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

gtgcggtttgtgatataatgaatgcttacctgagctttctgaatgcccacaaaattagaactgaataactgctagaactgacatttgcgttagcattaaggagtgagctgtgttggtcttccgaactcagcgagcttatatgtggttttcttttgggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCCTTTATTTCACTTACAGCGGTGAAAATACTTTCGGAGATTGTGTTGCTTG

Basic information

species Physcomitrella patens
transcript PP1S209_114V6.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S209_114V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ09352 (Selaginella moellendorffii), 3'ss of exon 4
gtgcggtttgtgatataatgaatgcttacctgagctttctgaatgcccacaaaattagaactgaataactgctagaactgacatttgcgttagcattaaggagtgagctgtgttggtcttccgaactca-gcgagcttatatgtggttttcttttgggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCCTTTATTTCACTTACAGCGGTGAAAATACTTTCGGAGATTGTGTTGCTTG
                                                                                                    |  ||||| ||   |   |    | | || |     | || |    | ||| |||   ||||| ||||||  |||| ||| |  | || || || ||||| ||||||||||||||||| || ||||| |||||||| || ||||| |||||  |    |     | 
----------------------------------------------------------------------------------------------------gtatgagccgtcgagacgt---aatcccacgtatattgatttacactgttcctttcc-ttttgtagCGGCATTGATATCGACCATCTACGAGGAGCACAAGGACGAGGATGGATTCCTCTACTTCACGTACAGCGGGGAGAATACCTTCGGCCAAGAAGAACACTA

upper sequence: PP1S209_114V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ35003 (Selaginella moellendorffii), 3'ss of exon 4
gtgcggtttgtgatataatgaatgcttacctgagctttctgaatgcccacaaaattagaactgaataactgctagaactgacatttgcgttagcattaaggagtgagctgtgttggtcttccgaactca-gcgagcttatatgtggttttcttttgggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCCTTTATTTCACTTACAGCGGTGAAAATACTTTCGGAGATTGTGTTGCTTG
                                                                                                    |  ||||| ||   |   |    | | || |     | || |    | ||| |||   ||||| ||||||  |||| ||| |  | || || || ||||| ||||||||||||||||| || ||||| |||||||| || ||||| |||||  |    |     | 
----------------------------------------------------------------------------------------------------gtatgagccgtcgagacgt---aatcccacgtatattgatttacactattcctttcc-ttttgtagCGGCATTGATATCGACCATCTACGAGGAGCACAAGGACGAGGATGGATTCCTCTACTTCACGTACAGCGGGGAGAATACCTTCGGCCAAGAAGAACACTA
















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|67575443|gb|BJ948267.1|BJ948267
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|162233637|gb|FC409396.1|FC409396
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|162266942|gb|FC443030.1|FC443030
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|162225361|gb|FC401165.1|FC401165
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|100416767|gb|BY993077.1|BY993077
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|162238593|gb|FC418163.1|FC418163
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|67698910|gb|BJ959143.1|BJ959143
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|100386838|gb|BY988107.1|BY988107
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|162200693|gb|FC377876.1|FC377876
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|162215669|gb|FC391709.1|FC391709
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|18331879|gb|BJ163891.1|BJ163891
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|162264864|gb|FC440639.1|FC440639
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|162225362|gb|FC401166.1|FC401166
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|162246388|gb|FC422420.1|FC422420
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|162200692|gb|FC377875.1|FC377875
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|7582945|gb|AW699109.1|AW699109
EST:     GAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: GAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|18339800|gb|BJ171827.1|BJ171827
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|6167639|gb|AW145903.1|AW145903
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|37830291|gb|BJ588303.1|BJ588303
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCNTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|162246361|gb|FC422419.1|FC422419
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|162173286|gb|FC350068.1|FC350068
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|162262384|gb|FC437711.1|FC437711
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|162233638|gb|FC409397.1|FC409397
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|162173285|gb|FC350067.1|FC350067
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|162215670|gb|FC391710.1|FC391710
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|162266941|gb|FC443029.1|FC443029
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|162270438|gb|FC447554.1|FC447554
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|162216853|gb|FC393035.1|FC393035
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|18350954|gb|BJ183005.1|BJ183005
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|162238594|gb|FC418164.1|FC418164
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
EST: gi|162216854|gb|FC393036.1|FC393036
EST:     TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAG                         CGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC
genomic: TTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCC

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), 35 (downstream exon)
Score: 28

TTAACAGTCGGACAGTTTGTATACGTCATAAGGAAGCGCATTAAGTTGAGTTCCGAGAAGGCCATCTTCATCTTTGTGAAGAATGTTCTTCCTCCTACAGgtgcggtttg ... ggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCCTTTATTTCACTTACAGCGGTGAAAATACTTTCGGAGATTGTGTTGCTTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttggtcttccgaactcagcgagcttatatgtggttttcttttgggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCCTTTATTTCACTTACAGCGGTGAAAATACTTTCGGAGATTGTGTTGCTTG
                                   ttttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcggtttgtgatataatgaatgcttacctgagctttctgaatgcccacaaaattagaactgaataactgctagaactgacatttgcgttagcattaaggagtgagctgtgttggtcttccgaactcagcgagcttatatgtggttttcttttgggttttgcagCGGCTATGATGTCGTCAGTTTATGACGAACACAAAGACGAGGATGGATTCCTTTATTTCACTTACAGCGGTGAAAATACTTTCGGAGATTGTGTTGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT