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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcctgcacatgcacgttgtgccaggtgtcgcgaacgttgcgctggccgtatggctgggatgcttccctgactgcctttgctcgccccacacctgctgcagGCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGTAAATGCAGCAGCTTCAGAGGTTGCTGCCTTTTAGCAGGAGATAGAGTGT

Basic information

species Chlamydomonas reinhardtii
transcript EDP05500
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP05500 (Chlamydomonas reinhardtii), 3'ss of exon 3
lower sequence: PP1S41_71V6.1 (Physcomitrella patens), 3'ss of exon 2
-gcctgcacatgcacgttgtgccaggtgtcgcgaacgttgcgctggccgtatggctgggatgcttccctgactgcctttgctcgccccacacctgctgcagGCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGTAAATGCAGCAG--CTTCAGAGGTTGCTGCCTTTTAGCAGGAGATAGAGTGT
   || | | ||       |  |   |  |   ||| |  | ||  |   |    |    ||  |   | | |   |  | ||      |      | |||| |||||||||||||| |||||||||||| | |||||  |  | ||||||| || | ||| |   |||| | ||  ||  |||||        ||  |    
cttcttctcttgatacagatatcgcattgcagaaac-tctcactcccacaagcaattcagtgtgtaagtaagtttttaagttcttgttcctttgtatacagGTGACATCCTGACTCTCCTGGAGTCTGAGAGAGAGGCTAGGAGGCTGCGGTGAA-GAAGCGGGATTTCACAAGTCTCTAGCTTTTTTTTTCCTATTTATCA-
















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|22071235|gb|BQ820573.1|BQ820573
EST:     GCAACGTGAAGGGCCCCGTCCGCGAGG                         GCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
genomic: GCAACGTGAAGGGCCCCGTCCGCGAGGgtgagcacgc ... cctgctgcagGCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
EST: gi|34988161|gb|CF562078.1|CF562078
EST:     CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGG                         GCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
genomic: CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGGgtgagcacgc ... cctgctgcagGCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
EST: gi|34988803|gb|CF562720.1|CF562720
EST:     CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGG                         GCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
genomic: CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGGgtgagcacgc ... cctgctgcagGCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
EST: gi|34993857|gb|CF567774.1|CF567774
EST:     CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGG                         GCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
genomic: CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGGgtgagcacgc ... cctgctgcagGCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
EST: gi|34989394|gb|CF563311.1|CF563311
EST:     CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGG                         GCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
genomic: CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGGgtgagcacgc ... cctgctgcagGCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
EST: gi|10783401|gb|AV640073.1|AV640073
EST:     CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGG                         GCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
genomic: CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGGgtgagcacgc ... cctgctgcagGCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
EST: gi|34993622|gb|CF567539.1|CF567539
EST:     CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGG                         GCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
genomic: CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGGgtgagcacgc ... cctgctgcagGCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
EST: gi|34989393|gb|CF563310.1|CF563310
EST:     CGACCAGAACCCCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGG                         GCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCCCCTGCGGT
genomic: CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGGgtgagcacgc ... cctgctgcagGCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
EST: gi|34983424|gb|CF557341.1|CF557341
EST:     CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGG                         GCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTTTTTT
genomic: CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGGgtgagcacgc ... cctgctgcagGCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
EST: gi|10789573|gb|AV645302.1|AV645302
EST:     CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGG                         GCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
genomic: CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGGgtgagcacgc ... cctgctgcagGCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
EST: gi|10125832|gb|BE724536.1|BE724536
EST:     CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGG                         GCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
genomic: CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGGgtgagcacgc ... cctgctgcagGCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
EST: gi|34988802|gb|CF562719.1|CF562719
EST:     ACCAGAACCGCCTGATCATGCGCAACGTGAAGGGGCCCCGTCCGCCGAGG                         GCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCNCCGCCGCCTGCG
genomic: ACCAGAACCGCCTGATCATGCGCAACGTGAAGGG-CCCCGTCCGC-GAGGgtgagcacgc ... cctgctgcagGCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGC-CCGCCGCCTGCG
EST: gi|34993422|gb|CF567339.1|CF567339
EST:     CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGG                         GCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCCCCTGCGGT
genomic: CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGGgtgagcacgc ... cctgctgcagGCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
EST: gi|34986739|gb|CF560656.1|CF560656
EST:     CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGG                         GCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
genomic: CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGGgtgagcacgc ... cctgctgcagGCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
EST: gi|34993148|gb|CF567065.1|CF567065
EST:     CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGG                         GCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
genomic: CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGGgtgagcacgc ... cctgctgcagGCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
EST: gi|34992624|gb|CF566541.1|CF566541
EST:     CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGG                         GCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
genomic: CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGGgtgagcacgc ... cctgctgcagGCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
EST: gi|15372414|gb|BI531840.1|BI531840
EST:     CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGG                         GCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
genomic: CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGGgtgagcacgc ... cctgctgcagGCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
EST: gi|34987662|gb|CF561579.1|CF561579
EST:     CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGG                         GCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
genomic: CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGGgtgagcacgc ... cctgctgcagGCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
EST: gi|34993615|gb|CF567532.1|CF567532
EST:     CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGG                         GCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
genomic: CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGGgtgagcacgc ... cctgctgcagGCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
EST: gi|10788274|gb|AV644946.1|AV644946
EST:     CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGG                         GCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
genomic: CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGGgtgagcacgc ... cctgctgcagGCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
EST: gi|6544748|gb|AV390532.1|AV390532
EST:     CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGG                         GCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
genomic: CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGGgtgagcacgc ... cctgctgcagGCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
EST: gi|10786077|gb|AV642749.1|AV642749
EST:     CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGG                         GCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
genomic: CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGGgtgagcacgc ... cctgctgcagGCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
EST: gi|10788170|gb|AV644842.1|AV644842
EST:     CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGG                         GCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT
genomic: CGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGGgtgagcacgc ... cctgctgcagGCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgtatggctgggatgcttccctgactgcctttgctcgccccacacctgctgcagGCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGTAAATGCAGCAGCTTCAGAGGTTGCTGCCTTTTAGCAGGAGATAGAGTGT
                   ccctgac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcctgcacatgcacgttgtgccaggtgtcgcgaacgttgcgctggccgtatggctgggatgcttccctgactgcctttgctcgccccacacctgctgcagGCGACATCCTGACTCTGCTGGAGTCTGAGCGTGAGGCCCGCCGCCTGCGGTAAATGCAGCAGCTTCAGAGGTTGCTGCCTTTTAGCAGGAGATAGAGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - acatgca
- - - - - - -cgttgtg