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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtattgagcctcttttaccttagtttcatcagtaaattgttaacatgcggttattgaattgtgtattattactttttgaagGTCACTTCAAGGAAACAGATTGACGGGTAGAATTCCAGAAGTTATTGGTCTAATGCAGGCTCTTGCTGTTTT

Basic information

species Arabidopsis thaliana
transcript AT5G62230.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G62230.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os06g03970.1 (Oryza sativa), 3'ss of exon 9
--------------------------------gtgagtattgagcctcttttaccttagtttcatcagtaaattgttaacatgcggt-tattgaattgtgtattattactttttgaagGTCACTTCAAGGAAACAGATTGACGGGTAGAATTCCAGAAGTTATTGGTCTAATGCAGGCTCTTGCTGTTTT
                                    ||| |  ||   ||    ||||     ||   |   ||  | |||  |  | | |||||   | |  ||||  | ||   ||||||||||||||||| ||| |||| || | ||||||||| || ||||| || ||||| |||||||||||| |
gtaagtgttcctgagttattgcaaatcctctaacatgtaatctgctgtttcactcttatgcatatagatgctttacttacagcctttatgttgaaccattt-ctattcatgttcatagGTCACTTCAAGGAAATAGACTGACTGGGAAAATTCCAGATGTGATTGGCCTGATGCAAGCTCTTGCTGTTCT

upper sequence: AT5G62230.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G082855_T03 (Zea mays), 3'ss of exon 9
----------gtga-gtattgagc-ctcttttaccttag-----tttcatcagtaaattgttaacatgcggttatt-gaattgtgtatt--attact-ttttgaagGTCACTTCAAGGAAACAGATTGACGGGTAGAATTCCAGAAGTTATTGGTCTAATGCAGGCTCTTGCTGTTTT
           ||| || ||||   ||  ||||  | ||     ||   |    | ||   || ||||| ||| || |  |||   |||  |||  | ||||  ||||||||||||||||| ||| |||  || | |||||| ||||| ||||| || |||||||||||||||||  |
gtaagtcttcctgatgtcttgaattcttctttaattcagcagacttgtgtactcatatatgtaccatgccgttctttgttttgatcattgcattgttgttttacagGTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGATTGGCCTCATGCAGGCTCTTGCTGTCCT

upper sequence: AT5G62230.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA20G29010.1 (Glycine max), 3'ss of exon 7
------------------------------------------------------------gtgagtattgagcctcttttaccttagtttcatcagtaaattgttaacatgcggttattgaattgtgtattattactttt-tgaagGTCACTTCAAGGAAACAGATTGACGGGTAGAATTCCAGAAGTTATTGGTCTAATGCAGGCTCTTGCTGTTTT
                                                            |  | |  ||  |   |       |  | ||||    |||   | |  ||     |  | |||| |  | |   | || |    ||||||||||||||||| ||||| || ||    ||||||||||| |||||| ||||||| || |||||  | ||
gtacgtatactttgactgaagttattttaattatggcactactgtgaatcacttttgtttgacaatggtggactggtgggggggtcatgtcatattgaaaggataagtatatttatgatcaattat-cactgcaatttctgcctagGTCACTTCAAGGAAATAGATTAACTGGGGAGATTCCAGAAGTGATTGGTTTAATGCAAGCCCTTGCAATATT

upper sequence: AT5G62230.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv16s0022g02030.t01 (Vitis vinifera), 3'ss of exon 9
-----------------------------------gtgagtattgagcctcttttaccttagtttcatcagtaa--attgttaacatgcggttattgaattgtgt---------attattactttttgaa---gGTCACTTCAAGGAAACAGATTGACGGGTAGAATTCCAGAAGTTATTGGTCTAATGCAGGCTCTTGCTGTTTT
                                     ||  | |||   |  ||||| |  |    | || | |  | ||||   |   | ||  |||  ||  |         | | ||  || || ||   ||||||| |||||||| |   | || || |  |||||||| || |||||||||||||| || |||||||||||
gtaagctttctagtttagatcattcttttggaaactggacaaatgaaagttatttacttggggaagagcattgatcaatgttgtgaaatgattggtgacatgatttaagataaaactcttggttctttaatcagGTCACTCCAAGGAAATAAGCTAACAGGAAAGATTCCAGAGGTGATTGGTCTAATGCAAGCCCTTGCTGTTTT

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|86063080|gb|DR358837.1|DR358837
EST:     ATAACAGGAGAGATTCCTTACAATATCGGCTTCCTCCAAGTTGCTACTCT                         GTCACTTCAAGGAAACAGATTGACGGGTAGAATTCCAGAAGTTATTGGTCT
genomic: ATAACAGGAGAGATTCCTTACAATATCGGCTTCCTCCAAGTTGCTACTCTgtgagtattg ... ctttttgaagGTCACTTCAAGGAAACAGATTGACGGGTAGAATTCCAGAAGTTATTGGTCT
EST: gi|86063078|gb|DR358835.1|DR358835
EST:     ATAACAGGAGAGATTCCTTACAATATCGGCTTCCTCCAAGTTGCTACTCT                         GTCACTTCAAGGAAACAGATTGACGGGTAGAATTCCAGAAGTTATTGGTCT
genomic: ATAACAGGAGAGATTCCTTACAATATCGGCTTCCTCCAAGTTGCTACTCTgtgagtattg ... ctttttgaagGTCACTTCAAGGAAACAGATTGACGGGTAGAATTCCAGAAGTTATTGGTCT
EST: gi|86063081|gb|DR358838.1|DR358838
EST:     ATAACAGGAGAGATTCCTTACAATATCGGCTTCCTCCAAGTTGCTACTCT                         GTCACTTCAAGGAAACAGATTGACGGGTAGAATTCCAGAAGTTATTGGTCT
genomic: ATAACAGGAGAGATTCCTTACAATATCGGCTTCCTCCAAGTTGCTACTCTgtgagtattg ... ctttttgaagGTCACTTCAAGGAAACAGATTGACGGGTAGAATTCCAGAAGTTATTGGTCT
EST: gi|86063079|gb|DR358836.1|DR358836
EST:     ATAACAGGAGAGATTCCTTACAATATCGGCTTCCTCCAAGTTGCTACTCT                         GTCACTTCAAGGAAACAGATTGACGGGTAGAATTCCAGAAGTTATTGGTCT
genomic: ATAACAGGAGAGATTCCTTACAATATCGGCTTCCTCCAAGTTGCTACTCTgtgagtattg ... ctttttgaagGTCACTTCAAGGAAACAGATTGACGGGTAGAATTCCAGAAGTTATTGGTCT
EST: gi|86063083|gb|DR358840.1|DR358840
EST:     ATAACAGGAGAGATTCCTTACAATATCGGCTTCCTCCAAGTTGCTACTCT                         GTCACTTCAAGGAAACAGATTGACGGGTAGAAATTCCAGAAGTTATTGGTC
genomic: ATAACAGGAGAGATTCCTTACAATATCGGCTTCCTCCAAGTTGCTACTCTgtgagtattg ... ctttttgaagGTCACTTCAAGGAAACAGATTGACGGGTAGAA-TTCCAGAAGTTATTGGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcagtaaattgttaacatgcggttattgaattgtgtattattactttttgaagGTCACTTCAAGGAAACAGATTGACGGGTAGAATTCCAGAAGTTATTGGTCTAATGCAGGCTCTTGCTGTTTT
           tgttaac  putative branch site (score: 2)
                                          ttacttttt  putative PPT
                        ttattgaattgtgtat  TA-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtattgagcctcttttaccttagtttcatcagtaaattgttaacatgcggttattgaattgtgtattattactttttgaagGTCACTTCAAGGAAACAGATTGACGGGTAGAATTCCAGAAGTTATTGGTCTAATGCAGGCTCTTGCTGTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT