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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttctgtgatttctatcttatttctattttttattttatgtttgtttattttttttagtttttttctgactgtccaatttgatgctggtgaagctaagGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGCTCGGCATCGTGGCGCCAAGTGTATGCTGTCGTTCTGGATAATAATCTAAACCTG

Basic information

species Physcomitrella patens
transcript PP1S98_84V6.2
intron # 1
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|162229735|gb|FC404019.1|FC404019
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGCTAAG                     
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTC--G---AGgtgagtggtg ... tgaagc
EST: gi|208368426|gb|DC935991.1|DC935991
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGCTAAG                     
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTC--G---AGgtgagtggtg ... tgaagc
EST: gi|100372576|gb|BY985666.1|BY985666
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGCTAAG                     
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTC--G---AGgtgagtggtg ... tgaagc
EST: gi|100416857|gb|BY993124.1|BY993124
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGCTAAG                     
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTC--G---AGgtgagtggtg ... tgaagc
EST: gi|208378757|gb|DC914731.1|DC914731
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGCTAAG                     
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTC--G---AGgtgagtggtg ... tgaagc
EST: gi|100452996|gb|CJ975548.1|CJ975548
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGCTAAG                     
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTC--G---AGgtgagtggtg ... tgaagc
EST: gi|67704222|gb|BJ964455.1|BJ964455
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAG                         C
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... tgaagctaag-
EST: gi|67704222|gb|BJ964455.1|BJ964455
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAG                         C
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... tgaagctaag-
EST: gi|67704222|gb|BJ964455.1|BJ964455
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAG                         C
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... tgaagctaag-
EST: gi|67704222|gb|BJ964455.1|BJ964455
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAG                         C
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... tgaagctaag-
EST: gi|67704222|gb|BJ964455.1|BJ964455
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAG                         C
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... tgaagctaag-
EST: gi|100418392|gb|BY957396.1|BY957396
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGCTAAG                     
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTC--G---AGgtgagtggtg ... tgaagc
EST: gi|100398110|gb|BY954093.1|BY954093
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGCTAAG                     
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTC--G---AGgtgagtggtg ... tgaagc
EST: gi|18328498|gb|BJ160503.1|BJ160503
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGCTAAG                     
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTC--G---AGgtgagtggtg ... tgaagc
EST: gi|208377991|gb|DC914368.1|DC914368
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAG                         GACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGCTCGGC
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... tgaagctaagGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGCTCGGC
EST: gi|162225034|gb|FC401450.1|FC401450
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAG                         GACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGCTCGGC
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... tgaagctaagGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGCTCGGC
EST: gi|67571140|gb|BJ943964.1|BJ943964
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAG                         GACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGCTCGGC
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... tgaagctaagGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGCTCGGC
EST: gi|100442029|gb|BY962922.1|BY962922
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAG                         GACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGCTCGGC
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... tgaagctaagGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGCTCGGC
EST: gi|100443881|gb|BY982109.1|BY982109
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGCTAAG                     
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTC--G---AGgtgagtggtg ... tgaagc
EST: gi|18348368|gb|BJ180416.1|BJ180416
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGCTAAG                     
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTC--G---AGgtgagtggtg ... tgaagc
EST: gi|208400107|gb|DC904755.1|DC904755
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGCTAAG                     
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTC--G---AGgtgagtggtg ... tgaagc
EST: gi|7148073|gb|AW509995.1|AW509995
EST:     TTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCTAGCTAAG                         GACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGCTCGG
genomic: TTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTC--G---AGgtgagtggtg ... tgaagctaagGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGCTCGG
EST: gi|208353978|gb|DC930118.1|DC930118
EST:     ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGCTAAG                     
genomic: ACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTC--G---AGgtgagtggtg ... tgaagc

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), 32 (downstream exon)
Score: 26

TTGGGGGCGTTGAAGCGGCAGCACTGCTACGATTGCGCTTCGTTAGAGCCACAGTTTGCCACATTTCGTTGTCGTCTGAGGAGAATCGGGCGGATTCGAGgtgagtggtg ... tgaagctaagGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGCTCGGCATCGTGGCGCCAAGTGTATGCTGTCGTTCTGGATAATAATCTAAACCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttattttttttagtttttttctgactgtccaatttgatgctggtgaagctaagGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGCTCGGCATCGTGGCGCCAAGTGTATGCTGTCGTTCTGGATAATAATCTAAACCTG
     ttttttttagtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttctgtgatttctatcttatttctattttttattttatgtttgtttattttttttagtttttttctgactgtccaatttgatgctggtgaagctaagGACACATGTGGAGTTCGGCCACAGTGCTGCTCCTTTTACTACCTGCTCGGCATCGTGGCGCCAAGTGTATGCTGTCGTTCTGGATAATAATCTAAACCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG