Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTACAAATGTCATGCCTGGCTGCGGATCCTCATTCTCCATCAAGGCTCATCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAGgtgcggctcgcaccttgtgcagaatatttttagtgttacatttttaacttcaatttctaatttctatacgtatgaaacag

Basic information

species Physcomitrella patens
transcript PP1S79_105V6.1
intron # 6
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|37842479|gb|BJ600487.1|BJ600487
EST:     TCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAG                         GCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTG
genomic: TCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAGgtgcggctcg ... tatgaaacagGCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTG
EST: gi|162256292|gb|FC432198.1|FC432198
EST:     TCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAG                         GCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTG
genomic: TCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAGgtgcggctcg ... tatgaaacagGCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTG
EST: gi|162259819|gb|FC435954.1|FC435954
EST:     TCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAG                         GCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTG
genomic: TCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAGgtgcggctcg ... tatgaaacagGCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTG
EST: gi|208367986|gb|DC955393.1|DC955393
EST:     TCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAG                         GCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTG
genomic: TCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAGgtgcggctcg ... tatgaaacagGCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTG
EST: gi|162276087|gb|FC452363.1|FC452363
EST:     TCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAG                         GCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTG
genomic: TCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAGgtgcggctcg ... tatgaaacagGCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTG
EST: gi|67577930|gb|BJ950097.1|BJ950097
EST:     TCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAG                         GCAACTATCTTGAGGA
genomic: TCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAGgtgcggctcg ... tatgaaacagGCAACTATCTTGAGGA
EST: gi|208352691|gb|DC921425.1|DC921425
EST:     TCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAG                         GCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTG
genomic: TCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAGgtgcggctcg ... tatgaaacagGCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTG
EST: gi|162256291|gb|FC432197.1|FC432197
EST:     TCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAG                         GCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTG
genomic: TCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAGgtgcggctcg ... tatgaaacagGCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTG
EST: gi|208377554|gb|DC922657.1|DC922657
EST:     TCCGTTNTAAGCATGCTGCTGAAGAGGCAGTTATGCAGNACTTTCCTGAG                         GCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTG
genomic: TCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAGgtgcggctcg ... tatgaaacagGCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTG
EST: gi|162259818|gb|FC435953.1|FC435953
EST:     TCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCTTGAG                         GCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTG
genomic: TCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAGgtgcggctcg ... tatgaaacagGCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTG
EST: gi|208367694|gb|DC955025.1|DC955025
EST:     TCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAG                         GCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTG
genomic: TCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAGgtgcggctcg ... tatgaaacagGCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTG
EST: gi|37846724|gb|BJ604732.1|BJ604732
EST:     TCCGTTNTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAG                         GCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTG
genomic: TCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAGgtgcggctcg ... tatgaaacagGCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTG
EST: gi|67578914|gb|BJ951081.1|BJ951081
EST:     TTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAG                         GCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTG
genomic: TTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAGgtgcggctcg ... tatgaaacagGCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTG
EST: gi|162276086|gb|FC452362.1|FC452362
EST:     TCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAG                         GCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTG
genomic: TCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAGgtgcggctcg ... tatgaaacagGCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTG
EST: gi|67577666|gb|BJ949833.1|BJ949833
EST:     TCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAG                         GCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTG
genomic: TCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAGgtgcggctcg ... tatgaaacagGCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTG
EST: gi|208393451|gb|DC942521.1|DC942521
EST:     TCCGTTCTAAGCATGCTGCTGAAAANGCAGTTATGCANAACTTTCCTGAG                         GCACCTATCTTGAGGACAGCGCCTTTGGTT
genomic: TCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAGgtgcggctcg ... tatgaaacagGCAACTATCTTGAGGACAGCGCCTTTGGTT

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), 23 (downstream exon)
Score: 4

CGTACAAATGTCATGCCTGGCTGCGGATCCTCATTCTCCATCAAGGCTCATCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAGgtgcggctcg ... tatgaaacagGCAACTATCTTGAGGACAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTGAATCGATGGGCCATCCAAGCTAAGAAACTTCCTTTTGTCCCCATACCAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTACAAATGTCATGCCTGGCTGCGGATCCTCATTCTCCATCAAGGCTCATCCGTTCTAAGCATGCTGCTGAAGAGGCAGTTATGCAGAACTTTCCTGAGgtgcggctcgcaccttgtgcagaatatttttagtgttacatttttaacttcaatttctaatttctatacgtatgaaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG