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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttagcatgaggttctaaagttacgcttcatttgatgaggagagtggaatttttgggagaactatttcatgcactgcttgtagtcgagcggatgatttcattgttgaggcttgccctgatgcataggtaggtgatactttgtgtagGTAATAAACTCAACAACTTGGATGTTGTTTACACACCGTGGTATAATCTGAGGAAGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAA

Basic information

species Physcomitrella patens
transcript PP1S199_23V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S199_23V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os05g13440.1 (Oryza sativa), 3'ss of exon 3
gtatgttagcatgaggttctaaagttacgcttcatttgatgaggagagtggaatttttgggagaactatttcatgcactgcttgtagtcgagcggatgatttcattgttgaggcttgccctgatgcataggtaggtgatactttgtgtagGTAATAAACTCAACAACTTGGATGTTGTTTACACACCGTGGTATAATCTGAGGAAGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAA
                                               | | || ||    || || | | | || |   | |   |          || ||||  |  |  || |     | |  || |  ||  |     ||| |  |||||||||    || ||| | ||||| ||||| ||||| ||||||||||| | |||||||| |  |||||| || || |||||||| ||||| ||||| ||
--------------------------------------------gttgggaaaattacatgataattctgtaatacctggttcaaaccttttgttttgctttccctagtttggttctttgtcagacacatttaatta----tttttacagGTAATAAGACTAATAACATTGATGTGGTTTATACACCATGGTATAATCTAAAGAAGACTCCATCCATGGATGTGGGTCAAGTTGGTTTTCACAACTCTAA
















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|37852008|gb|BJ610016.1|BJ610016
EST:     GAGCTTTTAGAAGATTGTGCTCAGCTCGTGAAGGCCAACTCCATCCCAAG                         GTAATAAACTCAACAACTTGGATGTTGTTTACACACCGTGGTATAATCTG
genomic: GAGCTTTTAGAAGATTGTGCTCAGCTCGTGAAGGCCAACTCCAT-CCAAGgtatgttagc ... ctttgtgtagGTAATAAACTCAACAACTTGGATGTTGTTTACACACCGTGGTATAATCTG
EST: gi|37852535|gb|BJ610543.1|BJ610543
EST:     TGAGCTTTTAGAAGATTGTGCTCAGCTCGTGAAGGCCAACTCCATCCAAG                         GTAATAAACTCAACAACTTGGATGTTGTTTACACACCGTGGTATAATCTGA
genomic: TGAGCTTTTAGAAGATTGTGCTCAGCTCGTGAAGGCCAACTCCATCCAAGgtatgttagc ... ctttgtgtagGTAATAAACTCAACAACTTGGATGTTGTTTACACACCGTGGTATAATCTGA
EST: gi|37837061|gb|BJ595069.1|BJ595069
EST:     TGAGCTTTTAGAAGATTGTGCTCAGCTCGTGAAGGCCAACTCCATCCAAG                         GTAATAAACTCAACAACTTGGATGTTGTTTACACACCGTGGTATAATCTGA
genomic: TGAGCTTTTAGAAGATTGTGCTCAGCTCGTGAAGGCCAACTCCATCCAAGgtatgttagc ... ctttgtgtagGTAATAAACTCAACAACTTGGATGTTGTTTACACACCGTGGTATAATCTGA
EST: gi|37848004|gb|BJ606012.1|BJ606012
EST:     TGAGCTTTTAGAAGATTGTGCTCAGCTCGTGAAGGCCAACTCCATCCAAG                         GTAATAAACTCAACAACTTGGATGTTGTTTACACACCGTGGTATAATCTGA
genomic: TGAGCTTTTAGAAGATTGTGCTCAGCTCGTGAAGGCCAACTCCATCCAAGgtatgttagc ... ctttgtgtagGTAATAAACTCAACAACTTGGATGTTGTTTACACACCGTGGTATAATCTGA
EST: gi|37830821|gb|BJ588833.1|BJ588833
EST:     TGAGCTTTTAGAAGATTGTGCTCAGCTCGTGAAGGCCAACTCCATCCAAG                         GTAATAAACTCAACAACTTGGATGTTGTTTACACACCGTGGTATAATCTGA
genomic: TGAGCTTTTAGAAGATTGTGCTCAGCTCGTGAAGGCCAACTCCATCCAAGgtatgttagc ... ctttgtgtagGTAATAAACTCAACAACTTGGATGTTGTTTACACACCGTGGTATAATCTGA
EST: gi|18359130|gb|BJ191190.1|BJ191190
EST:     TGAGCTTTTAGAAGATTGTGCTCAGCTCGTGAAGGCCAACTCCATCCAAG                         GTAATAAACTCAACAACTTGGATGTTGTTTACACACCGTGGTATAATCTGA
genomic: TGAGCTTTTAGAAGATTGTGCTCAGCTCGTGAAGGCCAACTCCATCCAAGgtatgttagc ... ctttgtgtagGTAATAAACTCAACAACTTGGATGTTGTTTACACACCGTGGTATAATCTGA
EST: gi|18351476|gb|BJ183528.1|BJ183528
EST:     TGAGCTTTTANAAGATTGTGCTCAGCTCGTGAAGGCCAACTCCATCCAAG                         GTAATAAACTCAACAACTTGGATGTTGTTTACACACCGTGGTATAATCTGA
genomic: TGAGCTTTTAGAAGATTGTGCTCAGCTCGTGAAGGCCAACTCCATCCAAGgtatgttagc ... ctttgtgtagGTAATAAACTCAACAACTTGGATGTTGTTTACACACCGTGGTATAATCTGA
EST: gi|18371814|gb|BJ203416.1|BJ203416
EST:     TGAGCTTTTANAAGATTGTGCTCAGCTCGTGAAGGCCAACTCCATCCAAG                         GTAATAAACTCAACAACTTGGATGTTGTTTACACACCGTGGTATAATCTGA
genomic: TGAGCTTTTAGAAGATTGTGCTCAGCTCGTGAAGGCCAACTCCATCCAAGgtatgttagc ... ctttgtgtagGTAATAAACTCAACAACTTGGATGTTGTTTACACACCGTGGTATAATCTGA
EST: gi|18367505|gb|BJ199588.1|BJ199588
EST:     TGAGCTTTTAGAAGATTGTGCTCAGCTCGTGAAGGCCAACTCCATCCAAG                         GTAATAAACTCAACAACTTGGATGTTGTTTACACACCCGTGGTATAATCTG
genomic: TGAGCTTTTAGAAGATTGTGCTCAGCTCGTGAAGGCCAACTCCATCCAAGgtatgttagc ... ctttgtgtagGTAATAAACTCAACAACTTGGATGTTGTTTACACACC-GTGGTATAATCTG
EST: gi|208346849|gb|DC913088.1|DC913088
EST:     TGAGCTTTTAGAAGATTGTGCTCAGCTCGTGAAGGCCAACTCCATCCAAG                         GTAATAAACTCAACAACTTGGATGTTGTTTACACACCGTGGTATAATCTGA
genomic: TGAGCTTTTAGAAGATTGTGCTCAGCTCGTGAAGGCCAACTCCATCCAAGgtatgttagc ... ctttgtgtagGTAATAAACTCAACAACTTGGATGTTGTTTACACACCGTGGTATAATCTGA

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), 34 (downstream exon)
Score: 9

CATGTCTACCTGAGAATGCACAAGGGCCAAACTATGGAGATGATCAGCCCTGAGCTTTTAGAAGATTGTGCTCAGCTCGTGAAGGCCAACTCCATCCAAGgtatgttagc ... ctttgtgtagGTAATAAACTCAACAACTTGGATGTTGTTTACACACCGTGGTATAATCTGAGGAAGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatttcattgttgaggcttgccctgatgcataggtaggtgatactttgtgtagGTAATAAACTCAACAACTTGGATGTTGTTTACACACCGTGGTATAATCTGAGGAAGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAA
                      ccctgat  putative branch site (score: 9)
                                          atacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttagcatgaggttctaaagttacgcttcatttgatgaggagagtggaatttttgggagaactatttcatgcactgcttgtagtcgagcggatgatttcattgttgaggcttgccctgatgcataggtaggtgatactttgtgtagGTAATAAACTCAACAACTTGGATGTTGTTTACACACCGTGGTATAATCTGAGGAAGACTCAAAGCATGGACGTTGGCCAAGTTGGCTTTCATAACTCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA