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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGAAGCTTGTTCGACCAAGAGTTCCATACCTCAAATATGGCCTCTTTATCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAGgtacatcttcctctcaacactttcacttaatctctcaacacccacaaatatcctgaaacaacattgatgtggttaacttgagcaatacgttctacgagac...

Basic information

species Physcomitrella patens
transcript PP1S101_169V6.1
intron # 7
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|37845451|gb|BJ603459.1|BJ603459
EST:     TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAG                         GCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
genomic: TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAGgtacatcttc ... tggatcacagGCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
EST: gi|37837490|gb|BJ595498.1|BJ595498
EST:     TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAG                         GCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
genomic: TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAGgtacatcttc ... tggatcacagGCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
EST: gi|162194475|gb|FC371115.1|FC371115
EST:     TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAG                         GCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
genomic: TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAGgtacatcttc ... tggatcacagGCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
EST: gi|162166009|gb|FC341814.1|FC341814
EST:     TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAG                         GCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
genomic: TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAGgtacatcttc ... tggatcacagGCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
EST: gi|37835482|gb|BJ593494.1|BJ593494
EST:     TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAG                         GCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
genomic: TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAGgtacatcttc ... tggatcacagGCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
EST: gi|37834995|gb|BJ593007.1|BJ593007
EST:     TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAG                         GCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
genomic: TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAGgtacatcttc ... tggatcacagGCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
EST: gi|37840690|gb|BJ598698.1|BJ598698
EST:     TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAG                         GCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
genomic: TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAGgtacatcttc ... tggatcacagGCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
EST: gi|37821522|gb|BJ579588.1|BJ579588
EST:     TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAG                         GCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
genomic: TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAGgtacatcttc ... tggatcacagGCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
EST: gi|37829381|gb|BJ587393.1|BJ587393
EST:     TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAG                         GCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
genomic: TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAGgtacatcttc ... tggatcacagGCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
EST: gi|37848000|gb|BJ606008.1|BJ606008
EST:     TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAG                         GCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
genomic: TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAGgtacatcttc ... tggatcacagGCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
EST: gi|37845807|gb|BJ603815.1|BJ603815
EST:     TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAG                         GCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
genomic: TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAGgtacatcttc ... tggatcacagGCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
EST: gi|208368471|gb|DC955124.1|DC955124
EST:     TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAG                         GCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
genomic: TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAGgtacatcttc ... tggatcacagGCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
EST: gi|37852983|gb|BJ610991.1|BJ610991
EST:     TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAG                         GCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
genomic: TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAGgtacatcttc ... tggatcacagGCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
EST: gi|37842052|gb|BJ600060.1|BJ600060
EST:     TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAG                         GCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
genomic: TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAGgtacatcttc ... tggatcacagGCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
EST: gi|37849754|gb|BJ607762.1|BJ607762
EST:     TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAG                         GCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG
genomic: TCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAGgtacatcttc ... tggatcacagGCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAG

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: 11 (upstream exon), 34 (downstream exon)
Score: 2

TTTGAAGCTTGTTCGACCAAGAGTTCCATACCTCAAATATGGCCTCTTTATCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAGgtacatcttc ... tggatcacagGCCTTGCACAGTCAAGACGTGTCGTTTATGGCCACCCTTTCAGCTCTTGAGAAATCCTCAATGCAGCCGGTGTTCAGTGAGATGTTATACGCAGTTGCAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGAAGCTTGTTCGACCAAGAGTTCCATACCTCAAATATGGCCTCTTTATCCGCCACATAATTGACGAAGAAAGCCCTCTTTATAATCTGGACATTGAGgtacatcttcctctcaacactttcacttaatctctcaacacccacaaatatcctgaaacaacattgatgtggttaacttgagcaatacgttctacgagac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaca