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'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCAGCAGCTATACCTGGTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAGgtactgacgtcacttccaaatcagtttagggtcgaatttgtgggttcttgagggtgtttttaggtgctggatcaagcgtaaagtgtctgcaggcccgattaaaatttgtgtgttcatgcag

Basic information

species Physcomitrella patens
transcript PP1S37_33V6.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S37_33V6.2 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA15G42300.2 (Glycine max), 5'ss of exon 7
AGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCAGCAGCTATACCTGGTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAGgtac-tgacgtcacttccaaatcagtttagggtcg--aatttgtgggttcttgagggtgttttta-ggtgctggatcaagcgtaaagtg-tctgcaggcccgattaaaatttgtgtgttcatgcag----------------------
 |||||||||||||||||||| ||||||||||||||||  ||| |  ||||||| || ||  | || || |   |  ||||||| || | ||| ||| |||||    |      |   ||||||  ||    |    | ||||    ||  | |   ||  | ||   | ||      |  ||    |  | |  |  |  | || | ||||   |||  |  |                        
GGGCATGTCAATTCCTGAATGCCAGAAAAAGCTTCCAGGTGCTTTTACTGGTGGGGAGCCTTTACCTGAGGCTGTACTGTGGCTTCTATTGACAGGAAAGgtatgcaatagttttagaaaatcaaattgaattaattattttgaatattactcataatgcatatataatccttttatgaaggtgttttaatatcaacacttggtttagattttgttgtataatctttgattcatacatttggtcacag

upper sequence: PP1S37_33V6.2 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA08G16770.1 (Glycine max), 5'ss of exon 7
AGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCAGCAGCTATACCTGGTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAGgtac-tgacgtcacttccaaatcagtttagggtcg--aatttg-----tgggttcttgagggtgttttta---ggtgctggatcaagcgtaa---agtgtctgcaggcccgattaaaatttgt-gtgttcatgcag--------------------
 |||||||||||||||||||| ||||||||||||||||  ||| | |||||||| || ||  | || || |   |  ||||||| || | ||| ||| |||||    |      |   ||||||  ||    |    | ||||     ||  | ||| |   ||  | ||     | || |  |||  ||     | | ||| ||   | | ||| | ||||| || |       |                    
GGGCATGTCAATTCCTGAATGCCAGAAAAAGCTTCCAGGTGCTTTTCCTGGTGGGGAGCCTTTGCCTGAGGCTGTACTGTGGCTTCTATTGACAGGAAAGgtatgcaatagttttagaaaatcaaattgaattaattattttgaatattgcttacttaataatgcatatatataatccttgtacaaaggtgttttaatatctacac-tctgtttagattttgttgtataatctttgattcatacacttggtcacag

upper sequence: PP1S37_33V6.2 (Physcomitrella patens), 5'ss of exon 6
lower sequence: AT3G60100.1 (Arabidopsis thaliana), 5'ss of exon 6
AGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCAGCAGCTATACCTGGTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAGgtactgacgtcacttccaaatcagtttagggtcgaatttgtgggttcttgagggtgtttttaggtgctggatcaagcgtaaagtgtctgcaggcccgattaaaatttgtgtgttcatgcag
||||||||| |||||||||||||||||||   | ||  |||||    |||| |  || ||  | || ||  |  || ||||||| || |  |||||| ||||      |  | |   ||| || ||||       |    |  |||          ||| ||  ||   |||| |  ||| ||| |   |         || |                  
AGGCATGTCGATTCCTGAATGTCAGAAAATATTACCTTCAGCTGAGTCTGGAGAAGAGCCCTTGCCTGAGAGTCTTCTGTGGCTTCTATTAACTGGAAAGgtgt----gataatcttaaaacattttatacataca---ataagtttcaac-----tttatatatgaatgatctaaagtatagttttccctcctttcggtatag-----------------

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|67712952|gb|BJ966401.1|BJ966401
EST:     GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAG                         GTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
genomic: GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAGgtactgacgt ... gttcatgcagGTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
EST: gi|162194038|gb|FC370213.1|FC370213
EST:     GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTGCGACTGGAGAG                         GTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
genomic: GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAGgtactgacgt ... gttcatgcagGTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
EST: gi|162202113|gb|FC378034.1|FC378034
EST:     GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTGCGACTGGAGAG                         GTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
genomic: GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAGgtactgacgt ... gttcatgcagGTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
EST: gi|162165709|gb|FC340890.1|FC340890
EST:     GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTGCGACTGGAGAG                         GTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
genomic: GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAGgtactgacgt ... gttcatgcagGTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
EST: gi|67574071|gb|BJ946895.1|BJ946895
EST:     GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAG                         GTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
genomic: GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAGgtactgacgt ... gttcatgcagGTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
EST: gi|208373915|gb|DC940426.1|DC940426
EST:     GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAG                         GTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
genomic: GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAGgtactgacgt ... gttcatgcagGTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
EST: gi|208398177|gb|DC908406.1|DC908406
EST:     GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAG                         GTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
genomic: GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAGgtactgacgt ... gttcatgcagGTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
EST: gi|100427449|gb|BY977503.1|BY977503
EST:     GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAG                         GNTCCAACCAAAGAGCAAGTCAATGCACTGAGTGGAGATTTGCGATCTCGC
genomic: GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAGgtactgacgt ... gttcatgcagGTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
EST: gi|162176173|gb|FC351915.1|FC351915
EST:     GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTGCGACTGGAGAG                         GTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
genomic: GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAGgtactgacgt ... gttcatgcagGTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
EST: gi|162233299|gb|FC409849.1|FC409849
EST:     GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTGCGACTGGAGAG                         GTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
genomic: GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAGgtactgacgt ... gttcatgcagGTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
EST: gi|208362586|gb|DC939510.1|DC939510
EST:     GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAG                         GTTCCAACCAAAGAGCAAGTCAATGCACTAAGTGAAGATTTGCGATCTCGC
genomic: GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAGgtactgacgt ... gttcatgcagGTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
EST: gi|162152562|gb|FC328840.1|FC328840
EST:     GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTGCGACTGGAGAG                         GTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
genomic: GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAGgtactgacgt ... gttcatgcagGTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
EST: gi|100352729|gb|BY945419.1|BY945419
EST:     GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAG                         GTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
genomic: GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAGgtactgacgt ... gttcatgcagGTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
EST: gi|162173170|gb|FC349237.1|FC349237
EST:     GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTGCGACTGGAGAG                         GTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
genomic: GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAGgtactgacgt ... gttcatgcagGTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
EST: gi|19783472|gb|BQ040017.1|BQ040017
EST:     GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAG                         GTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
genomic: GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAGgtactgacgt ... gttcatgcagGTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
EST: gi|162258522|gb|FC434737.1|FC434737
EST:     GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAG                         GTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC
genomic: GTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAGgtactgacgt ... gttcatgcagGTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGC

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), 34 (downstream exon)
Score: 22

AGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCAGCAGCTATACCTGGTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAGgtactgacgt ... gttcatgcagGTTCCAACCAAAGAGCAAGTCAATGCACTGAGTGAAGATTTGCGATCTCGCGCAAAAATCCCAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCAGCAGCTATACCTGGTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCCTTTCGACTGGAGAGgtactgacgtcacttccaaatcagtttagggtcgaatttgtgggttcttgagggtgtttttaggtgctggatcaagcgtaaagtgtctgcaggcccgattaaaatttgtgtgttcatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA