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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGAGCCGCAGCGAGAAGAAGAGCCGCAAGGCCATGCAGAAGCTGGGCATGAAGCCCGTCACTGGCGTGACTCGCGTGACCATCAAGAAGAGCAAGAACgtaaggattgcattgaagtccagtcaggccaggggttatgggaggggcgagctgcaggggacgggtacactgctgtggggggaaggggaagggggggcag...

Basic information

species Chlamydomonas reinhardtii
transcript EDO97954
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDO97954 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: LOC_Os03g02960.1 (Oryza sativa), 5'ss of exon 2
GCAGAGCCGCAGCGAGAAGAAGAGCCGCAAGGCCATGCAGAAGCTGGGCATGAAGCCCGTCACTGGCGTGACTCGCGTGACCATCAAGAAGAGCAAGAACgtaagga-ttgcattgaag-tccagtcaggccaggggttatgggaggggcgagctgcaggggacgggtacactgctgtggggggaaggggaagggggggcag
||||||| | |||||||||||||||||||||||||||  |||||| || ||||| |||||||| || || |   |  | ||||||||||    |||||| ||||| |  ||    |  | | ||  ||  | |    ||      |  |  ||    |  |         | | | ||| |    ||               
GCAGAGCAGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACGGGAGTCAGCAGGATTACCATCAAGAGAGCCAAGAATgtaagaaactgtgcagctgctgcaaacaatctattcattcgaatggaagacagaattaatgttttctctgaatcccgtgtgtttcag---------------

upper sequence: EDO97954 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: LOC_Os01g50360.1 (Oryza sativa), 5'ss of exon 3
GCAGAGCCGCAGCGAGAAGAAGAGCCGCAAGGCCATGCAGAAGCTGGGCATGAAGCCCGTCACTGGCGTGACTCGCGTGACCATCAAGAAGAGCAAGAACgtaagga-ttgcattgaagtc-cagtcaggccaggggttatgggaggggcgagctgcaggggacgggtacactgctgtggggggaaggggaagggggggcag
||||||| | |||||||||||||||||||||||||||  |||||| || ||||| |||||||| || || |   |  | |||||| |||    |||||| ||||| |  || |  |  |   ||  ||    |    ||      |  |  ||    |  |      |  |   | ||| |    ||               
GCAGAGCAGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACGGGAGTCAGCAGGATTACCATCGAGAGAGCCAAGAATgtaagaaactgtacagctgctgcaaacaatttattcattcgaatggaagacagagttaatgtttctctgaatc-ccgtgtgtttcag---------------

upper sequence: EDO97954 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: LOC_Os01g71230.2 (Oryza sativa), 5'ss of exon 3
GCAGAGCCGCAGCGAGAAGAAGAGCCGCAAGGCCATGCAGAAGCTGGGCATGAAGCCCGTCACTGGCGTGACTCGCGTGACCATCAAGAAGAGCAAGAACgtaaggattgcattgaagtccagtcaggccaggggttatgggaggggc---gagctgcaggggacgggtacact--gctgtggggggaaggggaagggggggcag
||||||  | |||||||| |||||| | || ||||||||||| || ||||||||| || ||||||| ||||  || || || ||||| |||||||||||||| ||   ||| |  ||   | || | ||||  | || | | |||  |   ||  ||      ||   | || |  |||            | |      |    
GCAGAGTAGGAGCGAGAAAAAGAGCAGGAAAGCCATGCAGAAACTTGGCATGAAGACCATCACTGGTGTGAGCCGTGTCACTATCAAAAAGAGCAAGAACgtgag--ctgctt--aatcactgttatgccattgtttcttgtaggctcacagaattgttatataccattgcattttgcttaacttttccctgcactaccag----

upper sequence: EDO97954 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: GRMZM2G171466_T01 (Zea mays), 5'ss of exon 2
GCAGAGCCGCAGCGAGAAGAAGAGCCGCAAGGCCATGCAGAAGCTGGGCATGAAGCCCGTCACTGGCGTGACTCGCGTGACCATCAAGAAGAGCAAGAACgtaaggat-----tgcattgaagtccagtcaggcc------aggggttatgggagg-ggcgagctgc--aggggacgggtacactgctgtggggggaaggggaagggggggcag---------------------------------------------------------------------
||||||||| |||||||||||||||||||||||||||  |||||| || ||||| |||||||| ||||| ||  |  | |||||||| |    |||||||||| | ||     |  ||  | | | | |   |||      | ||   | |  ||   || | ||    | |   || ||| ||   | |      |||      |   |                                                                         
GCAGAGCCGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACCGGCGTCACCAGGATAACCATCAAAAGAGCCAAGAACgtacgtatatctatatatatatgccaattattgccacaaggaaggaacacgatagatagctaactttttatgctccgtgtatacaattttacaaacaagatagtagatagatgcccgtgcaatttttagttagctcttgccttctcatattactgtcatgcgtgtctgtctcccttccttcag

upper sequence: EDO97954 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: GRMZM2G000923_T01 (Zea mays), 5'ss of exon 3
GCAGAGCCGCAGCGAGAAGAAGAGCCGCAAGGCCATGCAGAAGCTGGGCATGAAGCCCGTCACTGGCGTGACTCGCGTGACCATCAAGAAGAGCAAGAACgtaaggattgcattgaagtccagtcaggccag--gggttatgggaggggcgagctgcaggggacgggtacactgctgtggggggaaggggaagggggggcag
||| ||| | || ||||||||||||||||||||||||| |||||| |||||||||||| ||||||| || |  ||||| ||  | ||||| |||||||| ||||   |  |  |  | ||   |||  | |   || ||||       |    |||      | |  ||  ||  |    |                     
GCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAATgtaat--tcaccatttactcagatcacacaaactggcttatctttattgttgcctggctaacatga-tatgctatttccag---------------------

upper sequence: EDO97954 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: GRMZM2G465333_T01 (Zea mays), 5'ss of exon 3
GCAGAGCCGCAGCGAGAAGAAGAGCCGCAAGGCCATGCAGAAGCTGGGCATGAAGCCCGTCACTGGCGTGACTCGCGTGACCATCAAGAAGAGCAAGAACgtaaggattgcattgaagtccagtc-aggccaggggttatgggaggggcgagctgcaggggacgggtacactgctgtggggggaaggggaagggggggcag-----------
||| ||| | || ||||||||||||||||| ||||||| |||||| |||||||||||| ||||||| || |  || || ||  | ||||| |||||||| ||||   |  |   | |  |  | | |        ||| |  |     |  | |  |    |    |  | || |||  ||  ||   ||     |  ||            
GCAAAGCAGGAGTGAGAAGAAGAGCCGCAAAGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGTGTCACTGTGAAGAAAAGCAAGAATgtaat--tcaccacgcaaactggcctatctttattgttgtctggctaacatggtatatattatc--tttattgttgtctggctaacatgataaatgcacatatttttcccag

upper sequence: EDO97954 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: AT3G12390.1 (Arabidopsis thaliana), 5'ss of exon 3
GCAGAGCCGCAGCGAGAAGAAGAGCCGCAAGGCCATGCAGAAGCTGGGCATGAAGCCCGTCACTGGCGTGACTCGCGTGACCATCAAGAAGAGCAAGAACgtaaggattg---cattgaagtccagtcaggccaggggttatgggaggggcgagctgcaggggacgggtacactgctgtggggggaaggggaagggggggcag
 || ||| | || ||||||||||| ||||| |||||||  ||||| |||||||| ||| ||||||| || |  || || ||| |||| ||||||||||| ||  |  ||    | || |  | ||||||  |      || |   |    |            |    |   ||| | |||||  |   |    ||    |||
ACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGTTAGCCGAGTCACCGTCAAAAAGAGCAAGAATgtttgtgttttctctttaatattcagtcaatcttaat-ttcttttattcacacatcaggctttaatattgatctgttttggggacatttgctttggaacacag

upper sequence: EDO97954 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: Vv16s0098g00830.t01 (Vitis vinifera), 5'ss of exon 3
GCAGAGCCGCAGCGAGAAGAAGAGCCGCAAGGCCATGCAGAAGCTGGGCATGAAGCCCGTCACTGGCGTGACTCGCGTGACCATCAAGAAGAGCAAGAACgtaaggattgcattgaagtccagtcaggccaggggttatgggaggggcgagctgcaggggacgggtacactgctgtggggggaaggggaagggggggcag
||||||| | || |||||||||||||||||||| |||  |||||| |||||||| ||||| ||||| ||     | || ||||| ||||  |  || || ||||   ||    |||  ||   ||  |       || |   | |   |  ||  |   |     |   |||   | ||  |                  
GCAGAGCAGAAGTGAGAAGAAGAGCCGCAAGGCAATGTTGAAGCTCGGCATGAAACCCGTTACTGGTGTTGGAAGGGTCACCATTAAGAGAACAAAAAATgtaaaattttgtctgatttctgttcttgtattcacttgtatcatgaatgttctttaccagtt---tttcctgggcttggcag------------------

upper sequence: EDO97954 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: PP1S10_319V6.1 (Physcomitrella patens), 5'ss of exon 3
GCAGAGCCGCAGCGAGAAGAAGAGCCGCAAGGCCATGCAGAAGCTGGGCATGAAGCCCGTCACTGGCGTGACTCGCGTGACCATCAAGAAGAGCAAGAACgtaaggattgcattgaagtccagtcaggccaggggttatgggaggggcgagctg-caggggac--gggtacactgctgtggggggaaggggaagggggggcag
|||||||||  | |||||||| ||| | ||||||||||| ||||| |||||||||||||| || |  || || || || ||||||||||||||||| || ||| |  | |   |    ||   | |  |      | ||  ||      |  |  | ||| |   | ||  | || | |       ||   |   ||      
GCAGAGCCGTGGTGAGAAGAAAAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACCGATGTCACCCGAGTTACCATCAAGAAGAGCAAAAATgtatgcctcgtcatagcttcttttaacacgctatctaatctgaacatttatataaccgggaataagagtgtaatgttattttccatagttaatatggcca---

upper sequence: EDO97954 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: PP1S539_1V6.1 (Physcomitrella patens), 5'ss of exon 3
GCAGAGCCGCAGCGAGAAGAAGAGCCGCAAGGCCATGCAGAAGCTGGGCATGAAGCCCGTCACTGGCGTGACTCGCGTGACCATCAAGAAGAGCAAGAACgtaaggattgca--ttgaagtcc-agtcaggccaggggttatgggaggggcgagctgcaggggacgggtacactgctgtggggggaaggggaagggggggcag
|||||||||  | |||||||||||| | ||||||||||| ||||| |||||||||||||| ||||  || || || || || ||||||||||||||||| ||| |  |  |   || ||||   | ||  |   |  || |      | || | |||    | | | ||   || || |       |   |   ||     | 
GCAGAGCCGTGGTGAGAAGAAGAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACTGAAGTCACACGGGTTACTATCAAGAAGAGCAAGAATgtatgcctctcggcttaaagttttactcttgtttgacgtgaacctctgtgcaa-ctgttctgca-gagtgtgctactatcttccatatctgtctggtcaaaa-

upper sequence: EDO97954 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: PP1S122_100V6.1 (Physcomitrella patens), 5'ss of exon 3
GCAGAGCCGCAGCGAGAAGAAGAGCCGCAAGGCCATGCAGAAGCTGGGCATGAAGCCCGTCACTGGCGTGACTCGCGTGACCATCAAGAAGAGCAAGAACgtaaggattgcattgaagtccagtcaggccaggggttatgggaggggcg-agctgcaggggacgggtacactgctgtggggggaaggggaagggggggcag
|||||||||  | |||||||||||| | ||||||||||| ||||| |||||||| || ||| | ||||| || || ||||| ||||| |||||||||||||||||  |          |   | |  |||  | | |     |       |         || |  |  |     |      | |||     | | | || 
GCAGAGCCGTGGTGAGAAGAAGAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAACCAGTCCCCGGCGTCACCCGTGTGACAATCAAAAAGAGCAAGAACgtaagattcagtgctttctattgacgtgccttgcgcttcaaaaacaatataatctttaaagatgattttaaaatagacttttggaggactttgtgcg-cac

upper sequence: EDO97954 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: PP1S156_120V6.1 (Physcomitrella patens), 5'ss of exon 2
GCAGAGCCGCAGCGAGAAGAAGAGCCGCAAGGCCATGCAGAAGCTGGGCATGAAGCCCGTCACTGGCGTGACTCGCGTGACCATCAAGAAGAGCAAGAACgtaaggattg-cattgaagtccagtcaggccaggggttatgggaggggcgagctgcaggggacgggtacactgctgtggggggaaggggaagggggggcag
|||||| ||  | |||||||||||| | ||||||||||| |||||||| |||||||| || ||||| || ||  | ||||| |||||||| |||||||| |||     || || |    |    || |   |    || |       | || |         ||  | |   | ||| |   | |    |     | | | 
GCAGAGTCGTGGTGAGAAGAAGAGCAGGAAGGCCATGCAAAAGCTGGGTATGAAGCCTGTGACTGGTGTCACAAGGGTGACAATCAAGAAAAGCAAGAATgtatattctgacagtcctttatcatctgtttatttcttttttacctcgtgaaccttgcttctcgcat-cgtggatgttgtctggaatatatttttgcgtac

upper sequence: EDO97954 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: EFJ23805 (Selaginella moellendorffii), 5'ss of exon 3
GCAGAGCCGCAGCGAGAAGAAGAGCCGCAAGGCCATGCAGAAGCTGGGCATGAAGCCCGTCACTGGCGTGACTCGCGTGACCATCAAGAAGAGCAAGAACgtaaggattgcattgaagtccagtcaggccaggggttatgggaggggcgagctgcaggggacgggtacactgctgtggggggaaggggaagggggggcag
||| ||||| ||||||||||||||||| ||||| ||||||||||| || ||||||||||| ||||| || ||  | ||||| |||||||||||||| ||||||||  |||| |||          ||  |   |   ||   || | | | || |  |   | ||| |  | | |                         
GCAAAGCCGGAGCGAGAAGAAGAGCCGGAAGGCAATGCAGAAGCTCGGGATGAAGCCCGTGACTGGAGTAACGAGGGTGACGATCAAGAAGAGCAAAAACgtaagc-ttgcgttgg--------tagatcgaagagaat---agagactaacttc--gcttctggttctttccag-------------------------

upper sequence: EDO97954 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: EFJ21445 (Selaginella moellendorffii), 5'ss of exon 1
GCAGAGCCGCAGCGAGAAGAAGAGCCGCAAGGCCATGCAGAAGCTGGGCATGAAGCCCGTCACTGGCGTGACTCGCGTGACCATCAAGAAGAGCAAGAACgtaaggattgcattgaagtccagtcaggccaggggttatgggaggggcgagctgcaggggacgggtacactgctgtggggggaaggggaagggggggcag
                                                 ||||||||||| ||||| || ||  | ||||| |||||||||||||| ||||||||  |||| | | ||   |   ||   || |  ||     |   |  | |                                               
-------------------------------------------------ATGAAGCCCGTGACTGGAGTAACGAGGGTGACGATCAAGAAGAGCAAAAACgtaagc-ttgcgtagtagatgaaagagaatagagtctaacttcgctccttgttctttccag---------------------------------------

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|6550203|gb|AV395987.1|AV395987
EST:     TGAAGCCCGTCACTGGCGTGACTCGCGTGACCATCAAGAAGAGCAAGAAC                         ATTCTGTTCGTGATCCAGTCGCCCGATGTCTTCAAGAGCCCCGCCTCGGAC
genomic: TGAAGCCCGTCACTGGCGTGACTCGCGTGACCATCAAGAAGAGCAAGAACgtaaggattg ... ccacatgtagATTCTGTTCGTGATCCAGTCGCCCGATGTCTTCAAGAGCCCCGCCTCGGAC




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGAGCCGCAGCGAGAAGAAGAGCCGCAAGGCCATGCAGAAGCTGGGCATGAAGCCCGTCACTGGCGTGACTCGCGTGACCATCAAGAAGAGCAAGAACgtaaggattgcattgaagtccagtcaggccaggggttatgggaggggcgagctgcaggggacgggtacactgctgtggggggaaggggaagggggggcag

- - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcattga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatggga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgtgg