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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACCCTGGCCATCACCGACGACACCCGCATTCGCGCGGCCGTCCCCACCCTGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTGgtaagagattgtgctgtgctcggcgcacccagggccctcggtaggcgctcctagcatcgtgtgttgtcggcatgcataggtttctcgttccaccactggc...

Basic information

species Chlamydomonas reinhardtii
transcript EDO98586
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDO98586 (Chlamydomonas reinhardtii), 5'ss of exon 3
lower sequence: LOC_Os02g07260.1 (Oryza sativa), 5'ss of exon 2
CACCCTGGCCATCACCGACGACACCCGCATTCGCGCGGCCGTCCCCACCCTGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTGgtaagagattgtgctgtgctcggcgcacccagggccctcggtaggcgctcctagcatcgtgtgttgtcggcatgcataggtttctcgttccaccactggc--
| ||| |   |||||||||||||||||||| |||||| |||| |||||  | |||| ||| || || || || || |||||| | ||  ||   || ||||| || ||     |  ||| |  ||  ||  |  ||  | |      |     |||  |||   ||      |  ||   |||   |||| |    |||   
CGCCCAGAAGATCACCGACGACACCCGCATCCGCGCGTCCGTGCCCACTGTCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTGgtcagtgagcaccccctgc-catcgatccttgaccctcccgcgctttcgatctgcaaagtggcatgctactttagattt-ttttgggttctaggggtggatg

upper sequence: EDO98586 (Chlamydomonas reinhardtii), 5'ss of exon 3
lower sequence: GRMZM2G382914_T02 (Zea mays), 5'ss of exon 2
CACCCTGGCCATCACCGACGACACCCGCATTCGCGCGGCCGTCCCCACCCTGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTGgtaagagattgtgctgtgctcggcgcacccagggccctcggtaggcgctcctagcatcgtgtgttgtcggcatgcataggtttctcgttccaccactggc----
  ||| |   |||||||||||||||||||| |||||  ||||||||||| | |||| ||| || || || || || |||||| | ||  ||   |||||||| ||   | |  |    ||   ||| |    | |      ||| |  | ||  || |  | |   | | |  |    |||  |  | |               
TGCCCAGAAGATCACCGACGACACCCGCATCCGCGCCTCCGTCCCCACCATCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCACCTGgtgag---tcgctcccaccttcccgcccgtctgtcatatcatagtcaatactgccagc-cgcgcgatggcctagtcacggtgccatgatttggaggcaatttga
















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|161823510|gb|FC108510.1|FC108510
EST:     TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTG                         GGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTTGTG
genomic: TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTGgtaagagatt ... ttaaaaacagGGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
EST: gi|10126032|gb|BE724736.1|BE724736
EST:     TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTG                         GGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
genomic: TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTGgtaagagatt ... ttaaaaacagGGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
EST: gi|161791377|gb|FC077974.1|FC077974
EST:     CTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTG                         GGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTTGTG
genomic: CTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTGgtaagagatt ... ttaaaaacagGGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
EST: gi|161795111|gb|FC078255.1|FC078255
EST:     TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTG                         GGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTTGTG
genomic: TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTGgtaagagatt ... ttaaaaacagGGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
EST: gi|9459905|gb|BE452968.1|BE452968
EST:     TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTG                         GGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
genomic: TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTGgtaagagatt ... ttaaaaacagGGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
EST: gi|49469821|gb|BP097682.1|BP097682
EST:     TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTG                         GGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
genomic: TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTGgtaagagatt ... ttaaaaacagGGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
EST: gi|6551890|gb|AV397674.1|AV397674
EST:     TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTG                         GGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTG
genomic: TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTGgtaagagatt ... ttaaaaacagGGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTG
EST: gi|161808380|gb|FC098453.1|FC098453
EST:     TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTG                         GGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTTGTG
genomic: TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTGgtaagagatt ... ttaaaaacagGGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
EST: gi|161812620|gb|FC099437.1|FC099437
EST:     TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTG                         GGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTTGTG
genomic: TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTGgtaagagatt ... ttaaaaacagGGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
EST: gi|161799718|gb|FC085252.1|FC085252
EST:     TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTG                         GGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTTGTG
genomic: TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTGgtaagagatt ... ttaaaaacagGGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
EST: gi|239842030|gb|GR283887.1|GR283887
EST:     TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTG                         GGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
genomic: TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTGgtaagagatt ... ttaaaaacagGGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
EST: gi|161822387|gb|FC106808.1|FC106808
EST:     TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTG                         GGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTTGTG
genomic: TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTGgtaagagatt ... ttaaaaacagGGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
EST: gi|10786678|gb|AV643350.1|AV643350
EST:     TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTG                         GGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
genomic: TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTGgtaagagatt ... ttaaaaacagGGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
EST: gi|161799786|gb|FC083253.1|FC083253
EST:     TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTG                         GGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTTGTG
genomic: TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTGgtaagagatt ... ttaaaaacagGGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
EST: gi|9210917|gb|BE337832.1|BE337832
EST:     TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTG                         GGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
genomic: TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTGgtaagagatt ... ttaaaaacagGGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
EST: gi|161813926|gb|FC104552.1|FC104552
EST:     TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTG                         GGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTTGTG
genomic: TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTGgtaagagatt ... ttaaaaacagGGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
EST: gi|161802603|gb|FC089099.1|FC089099
EST:     TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTG                         GGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTTGTG
genomic: TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTGgtaagagatt ... ttaaaaacagGGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
EST: gi|161795396|gb|FC078553.1|FC078553
EST:     TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTG                         GGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTTGTG
genomic: TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTGgtaagagatt ... ttaaaaacagGGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
EST: gi|161820324|gb|FC105889.1|FC105889
EST:     TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTG                         GGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTTGTG
genomic: TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTGgtaagagatt ... ttaaaaacagGGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
EST: gi|10127475|gb|BE726179.1|BE726179
EST:     TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTG                         GGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
genomic: TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTGgtaagagatt ... ttaaaaacagGGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
EST: gi|15373411|gb|BI532837.1|BI532837
EST:     TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTG                         GGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
genomic: TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTGgtaagagatt ... ttaaaaacagGGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
EST: gi|22049242|gb|BQ808677.1|BQ808677
EST:     TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTG                         GGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
genomic: TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTGgtaagagatt ... ttaaaaacagGGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
EST: gi|10127829|gb|BE726533.1|BE726533
EST:     TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTG                         GGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG
genomic: TGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTGgtaagagatt ... ttaaaaacagGGTCGCCCGAAGGGCGGTCCCGAGGACAAGTACCGCCTGACCCCCGTGGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACCCTGGCCATCACCGACGACACCCGCATTCGCGCGGCCGTCCCCACCCTGAAGTACCTGCTGGACAACGGTGCTAAGGTCCTGCTGACCTCGCACCTGgtaagagattgtgctgtgctcggcgcacccagggccctcggtaggcgctcctagcatcgtgtgttgtcggcatgcataggtttctcgttccaccactggc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcaccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtttct