Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCTGAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagccttcctttgaggacctgcttttattttggatgtgctgcataaaatatccgcttgtagtttttaaaaaattatttgctataccaattattt...

Basic information

species Physcomitrella patens
transcript PP1S76_212V6.1
intron # 4
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|18325020|gb|BJ157016.1|BJ157016
EST:     GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAG                         TGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagc ... ctttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|18332989|gb|BJ165003.1|BJ165003
EST:     CAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAG                         TGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: CAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagc ... ctttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|162224580|gb|FC400476.1|FC400476
EST:     GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAG                         TGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagc ... ctttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|18348082|gb|BJ180129.1|BJ180129
EST:     GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAG                         TGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagc ... ctttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|67508569|gb|BJ941432.1|BJ941432
EST:     GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAG                         TGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagc ... ctttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|18345107|gb|BJ177148.1|BJ177148
EST:     GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAG                         TGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagc ... ctttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|37827453|gb|BJ585465.1|BJ585465
EST:     GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAG                         TGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagc ... ctttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|162250386|gb|FC426248.1|FC426248
EST:     GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAG                         TGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagc ... ctttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|37824297|gb|BJ582363.1|BJ582363
EST:     GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAG                         TGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagc ... ctttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|162250385|gb|FC426247.1|FC426247
EST:     GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAG                         TGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagc ... ctttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|162177237|gb|FC353394.1|FC353394
EST:     GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAG                         TGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagc ... ctttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|67691788|gb|BJ952021.1|BJ952021
EST:     GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAG                         TGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagc ... ctttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|208372787|gb|DC952674.1|DC952674
EST:     AGTGGATCAAGGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAG                         TGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: AGTGGATCAA-GGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagc ... ctttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|162224579|gb|FC400475.1|FC400475
EST:     GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAG                         TGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagc ... ctttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|162177238|gb|FC353395.1|FC353395
EST:     GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAG                         TGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagc ... ctttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT

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), 22 (downstream exon)
Score: 10

CTTCTGAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagc ... ctttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAAGATGCTATCAAAGCGGCGGTGAAGGACTACAAGTCCAAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCTGAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagccttcctttgaggacctgcttttattttggatgtgctgcataaaatatccgcttgtagtttttaaaaaattatttgctataccaattattt

- - - AGTGGA
- - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - -  AAGAAC