Skip to another splice site:
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 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCCACGGGAGGGCTGTGGAGAGGGCAGTCTCTTGCAGGGAAGCCAGCAGGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaatctttataaatgtttccccttctatcatttcttgtgcttctgacacttcagtggatgtggtctttgtaggtatggtaagcgtcatttccaa...

Basic information

species Physcomitrella patens
transcript PP1S475_5V6.1
intron # 3
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|162193827|gb|FC371302.1|FC371302
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|208385911|gb|DC956749.1|DC956749
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|162163406|gb|FC339732.1|FC339732
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|162207068|gb|FC382182.1|FC382182
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|67579381|gb|BJ951502.1|BJ951502
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|162228698|gb|FC405726.1|FC405726
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|162190185|gb|FC365927.1|FC365927
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|100359621|gb|BY947072.1|BY947072
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|162187749|gb|FC364661.1|FC364661
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|162239072|gb|FC418499.1|FC418499
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|162150320|gb|FC325864.1|FC325864
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|208363554|gb|DC939759.1|DC939759
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|162158189|gb|FC335232.1|FC335232
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|100361900|gb|BY947683.1|BY947683
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|208378489|gb|DC927186.1|DC927186
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|208362744|gb|DC950544.1|DC950544
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|162203315|gb|FC378775.1|FC378775
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|67692838|gb|BJ953071.1|BJ953071
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|100352993|gb|BY945553.1|BY945553
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACNACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|208375821|gb|DC926913.1|DC926913
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|162150321|gb|FC325865.1|FC325865
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|208356449|gb|DC914311.1|DC914311
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|208364585|gb|DC935370.1|DC935370
EST:     GGAATTTTTGTTANCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCANTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|208385419|gb|DC956631.1|DC956631
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|67694047|gb|BJ954280.1|BJ954280
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCT
EST: gi|208388933|gb|DC932961.1|DC932961
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|208383753|gb|DC928056.1|DC928056
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|162239073|gb|FC418500.1|FC418500
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|162245209|gb|FC422138.1|FC422138
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|162187750|gb|FC364662.1|FC364662
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|208386010|gb|DC956526.1|DC956526
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|100361247|gb|BY946987.1|BY946987
EST:     GAATTTTTGTTAGCACGGGCACTNCA-GGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GAATTTTTGTTAGCACGGGCACT-CAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
EST: gi|208373459|gb|DC931890.1|DC931890
EST:     GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGC                         GTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT
genomic: GGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGAT

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), 34 (downstream exon)
Score: 101

ATTCCACGGGAGGGCTGTGGAGAGGGCAGTCTCTTGCAGGGAAGCCAGCAGGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaat ... tggctcccagGTTGACAACCATCACGCAGTTGACACATCACGGGATGCTCTATGTCCCGATCGGATATACTTTTGGTGCTGGGATGTTCAAACTAGACGAGCCCAGAGGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTCCACGGGAGGGCTGTGGAGAGGGCAGTCTCTTGCAGGGAAGCCAGCAGGAATTTTTGTTAGCACGGGCACTCAAGGTGGAGGACAGGAGACTACCGCgtaagttaatctttataaatgtttccccttctatcatttcttgtgcttctgacacttcagtggatgtggtctttgtaggtatggtaagcgtcatttccaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA