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

gtaatcctctaaaatcattatttattcattcttttatcacgataacttattagtgttatttatccattttttgctgtggttgcatttgcccttcttgcgcttggccttgcctgatagcttcgtgaatgtctaggatgttaagagatagtgctgaatttcaatgcgtatggcagGTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCATCAGAGACGAAGGTTTCAGCATGGGCAAGACGTTTGAGCTAGGAGGACCA

Basic information

species Physcomitrella patens
transcript PP1S79_105V6.1
intron # 7
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|67573788|gb|BJ946612.1|BJ946612
EST:     CAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAA                         GTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCAT
genomic: CAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAAgtaatcctct ... cgtatggcagGTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCAT
EST: gi|37842479|gb|BJ600487.1|BJ600487
EST:     CAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAA                         GTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCAT
genomic: CAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAAgtaatcctct ... cgtatggcagGTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCAT
EST: gi|162259819|gb|FC435954.1|FC435954
EST:     CAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAA                         GTTGCAGCCTGTGCTTGT
genomic: CAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAAgtaatcctct ... cgtatggcagGTTGCAGCCTGTGCTTGT
EST: gi|208367986|gb|DC955393.1|DC955393
EST:     CAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAA                         GTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCAT
genomic: CAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAAgtaatcctct ... cgtatggcagGTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCAT
EST: gi|208352691|gb|DC921425.1|DC921425
EST:     CAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAA                         GTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCAT
genomic: CAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAAgtaatcctct ... cgtatggcagGTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCAT
EST: gi|162256291|gb|FC432197.1|FC432197
EST:     CAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAA                         GTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCAT
genomic: CAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAAgtaatcctct ... cgtatggcagGTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCAT
EST: gi|208377554|gb|DC922657.1|DC922657
EST:     CAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAA                         GTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCAT
genomic: CAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAAgtaatcctct ... cgtatggcagGTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCAT
EST: gi|162259818|gb|FC435953.1|FC435953
EST:     CAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAA                         GTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCAT
genomic: CAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAAgtaatcctct ... cgtatggcagGTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCAT
EST: gi|208367694|gb|DC955025.1|DC955025
EST:     CAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAA                         GTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCAT
genomic: CAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAAgtaatcctct ... cgtatggcagGTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCAT
EST: gi|67700542|gb|BJ960775.1|BJ960775
EST:     AAACTTCCTTTTGTCCCCATACCAGGAGATGGTNTGAGCAA                         GTTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCA
genomic: AAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAAgtaatcctct ... cgtatggcagG-TTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCA
EST: gi|67697174|gb|BJ957407.1|BJ957407
EST:     CAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAA                         GTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCAT
genomic: CAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAAgtaatcctct ... cgtatggcagGTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCAT
EST: gi|37846724|gb|BJ604732.1|BJ604732
EST:     CAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAA                         GTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCAT
genomic: CAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAAgtaatcctct ... cgtatggcagGTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCAT
EST: gi|67578914|gb|BJ951081.1|BJ951081
EST:     CAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAA                         GTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCAT
genomic: CAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAAgtaatcctct ... cgtatggcagGTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCAT
EST: gi|162276086|gb|FC452362.1|FC452362
EST:     CAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAA                         GTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCAT
genomic: CAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAAgtaatcctct ... cgtatggcagGTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCAT
EST: gi|67577666|gb|BJ949833.1|BJ949833
EST:     CAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAA                         GTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCAT
genomic: CAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAAgtaatcctct ... cgtatggcagGTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCAT

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: 29 (upstream exon), 30 (downstream exon)
Score: 11

CAGCGCCTTTGGTTGGTGTTGAGGACCGTTTGCTGAATCGATGGGCCATCCAAGCTAAGAAACTTCCTTTTGTCCCCATACCAGGAGATGGTCTGAGCAAgtaatcctct ... cgtatggcagGTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCATCAGAGACGAAGGTTTCAGCATGGGCAAGACGTTTGAGCTAGGAGGACCA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgtgaatgtctaggatgttaagagatagtgctgaatttcaatgcgtatggcagGTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCATCAGAGACGAAGGTTTCAGCATGGGCAAGACGTTTGAGCTAGGAGGACCA
                                   aatttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcctctaaaatcattatttattcattcttttatcacgataacttattagtgttatttatccattttttgctgtggttgcatttgcccttcttgcgcttggccttgcctgatagcttcgtgaatgtctaggatgttaagagatagtgctgaatttcaatgcgtatggcagGTTGCAGCCTGTGCTTGTAGTTGATGTAGCTGCAGCAGTCATTGCCGCCATCAGAGACGAAGGTTTCAGCATGGGCAAGACGTTTGAGCTAGGAGGACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA