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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAGgtacgcatactttttggttagagtcgtgaggttattgtcatttgtgcagtcaggaattggcttttcaatctcaaggaaaagctcgtttcgctattttttg...

Basic information

species Physcomitrella patens
transcript PP1S425_12V6.1
intron # 12
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|208363000|gb|DC946897.1|DC946897
EST:     CTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAG                         TTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTG
genomic: CTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAGgtacgcatac ... cccattgcagTTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTG
EST: gi|162186055|gb|FC361883.1|FC361883
EST:     CTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAG                         TTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTG
genomic: CTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAGgtacgcatac ... cccattgcagTTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTG
EST: gi|37828436|gb|BJ586448.1|BJ586448
EST:     CTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAG                         TTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTG
genomic: CTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAGgtacgcatac ... cccattgcagTTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTG
EST: gi|18334455|gb|BJ166472.1|BJ166472
EST:     CTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAG                         TTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTG
genomic: CTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAGgtacgcatac ... cccattgcagTTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTG
EST: gi|37844824|gb|BJ602832.1|BJ602832
EST:     CTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAG                         TTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTG
genomic: CTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAGgtacgcatac ... cccattgcagTTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTG
EST: gi|37848287|gb|BJ606295.1|BJ606295
EST:     CTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAG                         TTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTG
genomic: CTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAGgtacgcatac ... cccattgcagTTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTG
EST: gi|18339737|gb|BJ171764.1|BJ171764
EST:     CTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAG                         TTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTG
genomic: CTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAGgtacgcatac ... cccattgcagTTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTG
EST: gi|162191293|gb|FC366867.1|FC366867
EST:     CTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAG                         TTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTG
genomic: CTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAGgtacgcatac ... cccattgcagTTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTG
EST: gi|162158554|gb|FC334557.1|FC334557
EST:     CTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAG                         TTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTG
genomic: CTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAGgtacgcatac ... cccattgcagTTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTG
EST: gi|67700014|gb|BJ960247.1|BJ960247
EST:     CTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAG                         TTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTG
genomic: CTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAGgtacgcatac ... cccattgcagTTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTG
EST: gi|37823320|gb|BJ581386.1|BJ581386
EST:     CTATTGGGCAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAG                         TTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTG
genomic: CTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAGgtacgcatac ... cccattgcagTTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTG
EST: gi|162218504|gb|FC395081.1|FC395081
EST:     CTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAG                         TTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTG
genomic: CTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAGgtacgcatac ... cccattgcagTTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTG
EST: gi|162191294|gb|FC366868.1|FC366868
EST:     CTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAG                         TTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTG
genomic: CTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAGgtacgcatac ... cccattgcagTTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTG
EST: gi|162185240|gb|FC361750.1|FC361750
EST:     CTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAG                         TTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTG
genomic: CTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAGgtacgcatac ... cccattgcagTTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTG

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), 21 (downstream exon)
Score: 4

AGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAGgtacgcatac ... cccattgcagTTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAGgtacgcatactttttggttagagtcgtgaggttattgtcatttgtgcagtcaggaattggcttttcaatctcaaggaaaagctcgtttcgctattttttg

- - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaggaaaa