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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattccatcctacattttccccttctctggtctcttgtgttacctattcagcaatattaactagcttgtacgtctcctactttgtaactgcccga...

Basic information

species Physcomitrella patens
transcript PP1S72_57V6.4
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S72_57V6.4 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GRMZM2G445100_T02 (Zea mays), 5'ss of exon 10
TATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattccatcctacattttccccttctctggtctcttgtgttacctattcagcaatattaactagcttgtacgtctcctactttgtaactgcccga
 |||||||  ||||||||||| || |||||||| || |||||| ||||| |||||||||| ||||| || || || ||  |||||||    |||  |||        ||||         |    || | ||     |  |       ||  | ||||   |||  |  ||   |    |           
AATTTATGCAGTGCATGATGAAGCTAAGGACAAAGCTTTTGAGTTGGAGTTGAGCTGGATCTGTGAGGAATCGAAGCGCCAGCATCAGAAGgtac-tatggatattcacatgaagaatggcctctgtatgtttctccatttgaatttaaagctgaactcctttgctcacctgtcatacag-----------

upper sequence: PP1S72_57V6.4 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GRMZM2G445100_T01 (Zea mays), 5'ss of exon 10
TATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgta-----aatattccatcctacattttccccttctctggtctcttgtgttacctattcagcaatattaactagcttgtacgtctcctactttgtaactgcccga
 |||||||  ||||||||||| || |||||||| || |||||| ||||| |||||||||| ||||| || || || ||  |||||||    |||      ||||||      | | |  || ||      || |||    ||   | |  |||   | |   | |||     |||    |  |   || || |   
AATTTATGCAGTGCATGATGAAGCTAAGGACAAAGCTTTTGAGTTGGAGTTGAGCTGGATCTGTGAGGAATCGAAGCGCCAGCATCAGAAGgtactatggatattcacatgaagaatggcctctgtat--gtttctccatttgaatttaaagctgaactcctttgctcacctgtcatacaggtcccaaatgac---

upper sequence: PP1S72_57V6.4 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GLYMA05G14330.2 (Glycine max), 5'ss of exon 9
TATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattccatcctacattttccccttctctggtctct-tgtgttacctat--tcagcaatattaactagcttgtacgtctcctactttgtaactgcccga-
||| ||||| || ||||||||||| |||||||| |  |||||||| || ||||||||| | ||||| |||||||||||  | ||| |    ||||     |     |    |||      |  || ||  | ||  | |  | |  |  |   || |   || | | ||  |||  | |||  |  |||   |  
TATATATGGAGTTCATGATGAGGCAAAGGACAAAGATTTTGAGCTAGAAATGAGCTGGGTGTGTGATGAGTCAAACCGCCAACATGAGAAGgtaagg---ctggggtgtgcttttggtgacaatgatcaatgtgcttcatttgtgattggttgtaatt-ttatcatttatttcttttgcttcctggctgagagca

upper sequence: PP1S72_57V6.4 (Physcomitrella patens), 5'ss of exon 11
lower sequence: AT2G27020.1 (Arabidopsis thaliana), 5'ss of exon 9
TATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattccatcctacattttccccttctctggtctcttgtgttacctattcagcaatattaactagcttgtacgtctcctactttgtaactgcccga
 || ||     | || ||||| |||||||||||||| |||||  |||||||||||||||| || || |||||||| || ||||||||    ||||| |||  ||   |  |  |  | |     ||    ||     |  ||||||  ||   ||  ||  ||| ||   || ||                
CATCTACAAGCTACACGATGAAGCCAAGGACAAGGCTTTTGAATTGGAGATGAGCTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAGgtaaa-attttat---aagtgcttgcttatgaaggatgatttaaggagatattcataaaccatatataaattggactcgtcgtatag-------------

upper sequence: PP1S72_57V6.4 (Physcomitrella patens), 5'ss of exon 11
lower sequence: Vv08s0040g00410.t01 (Vitis vinifera), 5'ss of exon 9
TATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattccatcctacattttccccttctctggtctcttgtgttacctattcagcaatattaactagcttgtacgtctcctactttgtaactgcccga-----
 |||||||| || || |||||||||||||||||||| |||||| |||| ||||||||| ||||||| |||||||||||  |||||||    ||||    |  |   ||     ||    ||      |  |    | ||  ||      |    | ||| | |||   |  |   | |  | |||  | |      
CATTTATGGGGTACACGATGAGGCCAAGGACAAGGCATTTGAGTTGGAAATGAGCTGGGTTTGTGAGGAGTCAAACCGCCAGCATCAGAAGgtaatctcttgaattta-----tcaagatcaagaaacattaacttaactcatatcttgaagacatctaccctgttgattgcacccatgctcactagctggatagc

upper sequence: PP1S72_57V6.4 (Physcomitrella patens), 5'ss of exon 11
lower sequence: EFJ26741 (Selaginella moellendorffii), 5'ss of exon 10
TATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattccatcctacattttccccttctctggtctcttgtgttacctattcagcaatattaactagcttgtacgtctcctactttgtaactgcccga
 || || || || || || || ||||||||||| |||||||| ||||| |||||||||||||| |||||||| |||   ||||| |||   ||     | |||||  || | |  |      || ||| || || ||  ||| |  ||    ||  ||  |  |                           
CATCTACGGAGTTCACGACGAAGCCAAGGACAAAGCCTTTGAACTGGAAATGAGCTGGATTTGCGACGAGTCGAACAAGGAGCACCAAAAGgt---cttgccatcgcac-tctcgctacgtactagtccctcgtattttctaat--gcttgttttgctttccag---------------------------

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|18335635|gb|BJ167655.1|BJ167655
EST:     AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA                         GTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
genomic: AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattc ... gccaaagcagGTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
EST: gi|37840289|gb|BJ598297.1|BJ598297
EST:     AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA                         GTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
genomic: AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattc ... gccaaagcagGTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
EST: gi|208346631|gb|DC916897.1|DC916897
EST:     AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA                         GTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
genomic: AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattc ... gccaaagcagGTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
EST: gi|37844839|gb|BJ602847.1|BJ602847
EST:     AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA                         GTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
genomic: AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattc ... gccaaagcagGTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
EST: gi|208367520|gb|DC954952.1|DC954952
EST:     AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA                         GTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
genomic: AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattc ... gccaaagcagGTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
EST: gi|67693091|gb|BJ953324.1|BJ953324
EST:     AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA                         GTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
genomic: AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattc ... gccaaagcagGTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
EST: gi|37823229|gb|BJ581295.1|BJ581295
EST:     AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA                         GTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
genomic: AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattc ... gccaaagcagGTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
EST: gi|162272069|gb|FC447863.1|FC447863
EST:     AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA                         GTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
genomic: AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattc ... gccaaagcagGTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
EST: gi|162272070|gb|FC447864.1|FC447864
EST:     AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA                         GTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGC
genomic: AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattc ... gccaaagcagGTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGC
EST: gi|162267459|gb|FC444210.1|FC444210
EST:     AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA                         GTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
genomic: AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattc ... gccaaagcagGTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
EST: gi|208369160|gb|DC956035.1|DC956035
EST:     AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA                         GTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
genomic: AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattc ... gccaaagcagGTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
EST: gi|37823184|gb|BJ581250.1|BJ581250
EST:     AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA                         GTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
genomic: AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattc ... gccaaagcagGTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
EST: gi|208374326|gb|DC948386.1|DC948386
EST:     AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA                         GTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
genomic: AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattc ... gccaaagcagGTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
EST: gi|208363378|gb|DC946976.1|DC946976
EST:     AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA                         GTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
genomic: AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattc ... gccaaagcagGTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
EST: gi|208399219|gb|DC916574.1|DC916574
EST:     AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA                         GTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
genomic: AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattc ... gccaaagcagGTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
EST: gi|18336615|gb|BJ168638.1|BJ168638
EST:     AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA                         GTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
genomic: AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattc ... gccaaagcagGTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
EST: gi|162209436|gb|FC386069.1|FC386069
EST:     AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA                         GTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
genomic: AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattc ... gccaaagcagGTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
EST: gi|37847181|gb|BJ605189.1|BJ605189
EST:     AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA                         GTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
genomic: AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattc ... gccaaagcagGTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
EST: gi|208349231|gb|DC917995.1|DC917995
EST:     AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA                         GTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG
genomic: AGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattc ... gccaaagcagGTTCCGGCGGATTTATTGGCTGAAGCCAAGACTGCCGCAAAGGAAGCACAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattccatcctacattttccccttctctggtctcttgtgttacctattcagcaatattaactagcttgtacgtctcctactttgtaactgcccga

- - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA