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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcctcacacgacattcagcacgcactcgcccttacattgcttatctcacccaggagtatagttccttaccttcacaccgtcatcctcgcacccttggcagGTGGTGCGGAAGGTTGGGCGAGGGAAGTATAGCGAGGTGTTCGAGGGCGTCAACGTTGCAGCGGAGCCGCCCACGAAATGCATCATCAAAATCCTGAAGC

Basic information

species Chlamydomonas reinhardtii
transcript EDO97438
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDO97438 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: LOC_Os03g55490.1 (Oryza sativa), 3'ss of exon 1
------------------------gcctcacacgacattcagcacgcactcgcccttac-attgcttat-ctcacccaggagtatagttccttaccttcacaccgtcatcctcgcacccttggcagGTGGTGCGGAAGGTTGGGCGAGGGAAGTATAGCGAGGTGTTCGAGGGCGTCAACGTTGCAGCGGAGCCGCCCACGAAATGCATCATCAAAATCCTGAAGC
                        |    |   ||  |  | |   ||          | |  | || | |||     ||  |  | ||  ||                    | |    |   ||||| |||| ||| ||||| | |||||||| |||||||||||||||||  ||  ||   | | || | ||     ||  ||| | ||              
gtatgtatgagccatggtggtggcgggggagctgatctcgaacctccagatttgggggctagggtttgtgctctaatggggatgcactttgttgtgcgtgtgtgtagGGAGCAGGATGGGTACGAGGTGCTGCGCAAGCTTGGGAGGGGGAAGTACAGCGAGGTGTTCGAGGGATTC--CGGCCCGGGGGTGACGA----GAGGTGCGTTATT-------------

upper sequence: EDO97438 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: GRMZM2G138774_T01 (Zea mays), 3'ss of exon 2
gcctcacacg-acattcagcacgcactcgcccttacattgcttatctca---cccaggagtatagttccttaccttcacaccgtc-atcctcgca----------cccttggcagGTGGTGCGGAAGGTTGGGCGAGGGAAGTATAGCGAGGTGTTCGAGGGCGTCAACGTTGCAGCGGAGCCGCCCACGAAATGCATCATCAAAATCCTGAAGC
       | | |||   |||  |  |||| | ||||| ||     | ||      |   || ||     |||  |      ||||  |||  |||              |   ||||| |||||||||| ||| | |||||||| |||||||||||||| ||  ||   || |    |||||     |  | |||| ||||              
-----gtaggcacacgaagctggagctcggctttacactgtgatccccagatttgaatggtgtaaggttttatttctgatgcgtctgtccatgcagGAAGCAGGATGGGTACGAGGTGCTGCGGAAGGTGGGGAGGGGGAAGTACAGCGAGGTGTTCGAAGGGTTCCGGGTCG----GGAGCGATGAA--AGATGCGTCATT-------------

upper sequence: EDO97438 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: GRMZM2G112056_T01 (Zea mays), 3'ss of exon 1
gcctcacacg-acattcagcacgcactcgcccttacattgcttatctca---cccaggagtatagttccttaccttcacaccgtc-atcctcgca----------cccttggcagGTGGTGCGGAAGGTTGGGCGAGGGAAGTATAGCGAGGTGTTCGAGGGCGTCAACGTTGCAGCGGAGCCGCCCACGAAATGCATCATCAAAATCCTGAAGC
       | | ||||  |||  |  |||| | ||||| |      | ||      |   || ||     |||  |      ||||  |||  |||              |   ||||| |||||||||| ||| | |||||||| |||||||||||||| ||  ||   |       |||||       || |||| ||||              
-----gtaggcacatggagctggagctcggctttacactttgatccccagatttgaatggtgtaaggttttatttctgattcgtctgtccgtgcagGAAGCAGGATGGGTATGAGGTGCTGCGGAAGGTGGGGAGGGGGAAGTACAGCGAGGTGTTCGAAGGGTTCTGGGCCA----GGAGCGAT--GAGAGATGCGTCATT-------------

upper sequence: EDO97438 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: GRMZM2G154799_T01 (Zea mays), 3'ss of exon 1
gcctcacacgacattcagcacgcactcgcccttacattgcttatctca---cccaggagtatagttccttaccttcacaccgtc-atcctcgca----------cccttggcagGTGGTGCGGAAGGTTGGGCGAGGGAAGTATAGCGAGGTGTTCGAGGGCGTCAACGTTGCAGCGGAGCCGCCCACGAAATGCATCATCAAAATCCTGAAGC
     |  || ||   |||  |  |||| | ||||| ||     | ||      |   || ||     |||  |      ||||  |||  |||              |   ||||| |||||||||| ||| | |||||||| |||||||||||||| ||  ||   |  |    |||||       || |||| ||||              
---gtaggcg-cacggagctggagctcggctttacactgtgatccccagatttgaatggtgtaaggttttatttctgatgcgtctgtccgtgcagGAAGCAGGATGGGTACGAGGTGCTGCGGAAGGTGGGGAGGGGGAAGTACAGCGAGGTGTTCGAAGGGTTCCGGGCCG----GGAGCGAT--GAGAGATGCGTCATT-------------

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|22070308|gb|BQ819697.1|BQ819697
EST:     GCGACTACGAGCGGCTTTCTGTGTCTTGGGGCGACCAGGACAATTATGAG                         GTGGTGCGGAAGGTTGGGCGAGGGAAGTATAGCGAGGTGTTCGAGGGCGTC
genomic: GCGACTACGAGCGGCTTTCTGTGTCTTGGGGCGACCAGGACAATTATGAGgtgcgagcgg ... cccttggcagGTGGTGCGGAAGGTTGGGCGAGGGAAGTATAGCGAGGTGTTCGAGGGCGTC
EST: gi|161804206|gb|FC088079.1|FC088079
EST:     GACAATTATGAG                         GTGGTGCGGAAGGTTGGGCGAGGGAAGTATAGCGAGGTGTTCGAGGGCGTC
genomic: GACAATTATGAGgtgcgagcgg ... cccttggcagGTGGTGCGGAAGGTTGGGCGAGGGAAGTATAGCGAGGTGTTCGAGGGCGTC
EST: gi|161800270|gb|FC084426.1|FC084426
EST:     GCGACTACGAGCGGCTTTCTGTGTCTTGGGGCGACCAGGACAATTATGAG                         GTGGTGCGGAAGGTTGGGCGAGGGAAGTATAGCGAGGTGTTCGAGGGCGTC
genomic: GCGACTACGAGCGGCTTTCTGTGTCTTGGGGCGACCAGGACAATTATGAGgtgcgagcgg ... cccttggcagGTGGTGCGGAAGGTTGGGCGAGGGAAGTATAGCGAGGTGTTCGAGGGCGTC
EST: gi|161803595|gb|FC089415.1|FC089415
EST:     GCGACTACGAGCGGCTTTCTGTGTCTTGGGGCGACCAGGACAATTATGAG                         GTGGTGCGGAAGGTTGGGCGAGGGAAGTATAGCGAGGTGTTCGAGGGCGTC
genomic: GCGACTACGAGCGGCTTTCTGTGTCTTGGGGCGACCAGGACAATTATGAGgtgcgagcgg ... cccttggcagGTGGTGCGGAAGGTTGGGCGAGGGAAGTATAGCGAGGTGTTCGAGGGCGTC
EST: gi|15692144|gb|BI716449.1|BI716449
EST:     GCGACTACGAGCGGCTTTCTGTGTCTTGGGGCGACCAGGACAATTATGAG                         GTGGTGCGGAAGGTTGGGCGAGGGAAGTATAGCGAGGTGTTCGAGGGCGTC
genomic: GCGACTACGAGCGGCTTTCTGTGTCTTGGGGCGACCAGGACAATTATGAGgtgcgagcgg ... cccttggcagGTGGTGCGGAAGGTTGGGCGAGGGAAGTATAGCGAGGTGTTCGAGGGCGTC
EST: gi|14235702|gb|BG854518.1|BG854518
EST:     GCGACTACGAGCGGCTTTCTGTGTCTTGGGGCGACCAGGACAATTATGAG                         GTGGTGCGGAAGGTTGGGCGAGGGAAGTATAGCGAGGTGTTCGAGGGCGTC
genomic: GCGACTACGAGCGGCTTTCTGTGTCTTGGGGCGACCAGGACAATTATGAGgtgcgagcgg ... cccttggcagGTGGTGCGGAAGGTTGGGCGAGGGAAGTATAGCGAGGTGTTCGAGGGCGTC
EST: gi|161797321|gb|FC084873.1|FC084873
EST:     GCGACTACGAGCGGCTTTCTGTGTCTTGGGGCGACCAGGACAATTATGAG                         GTGGTGCGGAAGGTTGGGCGAGGGAAGTATAGCGAGGTGTTCGAGGGCGTC
genomic: GCGACTACGAGCGGCTTTCTGTGTCTTGGGGCGACCAGGACAATTATGAGgtgcgagcgg ... cccttggcagGTGGTGCGGAAGGTTGGGCGAGGGAAGTATAGCGAGGTGTTCGAGGGCGTC
EST: gi|15692080|gb|BI716385.1|BI716385
EST:     GCGACTACGAGCGGCTTTCTGTGTCTTGGGGCGACCAGGACAATTATGAG                         GTGGTGCGGAAGGTTGGGCGAGGGAAGTATAGCGAGGTGTTCGAGGGCGTC
genomic: GCGACTACGAGCGGCTTTCTGTGTCTTGGGGCGACCAGGACAATTATGAGgtgcgagcgg ... cccttggcagGTGGTGCGGAAGGTTGGGCGAGGGAAGTATAGCGAGGTGTTCGAGGGCGTC
EST: gi|10771979|gb|AV622802.1|AV622802
EST:     GCGACTACGAGCGGCTTTCTGTGTCTTGGGGCGACCAGGACAATTATGAG                         GTGGTGCGGAAGGTTGGGCGAGGGAAGTATAGCGAGGTGTTCGAGGGCGTC
genomic: GCGACTACGAGCGGCTTTCTGTGTCTTGGGGCGACCAGGACAATTATGAGgtgcgagcgg ... cccttggcagGTGGTGCGGAAGGTTGGGCGAGGGAAGTATAGCGAGGTGTTCGAGGGCGTC
EST: gi|15693129|gb|BI717434.1|BI717434
EST:     GCGACTACGAGCGGCTTTCTGTGTCTTGGGGCGACCAGGACAATTATGAG                         GTGGTGCGGAAGGTTGGGCGAGGGAAGTATAGCGAGGTGTTCGAGGGCGTC
genomic: GCGACTACGAGCGGCTTTCTGTGTCTTGGGGCGACCAGGACAATTATGAGgtgcgagcgg ... cccttggcagGTGGTGCGGAAGGTTGGGCGAGGGAAGTATAGCGAGGTGTTCGAGGGCGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacccaggagtatagttccttaccttcacaccgtcatcctcgcacccttggcagGTGGTGCGGAAGGTTGGGCGAGGGAAGTATAGCGAGGTGTTCGAGGGCGTCAACGTTGCAGCGGAGCCGCCCACGAAATGCATCATCAAAATCCTGAAGC
                 tccttac  putative branch site (score: 2)
                                           caccctt  putative PPT
           tatagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcctcacacgacattcagcacgcactcgcccttacattgcttatctcacccaggagtatagttccttaccttcacaccgtcatcctcgcacccttggcagGTGGTGCGGAAGGTTGGGCGAGGGAAGTATAGCGAGGTGTTCGAGGGCGTCAACGTTGCAGCGGAGCCGCCCACGAAATGCATCATCAAAATCCTGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- ctcacac
- - - - - acattca
- - - - - - - - - cacgcac
- - - - - - - - - - - - - - - cttacat
- - - - - - - - - - - - - - - - - - -tgcttat
- - - - - - - - - - - - - - - - - - - - - - -tcaccca