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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgcgcgagaaatttggagcacctcgttcgctcgcatggcccttagagccgcgcccccatcggccatggctatgcattgcgagcgagacgtctaacgcgcatgcatgcggctctcacgcaacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACTGTGGCTCAGATGATTAAGGGGAAAACGCCAGAGGAGATCCGCAAGACGT

Basic information

species Chlamydomonas reinhardtii
transcript EDP05410
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP05410 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: LOC_Os09g36830.1 (Oryza sativa), 3'ss of exon 1
gtaagcgcgcgagaaatttggagcacctcgttcgctcgcatggcccttagagccgcgcccccatcggccatggctatgcattgcgagcgagacgtctaacgcgcatgcatgcggctctcacgcaacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACTGTGGCTCAGATGATTAAGGGGAAAACGCCAGAGGAGATCCGCAAGACGT
        ||  ||   |||      ||| | |    |      || |  |           |||   ||||    | ||  |      |||    | | | |||||  || |  ||           ||||||| |||||||| ||||||||||| |||||||| |||||||||||||| |||||| | ||||| |||||||| || |||||||||||||||||||| |
-------tgctggatgattg-----tctcatgcttctgttgtatccatgtatattgttttttatcattcatg----tacaaagtcgattagat---tcatgtgcatgtttgtgtttc-----------agGCTGCAAACTACCTCAACATCAAGGGACTGCTGGATCTGACCTGCCAGACCGTGGCTGACATGATCAAGGGGAAGACACCAGAGGAGATCCGCAAGACCT

upper sequence: EDP05410 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: LOC_Os11g26910.1 (Oryza sativa), 3'ss of exon 1
gtaagcgcgcgagaaatttggagcacctcgttcgct-cgcatggcccttagagccgcgcccccatcggccatggctatgcattgcgagcgagacgtctaacgc-gcatgcatgcggctctcacgcaacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACTGTGGCTCAGATGATTAAGGGGAAAACGCCAGAGGAGATCCGCAAGACGT
                              |   ||  | ||  |  ||   || |       ||| |   |   ||  ||| | ||      | ||| |  |    |  ||  |  |||||     ||||||| ||||||||||| |||||||||||  |||||||||| || ||||||||||| ||| | ||||| |||||||| || || ||||||||||||||||| |
------------------------------tgaactatgtattccttttgtggctgaatgttgatctgtgct--ttagccatagtgattactgcttcttataccatgtttatttgattctcaaatcccacagGCCGCGAACTACCTCAACATCAAGGGGTTGCTGGACCTTACTTGCCAGACTGTTGCTGACATGATCAAGGGGAAGACTCCTGAGGAGATCCGCAAGACCT

upper sequence: EDP05410 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: GRMZM2G101446_T01 (Zea mays), 3'ss of exon 1
gtaagcgcgcgagaaatttggagcacctcgttcgctcgcatggcccttagagccgcgcccccatcggccatggctatgcattgcgagcgagacgtctaacgcgcatgcatgcggctctcacgcaacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACTGTGGCTCAGATGATTAAGGGGAAAACGCCAGAGGAGATCCGCAAGACGT
                       |||   |||   | |  ||    ||  | |   |     ||   |  |   |    |||          |  ||    |  || | |    | |  |      | ||||||| ||||| |||||||||||||||||||| ||||||||||| |||||||| ||| | ||||| ||||| || || ||||| ||||| |||||||| |
-----------------------cacactgttt--ttgtttgatttttgtatc---gtaattatatactgtaaattgtaattattgtttgagca-ctgcttctgattcgtttctccccta-attttatagGCTGCAAACTATCTGAACATCAAGGGTCTGCTCGACCTGACCTGTCAGACTGTTGCTGACATGATCAAGGGCAAGACACCAGAAGAGATTCGCAAGACCT

upper sequence: EDP05410 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: GRMZM2G032562_T01 (Zea mays), 3'ss of exon 1
gtaagcgcgcgagaaatttggagcacctcgttcgctcgcat-ggcccttagagccgcgcccccatcggccatggctatgcattgcgagcgagacgtctaacgcgcatgcatgcggctctcacgcaacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACTGTGGCTCAGATGATTAAGGGGAAAACGCCAGAGGAGATCCGCAAGACGT
                      |||        | | | || |||| ||| |          ||   |  ||   |||    |  ||       ||  |  |  ||||| | | ||  ||||       |||||||  |||||||| | ||||| || ||||||||||||||||||||| | || ||  | ||||| |||||||| || ||||||||||| ||| |||| |
--------------------aggcagaattggtgtttgtattggccattatattttgagtgtca--agaaataaatatattgtaggattatattgtg-actgtccatgc-tactgcattcac-------agGCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCCGTCGCGGACATGATCAAGGGGAAGACTCCAGAGGAGATACGCGAGACAT

upper sequence: EDP05410 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: GLYMA01G36850.2 (Glycine max), 3'ss of exon 1
gtaagcgcgcgagaaatttggagcacctcgttcgctcgcatggcccttagagccgcgcccccatcggccatggctatgcattgcgagcgagacgt-ctaacgcgcatgcatgcggctctcacgcaacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACTGTGGCTCAGATGATTAAGGGGAAAACGCCAGAGGAGATCCGCAAGACGT
                         | | ||| | |    ||| |  | ||       || |||   |  ||   ||  | |  |    |   || |||| ||   |  ||| | |  |    |     |||||||||||||| ||||||||||| | ||||||||||| || ||||| ||||| ||  | ||||| |||||||| || || ||||| || |||||||| |
-------------------------catggttggattatctgggcaatggaatg----ccacatatactctgttaat-tagtaggttaaatctgtactaatgcatgttaatgtgacaattttccttt-tagGCTGCGAACTACTTGAACATCAAGAGCCTGCTGGACCTTACATGCCAAACTGTAGCCGACATGATCAAGGGGAAGACTCCCGAGGAAATTCGCAAGACCT

upper sequence: EDP05410 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: GLYMA11G08440.1 (Glycine max), 3'ss of exon 1
gtaagcgcgcgagaaatttggagcacctcgttcgctcgcatggcccttagagc-cgcgcccccatcggccatggctatgcattgcgagcgagacgt-ctaacgcgcatgcatgcggctctcacgcaacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACTGTGGCTCAGATGATTAAGGGGAAAACGCCAGAGGAGATCCGCAAGACGT
                                 | | | || |    |  |   |    || |||   |  ||  |||  | |  |        || ||||  |  ||  ||| | |  |    |     ||||||| |||||| ||||||||||| | ||||||||||| || || || ||||| ||  | ||||| |||||||| || |||||||| || |||||||| |
-------------------------------atgtttgtattgtttgtgcattgcaatgccacataaactctgtttatttagtaggttaagtctgtactaatacatattaatgtgacaatttt-ctttttagGCTGCTAACTACTTGAACATCAAGAGCCTGCTGGACCTTACATGTCAAACTGTAGCCGACATGATCAAGGGGAAGACTCCAGAGGAAATTCGCAAGACCT

upper sequence: EDP05410 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: Vv18s0001g14860.t01 (Vitis vinifera), 3'ss of exon 2
gtaagcgcgcgagaaatttggagcacctcgttcgctcgcatggcccttagagccgcgcccccatcggccatggctatgcattgcgagcgagacgtctaacgcgcatgcatgcggctctcacgcaacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACTGTGGCTCAGATGATTAAGGGGAAAACGCCAGAGGAGATCCGCAAGACGT
                  ||| | ||    || | |  |||  |  ||      |     |||   |  |     ||  |  | | |   ||| |  ||   |  || ||  |  | ||| ||| ||         ||||| |||||||||||| |||| ||||| || || || |||||||||||| | ||||| ||||| || || ||||||||||| ||||| || |
--------------gtcatggcgaacaattttagatatcatatctatt----ttgatataccagtagaaagaaaaatttacagtg-gtttgacat--aatttgtgtgtatttgattttcagGCAGCA---------AACTATCTGAACATCAAGAGTCTCCTGGATCTTACTTGTCAGACTGTGGCTGACATGATAAAGGGCAAGACTCCAGAGGAGATTCGCAAAACTT

upper sequence: EDP05410 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: PP1S9_292V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------gtaagc-gcgcgagaaatttggagcacctcgttcgctcgcatggcccttagagccgcgcccccatcggccatggc-tatgcattgcgagcgagacgtctaacgcgcatgcatgcggctctcacgc------------aacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACTGTGGCTCAGATGATTAAGGGGAAAACGCCAGAGGAGATCCGCAAGACGT
                              |   || | ||| |  ||  || ||| | |   ||   ||     |   |     ||||   || ||    |||     |    | | | | ||| |     | | |    ||| |   ||  |                |||||| ||||||||| |||||||||||   ||||||||| |||| |||||||| |||||  | ||||| |||||||| ||||| ||||||||| | || ||||
gtaagtgatgtgcatgcgaccctgtttgttgcgtgcagggcgggggatggggtgcatcccag-cgggggcggaagcgcgatgatggcgcgtgcaacgtttgtggggcgagagaggagggggtgacttggggtgaggagttgtgctgacgtcggggtggtgaatgatgggaacagGCAGCGAACTACTTGAACATCAAGAACCTGCTGGACTTGACGTGCCAGACGGTGGCGGACATGATAAAGGGGAAGACGCCGGAGGAGATCAGGAAAACGT

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|14238265|gb|BG857081.1|BG857081
EST:     ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTG                         GCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
genomic: ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTGgtaagcgcgc ... cgcaacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
EST: gi|9028346|gb|BE238386.1|BE238386
EST:     ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTG                         GCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
genomic: ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTGgtaagcgcgc ... cgcaacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
EST: gi|16072985|gb|BI874981.1|BI874981
EST:     ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTG                         GCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
genomic: ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTGgtaagcgcgc ... cgcaacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
EST: gi|22048905|gb|BQ808451.1|BQ808451
EST:     ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTG                         GCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
genomic: ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTGgtaagcgcgc ... cgcaacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
EST: gi|10772658|gb|AV623481.1|AV623481
EST:     ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTG                         GCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
genomic: ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTGgtaagcgcgc ... cgcaacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
EST: gi|16073343|gb|BI875339.1|BI875339
EST:     ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTG                         GCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
genomic: ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTGgtaagcgcgc ... cgcaacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
EST: gi|23360499|gb|BU648319.1|BU648319
EST:     ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTG                         GCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
genomic: ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTGgtaagcgcgc ... cgcaacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
EST: gi|22059318|gb|BQ813369.1|BQ813369
EST:     ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTG                         GCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
genomic: ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTGgtaagcgcgc ... cgcaacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
EST: gi|14233097|gb|BG851913.1|BG851913
EST:     ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTG                         GCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
genomic: ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTGgtaagcgcgc ... cgcaacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
EST: gi|9458554|gb|BE452298.1|BE452298
EST:     ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTG                         GCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
genomic: ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTGgtaagcgcgc ... cgcaacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
EST: gi|10126354|gb|BE725058.1|BE725058
EST:     ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTG                         GCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
genomic: ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTGgtaagcgcgc ... cgcaacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
EST: gi|10776452|gb|AV633132.1|AV633132
EST:     ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTG                         GCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
genomic: ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTGgtaagcgcgc ... cgcaacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
EST: gi|8828365|gb|BE212095.1|BE212095
EST:     ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTG                         GCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
genomic: ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTGgtaagcgcgc ... cgcaacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
EST: gi|8514400|gb|BE122295.1|BE122295
EST:     ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTG                         GCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
genomic: ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTGgtaagcgcgc ... cgcaacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
EST: gi|22050919|gb|BQ809410.1|BQ809410
EST:     ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTG                         GCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
genomic: ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTGgtaagcgcgc ... cgcaacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
EST: gi|8287622|gb|BE025181.1|BE025181
EST:     ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTG                         GCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT
genomic: ATGATGAGTTCGTGAAGGTGGACCAGGCAACGCTGTTCGACCTCATCCTGgtaagcgcgc ... cgcaacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcattgcgagcgagacgtctaacgcgcatgcatgcggctctcacgcaacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACTGTGGCTCAGATGATTAAGGGGAAAACGCCAGAGGAGATCCGCAAGACGT
                                       ctctcac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcgcgcgagaaatttggagcacctcgttcgctcgcatggcccttagagccgcgcccccatcggccatggctatgcattgcgagcgagacgtctaacgcgcatgcatgcggctctcacgcaacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACTGTGGCTCAGATGATTAAGGGGAAAACGCCAGAGGAGATCCGCAAGACGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA