Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatgccttgagttctttctacttcaatacaccatcctatctgcagcctcttttctcaacttgattatgcttctatcttatcgaatgctctcttgtcttaatccttacgaatttgcatttatggctttcttcatgagttcagcagaaattgtatactgatgaagaagttggtttccagGTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATTGCAAGGAGGACACCAGGGTTCACCGGTGCCGACCTACAGAACTTGATGA

Basic information

species Physcomitrella patens
transcript PP1S44_78V6.1
intron # 2
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|162227325|gb|FC403917.1|FC403917
EST:     AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAG                         GTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
genomic: AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAGgtacatgcct ... tggtttccagGTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
EST: gi|162159396|gb|FC334664.1|FC334664
EST:     AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAG                         GTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
genomic: AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAGgtacatgcct ... tggtttccagGTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
EST: gi|162267864|gb|FC444465.1|FC444465
EST:     AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAG                         GTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
genomic: AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAGgtacatgcct ... tggtttccagGTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
EST: gi|19789489|gb|BQ041335.1|BQ041335
EST:     AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAG                         GTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
genomic: AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAGgtacatgcct ... tggtttccagGTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
EST: gi|162180447|gb|FC355868.1|FC355868
EST:     AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAG                         GTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
genomic: AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAGgtacatgcct ... tggtttccagGTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
EST: gi|162215553|gb|FC391346.1|FC391346
EST:     AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAG                         GTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
genomic: AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAGgtacatgcct ... tggtttccagGTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
EST: gi|162166771|gb|FC342740.1|FC342740
EST:     AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAG                         GTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
genomic: AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAGgtacatgcct ... tggtttccagGTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
EST: gi|100376379|gb|BY986138.1|BY986138
EST:     AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAG                         GTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
genomic: AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAGgtacatgcct ... tggtttccagGTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
EST: gi|162163190|gb|FC340244.1|FC340244
EST:     AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAG                         GTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
genomic: AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAGgtacatgcct ... tggtttccagGTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
EST: gi|162179553|gb|FC356593.1|FC356593
EST:     AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAG                         GTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
genomic: AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAGgtacatgcct ... tggtttccagGTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
EST: gi|162183816|gb|FC360733.1|FC360733
EST:     GTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAG                         GTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
genomic: GTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAGgtacatgcct ... tggtttccagGTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT

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), 35 (downstream exon)
Score: 30

ACCCGATGTCCTCGACTCCGCTCTTCTCCGACCTGGACGATTCGACAGGCAGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAGgtacatgcct ... tggtttccagGTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATTGCAAGGAGGACACCAGGGTTCACCGGTGCCGACCTACAGAACTTGATGA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttcttcatgagttcagcagaaattgtatactgatgaagaagttggtttccagGTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATTGCAAGGAGGACACCAGGGTTCACCGGTGCCGACCTACAGAACTTGATGA
                              tactgat  putative branch site (score: 30)
                                                tttcc  putative PPT
                      aaattgtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatgccttgagttctttctacttcaatacaccatcctatctgcagcctcttttctcaacttgattatgcttctatcttatcgaatgctctcttgtcttaatccttacgaatttgcatttatggctttcttcatgagttcagcagaaattgtatactgatgaagaagttggtttccagGTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATTGCAAGGAGGACACCAGGGTTCACCGGTGCCGACCTACAGAACTTGATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA