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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGAACCAGCGGAGGCAGCGGGTTGCGCACCGTACGACGGTTAAGGCTGCGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAGgtgaatgctgcgttttggatttcaactcaagttgtgcgaattccggtggctgcattggtgctggctccttggttgatgagagttgtacaagggagtcggt...

Basic information

species Physcomitrella patens
transcript PP1S15_485V6.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S15_485V6.2 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 2
TTTGAACCAGCGGAGGCAG-CGGGTTGCGCACCGTACGACGGTTAAGGCTGCGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAGgtgaatgctgcgttttggatttcaactcaagttgtgcgaattccggtggctgc-attggtgctggctccttggttgatgagagttgtacaagggagtcggt
    |  ||  | | ||   | |     |  |      | ||| || ||||| |||||| || ||||||| ||||||||||| |||||||||||| | |||||||   |     ||     ||  || ||  || | | ||||  |||  ||   |||  |        |  ||        |||| |        ||| | 
-ACCACGCAATGCACGCCTTCAGAGGAAGTGCAACTTCAGGGTAAAAGCTGCCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAGgtgagctccaaagttc----ttggacacatcttat-caaattttggtcactatgattcttagccttgaccaggcactcattagttatttctacatgtcag-

upper sequence: PP1S15_485V6.2 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G133698_T02 (Zea mays), 5'ss of exon 2
---TTTGAACCAGCGGAGGCAGCGGGTTGCGCACCGTACGACGGTTAAGGCTGCGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAGgtgaatgctgcgttttggatttcaactcaagttgtgcgaattccggtggctgcattggtgctggctccttggttgatgagagttgtacaagggagtcggt
      |||   |||    ||| ||   | | ||   |     || |  || || ||||||||| ||||||| ||||||||||| |||||||||||| | |||||||   |  |  |||  ||||  | |    |    ||| || | || |   | |        |||  ||| ||  |      |  |     |       
AGGGAAGAATGTGCGCCTTCAGAGGAGGGTGAACTTCAGA---GTAAGAGCAGCTAAGGAGCTGTACTTCAACAAGGATGGCTCAGCTATCAAGAAGCTCCAGgtgagctccacagtttttattt--attatgatataccgatttgctgttgacccttaaccaggcgctaattgttttttctcccctacatttcag-------

upper sequence: PP1S15_485V6.2 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G015989_T02 (Zea mays), 5'ss of exon 2
TTTGAACCAGCGGAGGCAGCGGGTTGCGCACCGTACGACGGTTAAGGCTGCGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAGgtgaatgctgcgttttggatttca----actcaagttgtgcgaattccggtggctgcattggtgctggctccttggttgatgagagtt--gtacaagggagtcggt
|  |  | ||  ||||| |||      | ||      | ||| || ||||| ||||||||||| ||||| ||||||||||| ||||||| ||| ||||| |||| |  |  |      || | |     ||  | |   ||     | | |     | ||   |   ||       ||  | |    |   |        ||| | 
TCCGCGCAAGATGAGGCCGCGAAGGAAGTACAACTTCAGGGTAAACGCTGCAAAGGAGCTGCATTTCAACAAGGATGGCTCGGCTATCAGGAAAATGCAAgtgagttttctgacaaacatataataacgcttgactaaggccgccgctgctcctcacgttcaagtgtgcgttgcacttacttattacttgattttcctatgtcag-

upper sequence: PP1S15_485V6.2 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 2
---TTTGAACCAGCGGAGGCAGCGGGTTGCGCACCGTACGACGGTTAAGGCTGCGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAGgtgaatgctgcgttttggatttcaactcaagttgtg-cgaattccggtggctgcattggtgctggctccttggttgatgagagttgtacaagggagtcggt
      |||   |||    ||| ||   ||  ||   |     || || || || ||||||||| ||||||| |||||||| || |||||||||||| | ||||||||    | | || ||        | |  |   | |||  | | |||||  | ||    | ||| |      || |      |      |    || | 
GGGGAAGAATGTGCGCCTTCAGAGGAGGGCTAACTTCAGA---GTAAAAGCGGCTAAGGAGCTGTACTTCAACAAGGATGGGTCAGCTATCAAGAAGCTCCAGgtgaag--cgagcttcgggcactcttttatttgaagacgatgtactgtggcctccttcac-caggcactaattgtgttttcgtcttcttctgtatctcag-

upper sequence: PP1S15_485V6.2 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 2
TTTGAACCAGCGGAGGCAGCGGGTTGCGCACCGTACGACGGTTAAGGCT---GCGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAGgtgaatgc-tgcgttttggatttcaactcaa---gttgtgcgaattccggtggctgcattggtgctggctccttggttgatgagagttgtacaagggagtcggt----------------
    ||     |    |  ||     | |    | | | | | || |||   || |||||  || | ||||| || ||||||||||||||||||||| ||||||||| |   || ||     | ||    ||||   ||| ||   |||  | ||  | |  ||     | ||   || |   |     ||           ||  |                
-ACAAAATGTTGTT--CTACGAAGGACACGATCTCCCAGGATCAATGCTATGGCAAAGGATTTGTATTTCAACAAAGATGGCTCTGCTATCAAGAAGCTGCAGgtgagtttgtgtgtaaaacacttttgatcaatatgttctgaacattttgttgattcctatgtattagactttctgatcattatctcttaagtcctaacatctttcaatttcctttttcag

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|162182315|gb|FC357186.1|FC357186
EST:     GCTCTGCTATCAAGAAGATGCAG                         GCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
genomic: GCTCTGCTATCAAGAAGATGCAGgtgaatgctg ... tcttgaacagGCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
EST: gi|67575198|gb|BJ948022.1|BJ948022
EST:     CGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAG                         GCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
genomic: CGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAGgtgaatgctg ... tcttgaacagGCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
EST: gi|162153515|gb|FC329609.1|FC329609
EST:     TATCAAGAAGATGCAG                         GCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
genomic: TATCAAGAAGATGCAGgtgaatgctg ... tcttgaacagGCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
EST: gi|208364523|gb|DC930913.1|DC930913
EST:     CGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAG                         GCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
genomic: CGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAGgtgaatgctg ... tcttgaacagGCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
EST: gi|162155281|gb|FC331218.1|FC331218
EST:     CGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAG                         GCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
genomic: CGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAGgtgaatgctg ... tcttgaacagGCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
EST: gi|67507453|gb|BJ940335.1|BJ940335
EST:     CGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAG                         GCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
genomic: CGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAGgtgaatgctg ... tcttgaacagGCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
EST: gi|162171512|gb|FC347814.1|FC347814
EST:     CGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAG                         GCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
genomic: CGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAGgtgaatgctg ... tcttgaacagGCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
EST: gi|18361532|gb|BJ193598.1|BJ193598
EST:     CGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAG                         GCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
genomic: CGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAGgtgaatgctg ... tcttgaacagGCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
EST: gi|162256596|gb|FC432906.1|FC432906
EST:     CGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAG                         GCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
genomic: CGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAGgtgaatgctg ... tcttgaacagGCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
EST: gi|100409963|gb|BY974341.1|BY974341
EST:     CGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAG                         GCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
genomic: CGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAGgtgaatgctg ... tcttgaacagGCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
EST: gi|67574539|gb|BJ947363.1|BJ947363
EST:     CGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAG                         GCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
genomic: CGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAGgtgaatgctg ... tcttgaacagGCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
EST: gi|18341885|gb|BJ173920.1|BJ173920
EST:     CGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAG                         GCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
genomic: CGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAGgtgaatgctg ... tcttgaacagGCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
EST: gi|67704538|gb|BJ964771.1|BJ964771
EST:     CGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAG                         GCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
genomic: CGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAGgtgaatgctg ... tcttgaacagGCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
EST: gi|162255427|gb|FC431841.1|FC431841
EST:     CGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAG                         GCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
genomic: CGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAGgtgaatgctg ... tcttgaacagGCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
EST: gi|162154271|gb|FC330402.1|FC330402
EST:     CGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAG                         GCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG
genomic: CGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAGgtgaatgctg ... tcttgaacagGCTGGAGTTGATAAGCTCGCGGATCTTGTGGGTGTCACCTTGGGCCCTAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGAACCAGCGGAGGCAGCGGGTTGCGCACCGTACGACGGTTAAGGCTGCGAAGGAGCTGCACTTCAATAAGGATGGCTCTGCTATCAAGAAGATGCAGgtgaatgctgcgttttggatttcaactcaagttgtgcgaattccggtggctgcattggtgctggctccttggttgatgagagttgtacaagggagtcggt

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG