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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttactttctcttactctatcaattatagttggtcacatgaatattggtgattgcaagcagagaatctaactggtggcattctctgcaatacagTGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGGCTTGACAGACGAAGACATCTTCGCTGGGAAGGTGACGGACAAGTGGAGG

Basic information

species Physcomitrella patens
transcript PP1S323_70V6.1
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|162221128|gb|FC397769.1|FC397769
EST:     CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGA                         TGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
genomic: CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGAgtgagttact ... tgcaatacagTGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
EST: gi|37823421|gb|BJ581487.1|BJ581487
EST:     GCCANCCAGCTCACCAATATCCATCGCGATGTTGGAGAAGA                         TGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
genomic: GCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGAgtgagttact ... tgcaatacagTGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
EST: gi|162195318|gb|FC370839.1|FC370839
EST:     CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGA                         TGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
genomic: CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGAgtgagttact ... tgcaatacagTGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
EST: gi|162233127|gb|FC408950.1|FC408950
EST:     CCTTCGCGATGTTGGAGAAGA                         TGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
genomic: CCTTCGCGATGTTGGAGAAGAgtgagttact ... tgcaatacagTGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
EST: gi|162279508|gb|FC455819.1|FC455819
EST:     CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGA                         TGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
genomic: CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGAgtgagttact ... tgcaatacagTGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
EST: gi|37838421|gb|BJ596429.1|BJ596429
EST:     CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGA                         TGCGAGGAGGGGAAGAGTGTACCTCCCACAGGGACGAACTGGCCCGATTTG
genomic: CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGAgtgagttact ... tgcaatacagTGCGAGGAGGGGAAGAGTGTACCTCCCACA-GGACGAACTGGCCCGATTTG
EST: gi|162195317|gb|FC370838.1|FC370838
EST:     CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGA                         TGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
genomic: CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGAgtgagttact ... tgcaatacagTGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
EST: gi|162167422|gb|FC343125.1|FC343125
EST:     TCGCGATGTTGGAGAAGA                         TGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
genomic: TCGCGATGTTGGAGAAGAgtgagttact ... tgcaatacagTGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
EST: gi|37841215|gb|BJ599223.1|BJ599223
EST:     CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGA                         TGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
genomic: CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGAgtgagttact ... tgcaatacagTGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
EST: gi|67578890|gb|BJ951057.1|BJ951057
EST:     TGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGA                         TGCGAGGAGGGGAAGAGTGTACCTCCCCACAGGACGAACTGGCCCGATTTG
genomic: TGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGAgtgagttact ... tgcaatacagTGCGAGGAGGGGAAGAGTGTACCT-CCCACAGGACGAACTGGCCCGATTTG
EST: gi|67692313|gb|BJ952546.1|BJ952546
EST:     CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGA                         TGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
genomic: CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGAgtgagttact ... tgcaatacagTGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
EST: gi|162194278|gb|FC368500.1|FC368500
EST:     CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGA                         TGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
genomic: CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGAgtgagttact ... tgcaatacagTGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
EST: gi|162155565|gb|FC331009.1|FC331009
EST:     CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGA                         TGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
genomic: CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGAgtgagttact ... tgcaatacagTGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
EST: gi|162263002|gb|FC438810.1|FC438810
EST:     CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGA                         TGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
genomic: CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGAgtgagttact ... tgcaatacagTGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
EST: gi|37821980|gb|BJ580046.1|BJ580046
EST:     CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGA                         TGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
genomic: CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGAgtgagttact ... tgcaatacagTGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
EST: gi|208347271|gb|DC917174.1|DC917174
EST:     CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGNTGGAGANGA                         TGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
genomic: CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGAgtgagttact ... tgcaatacagTGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
EST: gi|162213599|gb|FC389679.1|FC389679
EST:     CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGA                         TGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
genomic: CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGAgtgagttact ... tgcaatacagTGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
EST: gi|37838751|gb|BJ596759.1|BJ596759
EST:     CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGA                         TGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
genomic: CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGAgtgagttact ... tgcaatacagTGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
EST: gi|162178498|gb|FC354950.1|FC354950
EST:     CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGA                         TGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
genomic: CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGAgtgagttact ... tgcaatacagTGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
EST: gi|162196411|gb|FC373557.1|FC373557
EST:     CGCGATGTTGGAGAAGA                         TGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
genomic: CGCGATGTTGGAGAAGAgtgagttact ... tgcaatacagTGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
EST: gi|162279509|gb|FC455820.1|FC455820
EST:     CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGA                         TGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
genomic: CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGAgtgagttact ... tgcaatacagTGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
EST: gi|37852048|gb|BJ610056.1|BJ610056
EST:     CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGA                         TGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
genomic: CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGAgtgagttact ... tgcaatacagTGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
EST: gi|162162257|gb|FC338039.1|FC338039
EST:     CGCGATGTTGGAGAAGA                         TGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
genomic: CGCGATGTTGGAGAAGAgtgagttact ... tgcaatacagTGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
EST: gi|37836953|gb|BJ594961.1|BJ594961
EST:     CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGA                         TGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG
genomic: CTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGAgtgagttact ... tgcaatacagTGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGG

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: 26 (upstream exon), 35 (downstream exon)
Score: 29

ACCCTGAGTCGAAGGCCACTACACAAAGTGTATACAACGGTGCTCTGGCACTAGGAATTGCCAACCAGCTCACCAATATCCTTCGCGATGTTGGAGAAGAgtgagttact ... tgcaatacagTGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGGCTTGACAGACGAAGACATCTTCGCTGGGAAGGTGACGGACAAGTGGAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatattggtgattgcaagcagagaatctaactggtggcattctctgcaatacagTGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGGCTTGACAGACGAAGACATCTTCGCTGGGAAGGTGACGGACAAGTGGAGG
                         atctaac  putative branch site (score: 29)
                                      cattctct  putative PPT
                        aatctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttactttctcttactctatcaattatagttggtcacatgaatattggtgattgcaagcagagaatctaactggtggcattctctgcaatacagTGCGAGGAGGGGAAGAGTGTACCTCCCACAGGACGAACTGGCCCGATTTGGCTTGACAGACGAAGACATCTTCGCTGGGAAGGTGACGGACAAGTGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG