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

gtaagtcagcgttctacaagtgcttcttatgcttccatgtacttttatatttcccacttatgtggtgtctagtttgtaatcggagtaaagttggtttaagccttcttgtctgcgctgctatatttctttgaggtggaattgacagttggtaagcatgcatcaatcacattgtgtaagttggcttgcagGGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTGGTATGGGCTCTACTATTCTAGACGGAGCTGTTGTGGAGAAAGGTGCCAT

Basic information

species Physcomitrella patens
transcript PP1S207_12V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S207_12V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA04G03310.2 (Glycine max), 3'ss of exon 2
gtaagtcagcgttctacaagtgcttcttatgcttccatgtacttttatatttcccacttatgtggtgtctagtttgtaatcggagtaaagttggtttaagccttcttgtctgcgctgctatatttctttgaggtggaattgacagttggtaagcatgcatcaatcacattgtgtaagttggcttgcagGGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTGGTATGGGCTCTACTATTCTAGACGGAGCTGTTGTGGAGAAAGGTGCCAT
                                                                                         ||  ||   | |||| |||||     |   | | |  |     ||   | |   | | || ||   ||      | | ||| | |    ||    ||||| |||| | ||||  | ||||  |||||||||||||||||| | ||||||||||||||  | |   | || ||||| |  || || ||||||  ||||||
-----------------------------------------------------------------------------------------gtgagt---aacctttttgtcatgatta--agaatcgtgctgtgttctactcttaatgggaaattttg------ttaaattttttttactga---gcagGCCACAGTGCTGTTATCCATGGTTGTACTGTTGAGGACGAGGCTTTTGTTGGTATGGGTGCAATACTACTTGACGGTGTAGTAGTTGAGAAAAATGCCAT
















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|162233651|gb|FC409410.1|FC409410
EST:     CGTAAGTGGCAATGTTGAGCCTACTGTAATCGGCAATAGGGTCACTATTG                         GGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTG
genomic: CGTAAGTGGCAATGTTGAGCCTACTGTAATCGGCAATAGGGTCACTATTGgtaagtcagc ... tggcttgcagGGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTG
EST: gi|18369330|gb|BJ201416.1|BJ201416
EST:     CGTAAGTGGCAATGTTGAGCCTACTGTAATCGGCAATAGGGTCACTATTG                         GGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTG
genomic: CGTAAGTGGCAATGTTGAGCCTACTGTAATCGGCAATAGGGTCACTATTGgtaagtcagc ... tggcttgcagGGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTG
EST: gi|18363020|gb|BJ195092.1|BJ195092
EST:     CGTAAGTGGCAATGTTGAGCCTACTGTAATCGGCAATAGGGTCACTATTG                         GGCACAATTCTGTACTTCATGCGTGTACTGT
genomic: CGTAAGTGGCAATGTTGAGCCTACTGTAATCGGCAATAGGGTCACTATTGgtaagtcagc ... tggcttgcagGGCACAATTCTGTACTTCATGCGTGTACTGT
EST: gi|208349491|gb|DC905629.1|DC905629
EST:     CGTAAGTGGCAATGTTGAGCCTACTGTAATCGGCAATAGGGTCACTATTG                         GGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTG
genomic: CGTAAGTGGCAATGTTGAGCCTACTGTAATCGGCAATAGGGTCACTATTGgtaagtcagc ... tggcttgcagGGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTG
EST: gi|67697542|gb|BJ957775.1|BJ957775
EST:     CGTAAGTGGCAATGTTGAGCCTACTGTAATCGGCAATAGGGTCACTATTG                         GGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTG
genomic: CGTAAGTGGCAATGTTGAGCCTACTGTAATCGGCAATAGGGTCACTATTGgtaagtcagc ... tggcttgcagGGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTG
EST: gi|37834717|gb|BJ592729.1|BJ592729
EST:     CGTAAGTGGCAATGTTGAGCCTACTGTAATCGGCAATAGGGTCACTATTG                         GGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTG
genomic: CGTAAGTGGCAATGTTGAGCCTACTGTAATCGGCAATAGGGTCACTATTGgtaagtcagc ... tggcttgcagGGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTG
EST: gi|37840237|gb|BJ598245.1|BJ598245
EST:     CGTAAGTGGCAATGTTGAGCCTACTGTAATCGGCAATAGGGTCACTATTG                         GGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTG
genomic: CGTAAGTGGCAATGTTGAGCCTACTGTAATCGGCAATAGGGTCACTATTGgtaagtcagc ... tggcttgcagGGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTG
EST: gi|18350228|gb|BJ182279.1|BJ182279
EST:     CGTAAGTGGCAATGTTGAGCCTACTGTAATCGGCAATAGGGTCACTATTG                         GGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTG
genomic: CGTAAGTGGCAATGTTGAGCCTACTGTAATCGGCAATAGGGTCACTATTGgtaagtcagc ... tggcttgcagGGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTG
EST: gi|208381510|gb|DC919512.1|DC919512
EST:     CGTAAGTGGCAATGTTGAGCCTACTGTAATCGGCAATAGGGTCACTATTG                         GGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTG
genomic: CGTAAGTGGCAATGTTGAGCCTACTGTAATCGGCAATAGGGTCACTATTGgtaagtcagc ... tggcttgcagGGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTG
EST: gi|37850643|gb|BJ608651.1|BJ608651
EST:     CGTAAGTGGCAATGTTGAGCCTACTGTAATCGGCAATAGGGTCACTATTG                         GGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTG
genomic: CGTAAGTGGCAATGTTGAGCCTACTGTAATCGGCAATAGGGTCACTATTGgtaagtcagc ... tggcttgcagGGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTG
EST: gi|67574145|gb|BJ946969.1|BJ946969
EST:     CGTAAGTGGCAATGTTGAGCCTACTGTAATCGGCAATAGGGTCACTATTG                         GGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTG
genomic: CGTAAGTGGCAATGTTGAGCCTACTGTAATCGGCAATAGGGTCACTATTGgtaagtcagc ... tggcttgcagGGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTG
EST: gi|162233652|gb|FC409411.1|FC409411
EST:     CGTAAGTGGCAATGTTGAGCCTACTGTAATCGGCAATAGGGTCACTATTG                         GGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTG
genomic: CGTAAGTGGCAATGTTGAGCCTACTGTAATCGGCAATAGGGTCACTATTGgtaagtcagc ... tggcttgcagGGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTG
EST: gi|37829200|gb|BJ587212.1|BJ587212
EST:     TGGCAATGTTGAGCCTACTGTAATCGGCAATAGGGTCACTATTG                         GGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTG
genomic: TGGCAATGTTGAGCCTACTGTAATCGGCAATAGGGTCACTATTGgtaagtcagc ... tggcttgcagGGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTG

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: 20 (upstream exon), 16 (downstream exon)
Score: 1

TCAGAGACGAATATTCAGGACAATACTGTAGTACATGTAGCCAAAACCAACGTAAGTGGCAATGTTGAGCCTACTGTAATCGGCAATAGGGTCACTATTGgtaagtcagc ... tggcttgcagGGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTGGTATGGGCTCTACTATTCTAGACGGAGCTGTTGTGGAGAAAGGTGCCAT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaattgacagttggtaagcatgcatcaatcacattgtgtaagttggcttgcagGGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTGGTATGGGCTCTACTATTCTAGACGGAGCTGTTGTGGAGAAAGGTGCCAT
   aattgac  putative branch site (score: 1)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcagcgttctacaagtgcttcttatgcttccatgtacttttatatttcccacttatgtggtgtctagtttgtaatcggagtaaagttggtttaagccttcttgtctgcgctgctatatttctttgaggtggaattgacagttggtaagcatgcatcaatcacattgtgtaagttggcttgcagGGCACAATTCTGTACTTCATGCGTGTACTGTTGAGGACGAGTCGTTTGTTGGTATGGGCTCTACTATTCTAGACGGAGCTGTTGTGGAGAAAGGTGCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA