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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgttttgttgtttcttgttaacacacacacacgctctctcgcacacacacgcacgctcactcgcacacacatcaacacgcactcacacacatacacacagGTGGGCGACGCGCTGGCGCAGCCGTTCGAGGCCGGCGCCTTCGACCTGGTGTGGTCCATGGAGAGCGGCGAGCACATGCCCGACAAGAA

Basic information

species Chlamydomonas reinhardtii
transcript EDP02465
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP02465 (Chlamydomonas reinhardtii), 3'ss of exon 6
lower sequence: LOC_Os02g47310.1 (Oryza sativa), 3'ss of exon 2
----------------------------------------------------------------cgttttgttgtttcttgtta-acacacacac-acgctctctcgcacacacacgcacgctcactcgcacac------acatcaacacgcactcacacacatacacacagGTGGGCGACGCGCTGGCGCAGCCGTTCGAGGCCGGCGCCTTCGACCTGGTGTGGTCCATGGAGAGCGGCGAGCACATGCCCGACAAGAA
                                                                  | | | |||  || || | |   |||    ||  | ||          |     | | |||| |          ||  |||   |      ||    | |   || || || || ||  ||| |||||| ||    |  ||    || || || || |||||||||||||| |||||||||||||| |||||   
gtgcgtattactactgtttattctgttctaaaaaaaattctactgtttattcgtatcgggatttaatctcgctgtagctagtcatagttacatttgacaatatcagagggtttaagctctgattactcactgctggtgtgacgacaatctgtttaagcagGTCTCCTTTCAAGTTGGTGATGCATTGGAGCAGCCTTTTCCTGATGGGCAGTTTGATCTTGTCTGGTCCATGGAGAGTGGCGAGCACATGCCAGACAAAC-

upper sequence: EDP02465 (Chlamydomonas reinhardtii), 3'ss of exon 6
lower sequence: GRMZM2G035213_T01 (Zea mays), 3'ss of exon 2
-----cgtt-ttgttgtttct--tgttaacacacacacacgctctctcgcacacacacgcacgctcactcgcacacacatcaacacgcactcacacacatacacacagGTGGGCGACGCGCTGGCGCAGCCGTTCGAGGCCGGCGCCTTCGACCTGGTGTGGTCCATGGAGAGCGGCGAGCACATGCCCGACAAGAA
     |  |  || || | ||  | ||| | | |   ||   | |        |      ||| || | |   ||| |  |   ||| |       ||       || || |  || || |||| ||| |||||    | |||    ||||| |||||||||||||||||||| |||||||||||||| ||||||| 
gtgcccactgctgctgctcctcctcttacctctcttgcaaattgttataacggccggttaacg-tctcccttccaccccgcgtgacggagcagGTTACTC---TGCAAGTTGCTGATGCTCTGGAGCAACCGTTTCCTGACGGGCAGTTCGATCTGGTGTGGTCCATGGAGAGTGGCGAGCACATGCCGGACAAGA-

upper sequence: EDP02465 (Chlamydomonas reinhardtii), 3'ss of exon 6
lower sequence: GLYMA12G01690.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------cgttttgttgtttcttgttaacacacacacacgctctctcgca--cacacacgcacgctcactcgcacacacatcaacacgcactcacacacatacacacagGTGGGCGACGCGCTGGCGCAGCCGTTCGAGGCCGGCGCCTTCGACCTGGTGTGGTCCATGGAGAGCGGCGAGCACATGCCCGACAAGAA
                                                     ||| |   ||||    ||   |  || |   |       |   | ||| | |   | |      |   |||      | | |  ||    | |   ||||| |  ||||| ||   ||| || |||   | ||||   || || |||||||||||||||||||| || ||||| ||||| |||||   
gtcttcatttctcgacatgtttttagtatttatatttacgcattccaaggttctttataacttctatagaatctatgcatataatactatataaatatacaagtataataatatttgctttcatgtttctgtaattgcagGTTTCCTTTCAGGTTGCTGACGCTCTACAGCAACCATTCTCTGACGGCCAGTTTGATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAG-

upper sequence: EDP02465 (Chlamydomonas reinhardtii), 3'ss of exon 6
lower sequence: GLYMA12G01680.1 (Glycine max), 3'ss of exon 2
------cgttttgttgtttctt--gttaacacacacacacgctctctcgcacacacacgcacgctcactcgcacacacatcaacacgc----actcacacacatacacacagGTGGGCGACGCGCTGGCGCAGCCGTTCGAGGCCGGCGCCTTCGACCTGGTGTGGTCCATGGAGAGCGGCGAGCACATGCCCGACAAGAA
          | || ||   ||  | |     |     |   ||| |   |||||         |  || |||    | |  |   |     | |  ||    | |    |||| |  ||||| ||   ||| || |||  ||  ||    || || |||||||||||||||||||| || ||||| ||||| |||||   
cacatgtagctagtagtactttaaggtttttaatttctagtatctattttacacatgtttttaatttctagcatttgctttcatgtgtctgtaattgcagGTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAATTTGATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAG-

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|15693587|gb|BI717892.1|BI717892
EST:     CCAATGCGCTGAGCAAGGAGCAGGGCTTTGGCGACAAGCTGCAGTTCCAG                         GTGGGCGACGCGCTGGCGCAGCCGTTCGAGGCCGGCGCCTTCGACCTGGGT
genomic: CCAATGCGCTGAGCAAGGAGCAGGGCTTTGGCGACAAGCTGCAGTTCCAGgtgggtcgga ... atacacacagGTGGGCGACGCGCTGGCGCAGCCGTTCGAGGCCGGCGCCTTCGACCTGG-T
EST: gi|6543208|gb|AV388992.1|AV388992
EST:     CCAATGCGCTGAGCAAGGAGCAGGGCTTTGGCGACAAGCTGCAGTTCCAG                         GTGGGCGACGCGCTGGCGCAGCCGTTCGAGGCCGGCGCCTTCGACCTGGTG
genomic: CCAATGCGCTGAGCAAGGAGCAGGGCTTTGGCGACAAGCTGCAGTTCCAGgtgggtcgga ... atacacacagGTGGGCGACGCGCTGGCGCAGCCGTTCGAGGCCGGCGCCTTCGACCTGGTG
EST: gi|22061463|gb|BQ814260.1|BQ814260
EST:     CCAATGCGCTGAGCAAGGAGCAGGGCTTTGGCGACAAGCTGCAGTTCCAG                         GTGGGCGACGCGCTGGCGCAGCCGTTCGAGGCCGGCGCCTTCGACCTGGTG
genomic: CCAATGCGCTGAGCAAGGAGCAGGGCTTTGGCGACAAGCTGCAGTTCCAGgtgggtcgga ... atacacacagGTGGGCGACGCGCTGGCGCAGCCGTTCGAGGCCGGCGCCTTCGACCTGGTG
EST: gi|49461318|gb|BP089231.1|BP089231
EST:     CCAATGCGCTGAGCAAGGAGCAGGGCTTTGGCGACAAGCTGCAGTTCCAG                         GTGGGCGACGCGCTGGCGCAGCCGTTCGAGGCCGGCGCCTTCGACCTGGTG
genomic: CCAATGCGCTGAGCAAGGAGCAGGGCTTTGGCGACAAGCTGCAGTTCCAGgtgggtcgga ... atacacacagGTGGGCGACGCGCTGGCGCAGCCGTTCGAGGCCGGCGCCTTCGACCTGGTG
EST: gi|14237576|gb|BG856392.1|BG856392
EST:     CCAATGCGCTGAGCAAGGAGCAGGGCTTTGGCGACAAGCTGCAGTTCCAG                         GTGGGCGACGCGCTGGCGCAGCCGTTCGAGGCCGGCGCCTTCGACCTGGTG
genomic: CCAATGCGCTGAGCAAGGAGCAGGGCTTTGGCGACAAGCTGCAGTTCCAGgtgggtcgga ... atacacacagGTGGGCGACGCGCTGGCGCAGCCGTTCGAGGCCGGCGCCTTCGACCTGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacacgcacgctcactcgcacacacatcaacacgcactcacacacatacacacagGTGGGCGACGCGCTGGCGCAGCCGTTCGAGGCCGGCGCCTTCGACCTGGTGTGGTCCATGGAGAGCGGCGAGCACATGCCCGACAAGAA
                                  cactcac  putative branch site (score: 2)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgttttgttgtttcttgttaacacacacacacgctctctcgcacacacacgcacgctcactcgcacacacatcaacacgcactcacacacatacacacagGTGGGCGACGCGCTGGCGCAGCCGTTCGAGGCCGGCGCCTTCGACCTGGTGTGGTCCATGGAGAGCGGCGAGCACATGCCCGACAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- -tttgttg
- - - - - -ttcttgt
- - - - - - - - - - acacaca
- - - - - - - - - - - - - - - - - - - - - - - acacgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcacaca