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

...acttaacaaaaagcttttcgtgtacatactcctttccttacgtgcctgtttaatctttctgtatggaatgtttttctgacgttaacgttgggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAAGTTGACGTGGATGGTGGCAACAGTCGAGTG

Basic information

species Physcomitrella patens
transcript PP1S398_18V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S398_18V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os05g44050.1 (Oryza sativa), 3'ss of exon 4
acttaacaaaaagcttttcgtgtacatactcctttccttacgtgcctgtttaatctttctgtatggaatgtttttctgacgtta-acgttgggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAAGTTGACGTGGATGGTGGCAACAGTCGAGTG
                          || |   ||   ||      |  ||| || |     |||  || | | ||| || ||  | ||| |   || |||||||||||||| || || ||||| || ||||||||  |  | |||||||||||||| || || ||||||||||| || |||
-------------------------gtaatgtgttttcta------taattagtcatgaatcatgtcatttctgtctcactttggatgtttgactttacagGCAAGCCCATCAGACCCTGATAACTTCCCTTTTGTTCTTTTGGGCAACAAAGTTGATGTAGACGGTGGCAACAGCCGTGTG

upper sequence: PP1S398_18V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G158887_T02 (Zea mays), 3'ss of exon 3
acttaacaaaaagcttttcgtgtacatactcctttccttacgtgcctgtttaatctttctgta---tggaatgtttttctgacgtta-acgttgggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAAGTTGACGTGGATGGTGGCAACAGTCGAGTG
                     ||  | |   ||    |    |    ||| | |||  | | |     |  | ||| ||| || ||  | |||      ||||||| |||||||| ||||| |||||||| ||||||||  |  | || ||||||||||| || |||||||||||||| || |||
---------------------gtgaa-atatctccaatggtttattagttcagtctcacagcaatcctgtctttttatctaactttggatgtttccctctgcagGCTAGCCCATCAGATCCTGATAATTTCCCTTTTGTTCTGTTGGGTAACAAAGTTGATGTAGATGGTGGCAACAGCCGCGTG

upper sequence: PP1S398_18V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA12G04830.1 (Glycine max), 3'ss of exon 4
acttaacaaaaagcttttcgtgtacatactcctttccttacgtgcctgtttaatct-ttctgtatggaatgttt---ttctgacgttaacgttgggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAAGTTGACGTGGATGGTGGCAACAGTCGAGTG
                    ||    || |||| || |||      |  | || || |  |||   || | |     || | |  |    | |   | | ||||||||| || ||||||||||| |||||||||||||| ||| |||| |||||| | ||  | |||||||| |||||  |||||
-----------------gtatgcttttattcctctctttataaattttctcaagctatgttgtgcagattttacaacttttaagatgtgtgatcactttggcagGCAAGTCCTTCCGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAAATAGATATTGATGGTGGAAACAGCAGAGTG

upper sequence: PP1S398_18V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA11G12630.1 (Glycine max), 3'ss of exon 4
acttaacaaaaagcttttcgtgtacatactcctttc---cttacgtgcctgtttaatcttt-ctgtatggaatgtt---tttctgacgttaacgttgggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAAGTTGACGTGGATGGTGGCAACAGTCGAGTG
   |      |  | |||| |||| |   |  | ||    |||  |      | || || |  ||||  || | |     || | |  ||   | |   | | ||||||||| || || |||||||| |||||||||||||| ||| |||| |||||| | ||  | |||||||| |||||  |||||
gtatgcttttattcctttc-tgtataattttttctcagttttatctattatctcaagctatgttgtacagattttacaacttttaagatttgtgatcactttggcagGCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAAATAGATATTGATGGTGGGAACAGCAGAGTG

upper sequence: PP1S398_18V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv03s0063g02420.t01 (Vitis vinifera), 3'ss of exon 5
-------acttaacaaaaagcttttcgtgtacatactcctttccttacgtgcctgtttaatctttctgtatggaat-gtttttctgacgttaacgttgggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAAGTTGACGTGGATGGTGGCAACAGTCGAGTG
         ||||| | ||     |  ||| | ||  | |||   || |    |||| | |      ||  | | | ||  |  |||  |  | |||   |  |||||||||| || || |||||||| ||||| |||||||| || ||||| ||||| ||||| ||||||||||| |||||  | |||
tgaatagggttaactagaa-----taatgtccttaagcatttatctatg-atttgttaattagaaaagttggaagttgtgctgatgatttggaggttc--ttctgcagGCAAGTCCTTCAGATCCAGAAAATTTCCCTTTTGTTGTTCTAGGAAACAAGGTTGATGTGGATGGTGGAAACAGCAGGGTG

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|162275204|gb|FC451180.1|FC451180
EST:     TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAA                         GCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
genomic: TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgt ... ggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
EST: gi|162239905|gb|FC415744.1|FC415744
EST:     TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAA                         GCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
genomic: TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgt ... ggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
EST: gi|22491664|gb|BU051587.1|BU051587
EST:     TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAA                         GCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
genomic: TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgt ... ggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
EST: gi|162278758|gb|FC454868.1|FC454868
EST:     TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAA                         GCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
genomic: TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgt ... ggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
EST: gi|37826297|gb|BJ584309.1|BJ584309
EST:     AATTTTTGATTCAA                         GCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
genomic: AATTTTTGATTCAAgtaagtttgt ... ggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
EST: gi|162239904|gb|FC415743.1|FC415743
EST:     TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAA                         GCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
genomic: TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgt ... ggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
EST: gi|100394822|gb|BY989942.1|BY989942
EST:     TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAA                         GCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
genomic: TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgt ... ggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
EST: gi|208390030|gb|DC938085.1|DC938085
EST:     TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAA                         GCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
genomic: TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgt ... ggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
EST: gi|208365879|gb|DC951136.1|DC951136
EST:     TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAA                         GCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
genomic: TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgt ... ggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
EST: gi|18342622|gb|BJ174657.1|BJ174657
EST:     TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAA                         GCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
genomic: TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgt ... ggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
EST: gi|100391677|gb|BY989497.1|BY989497
EST:     TGAAGGCATTTGATAACCTTGTAAACTGGCGGGACGAATTTTTGATTCAA                         GCAAGCCCATCCGATCCAGAT
genomic: TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgt ... ggtgttgcagGCAAGCCCATCCGATCCAGAT
EST: gi|162278757|gb|FC454867.1|FC454867
EST:     TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAA                         GCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
genomic: TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgt ... ggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA

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: 31 (upstream exon), 35 (downstream exon)
Score: 13

CTTTTACCGTGGTGCAGATTGTTGTGTCCTTGTCTATGACGTTAATGTTATGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgt ... ggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAAGTTGACGTGGATGGTGGCAACAGTCGAGTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtttaatctttctgtatggaatgtttttctgacgttaacgttgggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAAGTTGACGTGGATGGTGGCAACAGTCGAGTG
                     aatgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttaacaaaaagcttttcgtgtacatactcctttccttacgtgcctgtttaatctttctgtatggaatgtttttctgacgttaacgttgggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAAGTTGACGTGGATGGTGGCAACAGTCGAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG