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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCAGCTGTTATGGGCATCGGTCCTGCTGTTGCCATTCCTGCTGCTATCAAGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctttactttcgtacaattcaagtatgatgcgttcggcagtatctcataaatacgtaaacattggtctaaaattacgacggaggatgtaaagttacagatgattggccctttgcag

Basic information

species Physcomitrella patens
transcript PP1S67_59V6.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S67_59V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GRMZM5G848768_T03 (Zea mays), 5'ss of exon 11
TCCAGCTGTTATGGGCATCGGTCCTGCTGTTGCCATTCCTGCTGCTATCAAGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctttactttcgtacaattcaagtatgatgcgttcggcagtatctcataaatacgtaaacattggtctaaaattacgacggaggatgtaaagttacagatgattggccctttgcag
|||||||||||||||| | |||||||| || ||||||||||||||| | ||| | || ||| | |||||    ||||||||| | |||||| | || |||||  ||| |  | |  | |   ||  |       | |  ||  |  | | ||   || |  | |  | ||    |    | |   |                                    
TCCAGCTGTTATGGGCGTTGGTCCTGCCGTGGCCATTCCTGCTGCTGTGAAGTCTGCAGGCCTTGAGATTGGAGACATTGATTTGTTTGAACTGAATGAGgtc-tgtgtcgattgccttg--atctacaccctcttctctcacctatttatccataacatctgattactgaatcatccatgcttag------------------------------------

upper sequence: PP1S67_59V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GRMZM2G152442_T01 (Zea mays), 5'ss of exon 3
TCCAGCTGTTATGGGCATCGGTCCTGCTGTTGCCATTCCTGCTGCTATCAAGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctttactttcgtacaattcaagtatgatgcgttcggcagtatctcataaatacgtaaacattggtctaaaattacgacggaggatgtaaagttacagatgattggccctttgcag
|||||||| ||||||| | ||||||||||| ||||||||||||||| | |||   || ||| | || ||    ||||||||| | |||||| | || |||||  ||| |  | |  | |   ||  |  |    | |  ||  |  | | ||   || |  | |  | ||    |    | |   |                                    
TCCAGCTGATATGGGCGTTGGTCCTGCTGTGGCCATTCCTGCTGCTGTGAAGTTTGCAGGCCTTGAAATTGGAGACATTGATTTGTTTGAACTGAATGAGgtc-tgtgtcgattgccttg--atctacatcctcttctctcacctatttatccataacatctgattactgaatcatccatgcttag------------------------------------
















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|208349666|gb|DC917844.1|DC917844
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|37852541|gb|BJ610549.1|BJ610549
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|208360248|gb|DC950221.1|DC950221
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|37821132|gb|BJ579198.1|BJ579198
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|37834213|gb|BJ592225.1|BJ592225
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|162187341|gb|FC363499.1|FC363499
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|37841276|gb|BJ599284.1|BJ599284
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|67691376|gb|BJ951609.1|BJ951609
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|162184203|gb|FC360470.1|FC360470
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|18333988|gb|BJ166004.1|BJ166004
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|18336719|gb|BJ168742.1|BJ168742
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|67728120|gb|BJ978379.1|BJ978379
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|208396520|gb|DC915832.1|DC915832
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|162271372|gb|FC446945.1|FC446945
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|208372620|gb|DC944613.1|DC944613
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|162230710|gb|FC406341.1|FC406341
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|162264637|gb|FC441635.1|FC441635
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|18340820|gb|BJ172851.1|BJ172851
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|37835724|gb|BJ593736.1|BJ593736
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|37843391|gb|BJ601399.1|BJ601399
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|208397944|gb|DC916699.1|DC916699
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|162213623|gb|FC389703.1|FC389703
EST:     GAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: GAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|162187340|gb|FC363498.1|FC363498
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|67726107|gb|BJ976366.1|BJ976366
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|37836846|gb|BJ594854.1|BJ594854
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|37835435|gb|BJ593447.1|BJ593447
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|162184204|gb|FC360471.1|FC360471
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|18340130|gb|BJ172158.1|BJ172158
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|162271371|gb|FC446944.1|FC446944
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|208368854|gb|DC947412.1|DC947412
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|162241361|gb|FC416992.1|FC416992
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
EST: gi|67698741|gb|BJ958974.1|BJ958974
EST:     AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAG                         GCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG
genomic: AGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAG

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: 19

TCCAGCTGTTATGGGCATCGGTCCTGCTGTTGCCATTCCTGCTGCTATCAAGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctt ... ccctttgcagGCGTTTGCATCACAGTTCACATACTGTGCTCAAGAGTTGGGACTAGATGAGGAGAAAATCAATGTGAATGGAGGTGCTATAGCTCTTGGCCATCCTCTTG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCAGCTGTTATGGGCATCGGTCCTGCTGTTGCCATTCCTGCTGCTATCAAGGCAGCTGGCTTGGAGATCAACGACATTGATCTTTTTGAAATTAACGAGgtaatgtctttactttcgtacaattcaagtatgatgcgttcggcagtatctcataaatacgtaaacattggtctaaaattacgacggaggatgtaaagttacagatgattggccctttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA