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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttgaggatcagaaattttggtctattactgtcttcaatagcattgtacttattttgtttcccccattttatttgatattagGTATCCTCTTGGCCGTGTGATTGGAGGAACTGTTTACCCTGGGTTAACTTTGACTGCTGGAACCATCTGGTG

Basic information

species Arabidopsis thaliana
transcript AT5G19690.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G19690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os05g44360.1 (Oryza sativa), 3'ss of exon 3
----gtaatttgaggatcagaaattttggtctattactgtcttcaatagcat------tgtacttattt---tgtttcccccatttt--atttgatattagGTATCCTCTTGGCCGTGTGATTGGAGGAACTGTTTACCCTGGGTTAACTTTGACTGCTGGAACCATCTGGTG
      || | || |    | | | |||    || |   | |  ||||| ||      |   | || ||   || |||||    | |   ||   | |||||||||| ||||||||||||||||| || ||||| || ||||| || || ||||| ||||||||||| |||||
tatcaaaagtagatgga-gggagtattgtgtaatcatgatgtaaaatagaatgtgtaatacgcctacttggctgattcccttgctgttgcttctgttttagGTATCCCCTTGGCCGTGTGATTGGCGGCACTGTGTATCCTGGTTTGACATTGACAGCTGGAACCATTTGGTG

upper sequence: AT5G19690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G060611_T02 (Zea mays), 3'ss of exon 3
------------gtaatttgaggatcaga-aattttggtctattactgtcttcaatag------cattgtacttattttgtttcccccattttatttgata--ttagGTATCCTCTTGGCCGTGTGATTGGAGGAACTGTTTACCCTGGGTTAACTTTGACTGCTGGAACCATCTGGTG
              ||  |    | ||   | | |||  | ||| |||| |  ||          | |   || |||| ||| |      |     || |   ||||||| || |||||||||||||| || || ||||| || |||||||| || |||||||||||||| || |||||
gtaagggcagctccaaactatcaaccatttagtattgcgcaatttctgtgtggaaggaatcaattactcggctgatttcgttgctgttgctgctgctgctgctttagGTACCCCCTTGGCCGTGTGATCGGTGGCACTGTGTATCCTGGGTTGACATTGACTGCTGGAACTATGTGGTG

upper sequence: AT5G19690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv11s0016g03320.t01 (Vitis vinifera), 3'ss of exon 3
------gtaatttgagg-atcagaaat--tttggt--ctattactgtcttcaatagcattgtacttattttgtttcc-------cccattttatttgatattagGTATCCTCTTGGCCGTGTGATTGGAGGAACTGTTTACCCTGGGTTAACTTTGACTGCTGGAACCATCTGGTG
       | |||  |    || || ||  | ||||  | ||   |||  |||       | | ||||  |||||           |  || || ||    | |||||||||||||| ||||||||||| || ||||||||||| || || || || || || ||  |||| |||||
gtaatcattattaaaactgtccgatatgttctggtgaccatgtttgtgctcacgttatctttccttaagttgttaatgacagtatctgttctacttccattaagGTATCCTCTTGGTCGTGTGATTGGTGGCACTGTTTACCCAGGATTGACCTTAACAGCAGGCTCCATATGGTG

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|163967867|gb|EL970675.1|EL970675
EST:     TCGAAGAATGGAATATACGAGTTCTGGAATTGGTTTGATGATAGGACCTG                         GTATCCTCTTTGGCCGTGTGATTGGAGGAACTGTT-ACCCTGGGTTAACTT
genomic: TCGAAGAATGGAATATACGAGTTCTGGAATTGGTTTGATGATAGGACCTGgtaatttgag ... ttgatattagGTATCCTCTT-GGCCGTGTGATTGGAGGAACTGTTTACCCTGGGTTAACTT
EST: gi|164071106|gb|EL977197.1|EL977197
EST:     TCGAAGAATGGAATATACGAGTTCTGGAATTGGTTTGATGATAGGACCTG                         GTATCCTCTTGGCCGTGTGATTGGAGGAACTGTTTACCCTGGGTTAACTTT
genomic: TCGAAGAATGGAATATACGAGTTCTGGAATTGGTTTGATGATAGGACCTGgtaatttgag ... ttgatattagGTATCCTCTTGGCCGTGTGATTGGAGGAACTGTTTACCCTGGGTTAACTTT
EST: gi|164080409|gb|ES181529.1|ES181529
EST:     GTTCTGGAATTGGTTTGATGATAGGACCTG                         GTATCCTCTTGGCCGTGTGATTGGAGGAACTGTTTACCCTGGGTTAACTTT
genomic: GTTCTGGAATTGGTTTGATGATAGGACCTGgtaatttgag ... ttgatattagGTATCCTCTTGGCCGTGTGATTGGAGGAACTGTTTACCCTGGGTTAACTTT
EST: gi|86067003|gb|DR362760.1|DR362760
EST:     TCGAAGAATGGAATATACGAGTTCTGGAATTGGTTTGATGATCGGACCTG                         GTATCCTCTTGGCCGTGTGATTGGAGGAACTGTTTACCCTGGGTTAACTTT
genomic: TCGAAGAATGGAATATACGAGTTCTGGAATTGGTTTGATGATAGGACCTGgtaatttgag ... ttgatattagGTATCCTCTTGGCCGTGTGATTGGAGGAACTGTTTACCCTGGGTTAACTTT
EST: gi|164191038|gb|EL983806.1|EL983806
EST:     TCGAAGAATGGAATATACGAGTTCTGGAATTGGTTTGATGATAGGACCTG                         GTATCCTCTTGGCCGTGTGATTG-AGGAACTGTT-ACCCTGGGTTAACTTT
genomic: TCGAAGAATGGAATATACGAGTTCTGGAATTGGTTTGATGATAGGACCTGgtaatttgag ... ttgatattagGTATCCTCTTGGCCGTGTGATTGGAGGAACTGTTTACCCTGGGTTAACTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgtcttcaatagcattgtacttattttgtttcccccattttatttgatattagGTATCCTCTTGGCCGTGTGATTGGAGGAACTGTTTACCCTGGGTTAACTTTGACTGCTGGAACCATCTGGTG
                                           atttgat  putative branch site (score: 5)
                         ttttgtttcccccatt  CT-rich tract
                                      attttatttgatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttgaggatcagaaattttggtctattactgtcttcaatagcattgtacttattttgtttcccccattttatttgatattagGTATCCTCTTGGCCGTGTGATTGGAGGAACTGTTTACCCTGGGTTAACTTTGACTGCTGGAACCATCTGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA