genomic: ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAGgtaagaatac ... tgtgttgcagACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
EST: gi|162230790|gb|FC406421.1|FC406421
EST:     ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAG                         ACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
genomic: ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAGgtaagaatac ... tgtgttgcagACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
EST: gi|18342355|gb|BJ174390.1|BJ174390
EST:     ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAG                         ACATTCGATGGGGTTTTCTTGA
genomic: ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAGgtaagaatac ... tgtgttgcagACATTCGATGGGGTTTTCTTGA
EST: gi|162227523|gb|FC403465.1|FC403465
EST:     ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAG                         ACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
genomic: ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAGgtaagaatac ... tgtgttgcagACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
EST: gi|162259014|gb|FC435125.1|FC435125
EST:     ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAG                         ACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
genomic: ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAGgtaagaatac ... tgtgttgcagACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
EST: gi|162259015|gb|FC435126.1|FC435126
EST:     ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAG                         ACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
genomic: ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAGgtaagaatac ... tgtgttgcagACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
EST: gi|208391789|gb|DC937979.1|DC937979
EST:     ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAG                         ACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG
genomic: ATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAGgtaagaatac ... tgtgttgcagACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTG

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: 15

TGTGAATAATATGCACCCCAAGACTAGGAAGACCATGCAATTGTTGCGCTTGAAACAGgtaagaatac ... tgtgttgcagACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaatcagccgccatatagtcgaccttttcatgacatgaaggatgtgtgttgcagACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGG
             atatagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaatactttacttgaactttcatatgcctctcttttgtttaattgcctaatgaaattggaatgctcagttttagggtactgggaatcagccgccatatagtcgaccttttcatgacatgaaggatgtgtgttgcagACATTCGATGGGGTTTTCTTGAAAGTCAACGAATCTACCATGAGCTTGTTGCGACGAGTGGAGCCATATGTGATCTACGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG