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

gtatgctgttcgtgattccagaagacaccagattatgttagctccattttatcttcgctttaaatttagagaatgctgttttatgaagctcattaaagcatgaaagtaaatgtcttcattttttctaactgtatcgcgcagGTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCCAAGGCAGCCGGTTGGGGTGTTATGGTCAGCCACCGAAGTGGAGAGACTG

Basic information

species Physcomitrella patens
transcript PP1S76_97V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S76_97V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G034848_T01 (Zea mays), 3'ss of exon 4
----gtatgctgttcgtgattccagaagacaccagattatgttagctccattttatcttcgctttaaatttagagaatgctgtttta-tgaagctca--ttaaagcatgaaagtaaatgtcttcattttttctaac-tgtatcgcgcagGTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCCAAGGCAGCCGGTTGGGGTGTTATGGTCAGCCACCGAAGTGGAGAGACTG
      ||  | |     |||  | | |      |||     |   |     |  |    |   | ||  |   || ||| |  | | |  || | |  ||  |     ||| ||||||||||  ||     |    ||  |    ||||| || || || ||  |||| || || || |||||||||||||||||||| || || || ||||||||||| |||||||||||| ||||||| || || |
gtaaccattttctaaacaatttgaaatggagtacgatatgcctttttttgcatccttccagtgctgaacatcatgactgcggaataactcgagataagcttgcactgaaaaactaaatgtctttgttaaaattggtgtgccttttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTCAAGCTGCCCTGGATTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCG

upper sequence: PP1S76_97V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G009030_T01 (Zea mays), 3'ss of exon 4
---------------gtatgctgtt-cgtgattccagaagacaccagattatgttagctccatttta--tcttcgctttaaatttagagaatgctgtttta-tgaagctca--ttaaagcatgaaagtaaatgtcttcattttttctaactgtatcgc---gcagGTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCCAAGGCAGCCGGTTGGGGTGTTATGGTCAGCCACCGAAGTGGAGAGACTG
                 |  |||    |   | | | |   |   |  || | || ||| | ||  |  |||   | | |    |  | ||   | | |   |  || | |  ||  |     ||| ||||||||||  ||     |   |||| |      ||||| || || || ||  |||| || || || ||| ||||||| || ||||| || || || ||||||||||| |||||||||||| ||||||| || || |
gtaaccatttactaaacaatctgaaatggagtactatatacccttaatttttttttgcttccttccagttctcaacatcatgactgcaaaacagtatctagctcgagataagcttgcactgcaaaactaaatgtctttgttaaaattgg-tgtacctttttccagGTCAACCAGATTGGTACTGTCACTGAATCAATTGAAGCTGCTCTCGATTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCG

upper sequence: PP1S76_97V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ26490 (Selaginella moellendorffii), 3'ss of exon 5
gtatgctgttcgtgattccagaagacaccagattatgttagctccattttatcttcgctttaaatttagagaatgctgttttatgaagctcattaaagcatgaaagtaaatgtcttcattttttctaactgtatcgcgcagGTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCCAAGGCAGCCGGTTGGGGTGTTATGGTCAGCCACCGAAGTGGAGAGACTG
                                                                |    |   ||  |  ||       |  | |  | ||  ||     | | ||  || |||      |  |   |||||| |||||  |||| || || || || ||||| ||||| ||  ||||||| || || || || |||||||||||||| |||||| ||||||||||||| |
---------------------------------------------------------------gtaagcacggtgtcgccttccatcatttctcatggaatcgaatcc--ttttttttttcttttctttcgctttttgcagGTGAATCAGGTCGGCTCCGTGACTGAATCCATCCAAGCAGCTTTGGATTCAAAAGCTGCTGGATGGGGTGTTATGGTGAGCCACAGAAGTGGAGAGACCG

upper sequence: PP1S76_97V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ26799 (Selaginella moellendorffii), 3'ss of exon 4
gtatgctgttcgtgattccagaagacaccagattatgttagctccattttatcttcgctttaaatttagagaatgctgttttatgaagctcattaaagcatgaaagtaaatgtcttcattttttctaactgtatcgcgcagGTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCCAAGGCAGCCGGTTGGGGTGTTATGGTCAGCCACCGAAGTGGAGAGACTG
                                                                |    |   ||  |  ||       |  | |  | ||  ||     | | ||  || |||      |  |   |||||| |||||  |||| || || || || ||||| ||||| ||  ||||||| || || || || |||||||||||||| |||||| ||||||||||||| |
---------------------------------------------------------------gtaagcacggtgtcgccttccatcatttctcatggaatagaatcc--ttttttttttcttttctttcgctttttgcagGTGAATCAGGTCGGCTCCGTGACTGAATCCATCCAAGCAGCTTTGGATTCAAAAGCTGCTGGATGGGGTGTTATGGTGAGCCACAGAAGTGGAGAGACCG

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|208371720|gb|DC951622.1|DC951622
EST:     AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAG                         GTAAATCAGATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
genomic: AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAGgtatgctgtt ... tatcgcgcagGTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
EST: gi|67693606|gb|BJ953839.1|BJ953839
EST:     AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAG                         GTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
genomic: AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAGgtatgctgtt ... tatcgcgcagGTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
EST: gi|208367450|gb|DC943909.1|DC943909
EST:     AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAG                         GTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
genomic: AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAGgtatgctgtt ... tatcgcgcagGTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
EST: gi|18332690|gb|BJ164703.1|BJ164703
EST:     TATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAG                         GTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
genomic: TATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAGgtatgctgtt ... tatcgcgcagGTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
EST: gi|67570333|gb|BJ943157.1|BJ943157
EST:     AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAG                         GTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
genomic: AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAGgtatgctgtt ... tatcgcgcagGTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
EST: gi|208364752|gb|DC943626.1|DC943626
EST:     AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAG                         GTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
genomic: AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAGgtatgctgtt ... tatcgcgcagGTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
EST: gi|67725691|gb|BJ975950.1|BJ975950
EST:     AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAG                         GTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
genomic: AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAGgtatgctgtt ... tatcgcgcagGTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
EST: gi|67727971|gb|BJ978230.1|BJ978230
EST:     AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAG                         GTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
genomic: AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAGgtatgctgtt ... tatcgcgcagGTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
EST: gi|208374157|gb|DC945203.1|DC945203
EST:     AAATTTCTGAGGCTATCTCAAAGCAAGTCTGCAACGCTCTGTTGTTGAAG                         GTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
genomic: AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAGgtatgctgtt ... tatcgcgcagGTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
EST: gi|37839773|gb|BJ597781.1|BJ597781
EST:     CTGTTGTTGAAG                         GTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
genomic: CTGTTGTTGAAGgtatgctgtt ... tatcgcgcagGTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
EST: gi|67698210|gb|BJ958443.1|BJ958443
EST:     AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAG                         GTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
genomic: AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAGgtatgctgtt ... tatcgcgcagGTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
EST: gi|208371256|gb|DC944420.1|DC944420
EST:     AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAG                         GTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
genomic: AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAGgtatgctgtt ... tatcgcgcagGTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
EST: gi|208386286|gb|DC952999.1|DC952999
EST:     AAANTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAG                         GTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
genomic: AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAGgtatgctgtt ... tatcgcgcagGTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
EST: gi|208366457|gb|DC955570.1|DC955570
EST:     AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAG                         GTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
genomic: AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAGgtatgctgtt ... tatcgcgcagGTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
EST: gi|208347383|gb|DC925351.1|DC925351
EST:     AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAG                         GTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
genomic: AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAGgtatgctgtt ... tatcgcgcagGTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
EST: gi|208361853|gb|DC950125.1|DC950125
EST:     AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAG                         GTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
genomic: AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAGgtatgctgtt ... tatcgcgcagGTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
EST: gi|67697196|gb|BJ957429.1|BJ957429
EST:     AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAG                         GTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
genomic: AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAGgtatgctgtt ... tatcgcgcagGTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
EST: gi|208368997|gb|DC955082.1|DC955082
EST:     AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAG                         GTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC
genomic: AAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAGgtatgctgtt ... tatcgcgcagGTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCC

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: 6

CATTGATACCCAAATCGTTGGCGACGACCTTCTTGTTACTAACCCCAAGAAAATTTCTGAGGCTATCTCAAAGCAAGCCTGCAACGCTCTGTTGTTGAAGgtatgctgtt ... tatcgcgcagGTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCCAAGGCAGCCGGTTGGGGTGTTATGGTCAGCCACCGAAGTGGAGAGACTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctcattaaagcatgaaagtaaatgtcttcattttttctaactgtatcgcgcagGTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCCAAGGCAGCCGGTTGGGGTGTTATGGTCAGCCACCGAAGTGGAGAGACTG
                                    ttctaac  putative branch site (score: 6)
                            ttcattttttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctgttcgtgattccagaagacaccagattatgttagctccattttatcttcgctttaaatttagagaatgctgttttatgaagctcattaaagcatgaaagtaaatgtcttcattttttctaactgtatcgcgcagGTAAATCAAATCGGGTCTGTAACGGAGTCCATTCAAGCTGCCCTGGATTCCAAGGCAGCCGGTTGGGGTGTTATGGTCAGCCACCGAAGTGGAGAGACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA