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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccagtgcctggcggacattccgcttacgctacgtgccctggggtccgttgcgatatggtgtgctgcccttaccctcttccgcttcccgcccctctcccagGCCCCTACTCTGAGAACTCGACCCCCGCCTACCTGACTGGCGAGTTCCCCGGCGACTACGGCTGGGACACTGCCGGTCTGTCGGCTGACCCGGAGACCTT

Basic information

species Chlamydomonas reinhardtii
transcript EDP01725
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP01725 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: GRMZM2G414192_T01 (Zea mays), 3'ss of exon 1
--------ccagtgcctggcggacattccgcttacgcta-----cgtgccctggg-gtccgttgcgatatg-gtgt--gctgcccttaccctcttccgcttc--ccgcccct--ctcccagGCCCCTACTCTGAGAACTCGACCCCCGCCTACCTGACTGGCGAGTTCCCCGGCGACTACGGCTGGGACACTGCCGGTCTGTCGGCTGACCCGGAGACCTT
        |   |||    || |   | | |||  |  |     |  || | ||  ||  |    ||  || |||   ||||||     |   | | ||      ||||||      |  ||||| | ||| ||| |   ||| ||  | |||||||| ||||||||||||||||||||||| |||||||| ||                           
gtacgtgccttctgctctccgcatgcttcccttgtgtcaatcagctcgctcgggaagtgagaactgacgtgcgtgctggctgcctgctgcagGTACGGCCCTGATCGCCCCAAGTATCTTGGCCCGTTCTCCGAGCA---GACGCCGTCGTACCTGACCGGCGAGTTCCCCGGCGACTACGGGTGGGACACCGCG--------------------------

upper sequence: EDP01725 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: GRMZM2G105518_T01 (Zea mays), 3'ss of exon 1
--------ccagtgcctggcggacattccgcttac--------gctacgtgccctggggtccgttgcgatatg-gtgtgctgcccttaccctcttccgcttcccgccc---ctctcccagGC------CCCTACTCTGAGAACTCGACCCCCGCCTACCTGACTGGCGAGTTCCCCGGCGACTACGGCTGGGACACTGCCGGTCTGTCGGCTGACCCGGAGACCTT
         |  |||   ||   |||||   | ||        |    | |  ||| |      ||  | |   ||  |||| |     |  | | |   | |  |||   |   |||| |       |||   |||  || |  |||  |  | |||||||| ||||||||||||||||||||||| |||||||| ||                           
gtacgtgctccctgcgccgcattcattcgtgtcactaagaggagaggtgaggactgtgagtaactgacagacacgtacgctgactgctgctgcatgcagGTACGACCCTGACCGCCCCAAGTACCTTGCCCCGTTCTCCGAGCA-GACGTCGTCGTACCTGACGGGCGAGTTCCCCGGCGACTACGGGTGGGACACCGCG--------------------------

upper sequence: EDP01725 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: GRMZM2G057281_T02 (Zea mays), 3'ss of exon 2
-------------ccagtgcctggcggacattccgcttacgctacgtgccctggggtccgttg-cgatatggtgtgctgcccttaccctcttccgcttcccgcccctctcccagGCCCCTACTCTGAGAACTCGACCCCCGCCTACCTGACTGGCGAGTTCCCCGGCGACTACGGCTGGGACACTGCCGGTCTGTCGGCTGACCCGGAGACCTT-
             |||  | ||  |||    |||    | |   ||| |  |||  ||  |     ||  |||    |   || ||     | | |    |||  |  |  |||| |      ||| |    || |||   ||      | |  |  |  |||         | |  |      | || | | | ||  |  ||||| |||    
gtacgtggagcatccatcgtctatcgg----tccatccatggcccgt-cgatggtttcaatcaataatcaggtaaaatcgactaacgagagtgctcgcttcgcttccattgcagGGCAACGACCTGTGG-TACGGCCCGGACCGCGTCAAGTACCTGGGCCCCTTCTCCGCCCAGACGCCCTCGTACCTGACCGGCGAGTTCCCCGGCGACTACG

upper sequence: EDP01725 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: PP1S51_305V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------ccagtgcctggcggacattccgcttacgctacg-tgccctggggtccgttgcgatatggtgtgctgcccttaccctcttccgcttcccgcccct--ctcccagGCCCCTACTCTGAGAACTCGACCCCCGCCTACCTGACTGGCGAGTTCCCCGGCGACTACGGCTGGGACACTGCCGGTCTGTCGGCTGACCCGGAGACCTT
                             ||||| | | | |  |         | || |  |  | |  |||      || || | || |||    |    |     |||  | | ||     ||   ||||| | ||| |   |   ||||||  | || |||| |||||||||| ||||||||||||| |||||||| ||                           
ggggttgcaagggagccccattccgagagagtgcattgtgaatgtggaatccgggatagggcgaaccgatgtctaagtggaaattg-gtactggtggtcagGTACGGAGCTGACAGGCCAAAGTTCTTGGGCCCATTCTCCGGCGA---GACCCCGTCATATCTGAATGGCGAGTTCGCCGGCGACTACGGATGGGACACCGCT--------------------------

upper sequence: EDP01725 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: PP1S27_97V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------------------ccagtgcctggcggac-attccgcttacgctac-gtgccctggggtccgttgcgatatggt-gtgctgcccttaccctcttccgcttcccgcccctctcccagGCCCCTACTCTGAGAACTCGACCCCCGCCTACCTGACTGGCGAGTTCCCCGGCGACTACGGCTGGGACACTGCCGGTCTGTCGGCTGACCCGGAGACCTT
                                 | |   | |||    ||| |||  | |||  |   |||       | | ||||||  | ||  |||   |||  |      |  |||     | |   |||||||| |||||   |   ||||||  | ||||||||||| |||||| |||| |||||||| |||||||||||                           
aacgtactcctgttcaccgctgccgaggtgattgagaacgccgggttgttctgctccccctattgcttcctaatagtagct-cgatatatttgtaatgcagGTACGGTGCCGACCGACCCAAGTATTT---AGGCCCCTTCTCTGGAGA---GACCCCTTCATACCTGACTGGTGAGTTCGCCGGTGACTACGGGTGGGACACTGCT--------------------------

upper sequence: EDP01725 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: PP1S254_3V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------------------ccagtgcc--tggcggacattccgcttacgctacgtgccctggggtccgttgcgatatggtgtgctgcccttaccctcttccgcttcccgcccctctcccagGCCCCTACTCTGAGAACTCGACCCCCGCCTACCTGACTGGCGAGTTCCCCGGCGACTACGGCTGGGACACTGCCGGTCTGTCGGCTGACCCGGAGACCTT
                                || |||  ||  |  ||        |   |  | |  ||   ||   |    | |||   ||||||   |||  ||  |||     | |||   ||   || || | ||| |  |||   |||||| ||||| |||  ||||||||||| || |||||||| |||||||||||                           
attgttcgcatcatgttgacatcgtcgttcttagagccgatgttgaccaccaaaggaattttttgagagctctagttaatcaatacatgcaatgctgcagGTACGGTC--CCGACAGGC-CCCTGTTCTTGGGTCCTTTCTCCGGTAAC---ACCCCCTCCTACTTGAAGGGCGAGTTCCCTGGTGACTACGGATGGGACACTGCT--------------------------

upper sequence: EDP01725 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: EFJ11993 (Selaginella moellendorffii), 3'ss of exon 1
------------------ccagtgcctggcggacattccgcttacgctacgtgccctggggtccgttgcgat-atggtgtgctgcccttaccctcttc-------cgcttcccgcccctc-----tcccagGCCCCTACTCTGAGAACTCGACCCCCGCCTACCTGACTGGCGAGTTCCCCGGCGACTACGGCTGGGACACTGCCGGTCTGTCGGCTGACCCGGAGACCTT
                   ||||  ||| |     ||      || | |  | |   | | ||      ||| || ||  |||  | ||    | | |        | | |   ||   |     |||  ||||||| ||| ||| |   ||| ||| ||||||| || |||||||| || ||||||||||||||||| || ||                           
tcgagctcttcaaagctcacagtcgctgacttg-gttgtctccacaccatttccttcgagctcttgaaagatcatagt-cgctaactttgttgtatccacagGTATGGTCCAGACCGACCAAAGTTCCTCGGCCCCTTCTCCGAGCA---GACACCCTCCTACCTCACCGGCGAGTTTCCTGGCGACTACGGCTGGGATACCGCG--------------------------

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|161806945|gb|FC093183.1|FC093183
EST:     CAAGAGCTCTGGCGTTGAGTTCTATGGCCCCAACCGCGCCAAGTGGCTGG                         GCCCCTACTCTGAGAACTCGACCCCCGCCTACCTGACTGGCGAGTTCCCCG
genomic: CAAGAGCTCTGGCGTTGAGTTCTATGGCCCCAACCGCGCCAAGTGGCTGGgtgagtgcgc ... cctctcccagGCCCCTACTCTGAGAACTCGACCCCCGCCTACCTGACTGGCGAGTTCCCCG
EST: gi|161797166|gb|FC087149.1|FC087149
EST:     CAAGAGCTCTGGCGTTGAGTTCTATGGCCCCAACCGCGCCAAGTGGCTGG                         GCCCCTACTCTGAGAACTCGACCCCCGCCTACCTGACTGGCGAGTTCCCCG
genomic: CAAGAGCTCTGGCGTTGAGTTCTATGGCCCCAACCGCGCCAAGTGGCTGGgtgagtgcgc ... cctctcccagGCCCCTACTCTGAGAACTCGACCCCCGCCTACCTGACTGGCGAGTTCCCCG
EST: gi|49460310|gb|BP088223.1|BP088223
EST:     CAAGAGCTCTGGCGTTGAGTTCTATGGCCCCAACCGCGCCAAGTGGCTGG                         GCCCCTACTCTGAGAACTCGACCCCCGCCTACCTGACTGGCGAGTTCCCCG
genomic: CAAGAGCTCTGGCGTTGAGTTCTATGGCCCCAACCGCGCCAAGTGGCTGGgtgagtgcgc ... cctctcccagGCCCCTACTCTGAGAACTCGACCCCCGCCTACCTGACTGGCGAGTTCCCCG
EST: gi|49463248|gb|BP091161.1|BP091161
EST:     CAAGAGCTCTGGCGTTGAGTTCTATGGCCCCAACCGCGCCAAGTGGCTGG                         GCCCCTACTCTGAGAACTCGACCCCCGCCTACCTGACTGGCGAGTTCCCCG
genomic: CAAGAGCTCTGGCGTTGAGTTCTATGGCCCCAACCGCGCCAAGTGGCTGGgtgagtgcgc ... cctctcccagGCCCCTACTCTGAGAACTCGACCCCCGCCTACCTGACTGGCGAGTTCCCCG
EST: gi|10776611|gb|AV633291.1|AV633291
EST:     CAAGAGCTCTGGCGTTGAGTTCTATGGCCCCAACCGCGCCAAGTGGCTGG                         GCCCCTACTCTGAGAACTCGACCCCCGCCTACCTGACTGGCGAGTTCCCCG
genomic: CAAGAGCTCTGGCGTTGAGTTCTATGGCCCCAACCGCGCCAAGTGGCTGGgtgagtgcgc ... cctctcccagGCCCCTACTCTGAGAACTCGACCCCCGCCTACCTGACTGGCGAGTTCCCCG
EST: gi|9441487|gb|BE441977.1|BE441977
EST:     CAAGAGCTCTGGCGTTGAGTTCTATGGCCCCAACCGCGCCAAGTGGCTGG                         GCCCCTACTCTGAGAACTCGACCCCCGCCTACCTGACTGGCGAGTTCCCCG
genomic: CAAGAGCTCTGGCGTTGAGTTCTATGGCCCCAACCGCGCCAAGTGGCTGGgtgagtgcgc ... cctctcccagGCCCCTACTCTGAGAACTCGACCCCCGCCTACCTGACTGGCGAGTTCCCCG
EST: gi|49461465|gb|BP089378.1|BP089378
EST:     CAAGAGCTCTGGCGTTGAGTTCTATGGCCCCAACCGCGCCAAGTGGCTGG                         GCCCCTACTCTGAGAACTCGACCCCCGCCTACCTGACTGGCGAGTTCCCCG
genomic: CAAGAGCTCTGGCGTTGAGTTCTATGGCCCCAACCGCGCCAAGTGGCTGGgtgagtgcgc ... cctctcccagGCCCCTACTCTGAGAACTCGACCCCCGCCTACCTGACTGGCGAGTTCCCCG
EST: gi|7426818|gb|AW660991.1|AW660991
EST:     CAAGAGCTCTGGCGTTGAGTTCTATGGCCCCAACCGCGCCAAGTGGCTGG                         GCCCCTACTCTGAGAACTCGACCCCCGCCTACCTGACTGGCGAGTTCCCCG
genomic: CAAGAGCTCTGGCGTTGAGTTCTATGGCCCCAACCGCGCCAAGTGGCTGGgtgagtgcgc ... cctctcccagGCCCCTACTCTGAGAACTCGACCCCCGCCTACCTGACTGGCGAGTTCCCCG
EST: gi|49462798|gb|BP090711.1|BP090711
EST:     CAAGAGCTCTGGCGTTGAGTTCTATGGCCCCAACCGCGCCAAGTGGCTGG                         GCCCCTACTCTGAGAACTCGACCCCCGCCTACCTGACTGGCGAGTTCCCCG
genomic: CAAGAGCTCTGGCGTTGAGTTCTATGGCCCCAACCGCGCCAAGTGGCTGGgtgagtgcgc ... cctctcccagGCCCCTACTCTGAGAACTCGACCCCCGCCTACCTGACTGGCGAGTTCCCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttgcgatatggtgtgctgcccttaccctcttccgcttcccgcccctctcccagGCCCCTACTCTGAGAACTCGACCCCCGCCTACCTGACTGGCGAGTTCCCCGGCGACTACGGCTGGGACACTGCCGGTCTGTCGGCTGACCCGGAGACCTT
                    cccttac  putative branch site (score: 3)
               tgctgcccttaccctc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccagtgcctggcggacattccgcttacgctacgtgccctggggtccgttgcgatatggtgtgctgcccttaccctcttccgcttcccgcccctctcccagGCCCCTACTCTGAGAACTCGACCCCCGCCTACCTGACTGGCGAGTTCCCCGGCGACTACGGCTGGGACACTGCCGGTCTGTCGGCTGACCCGGAGACCTT

- - - - - - - acattcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgtg