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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcaatattttctatcactctggagctacatgattcgttaagaaccaactactatgttattaaagaataaatgaatatattatgtatattttctttcagGATTGGCTAACCCTGCTCCGATTATTCAAACTTTCTATGCTGAGGATGAAATTTTCAATGATGTCAAGCTGGATGGGGTTGTCACTCTGGTTGATGCTAA

Basic information

species Arabidopsis thaliana
transcript AT1G15730.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G15730.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g55630.1 (Oryza sativa), 3'ss of exon 3
gttcaatattttctatcactctggagctacatgattcgttaagaaccaactactatgttattaaagaataaatgaatatattatgtatattttctttc-agGATTGGCTAACCCTGCTCCGATTATTCAAACTTTCTATGCTGAGGATGAAATTTTCAATGATGTCAAGCTGGATGGGGTTGTCACTCTGGTTGATGCTAA
 ||    |   |  |   |    ||| | |||  |||      |  ||   | ||| | |||| |  | |  |  | |  |    | | ||  ||||| ||| || || || || || || ||||| || ||||||||||| || |||  | |||| |||||||||||||||||||| ||||| ||| | || ||||| ||
-ttgtccacaattgaaatcctcagagattcatttttcaaagctactcattaattatttaattatatgaaattttcacacttgtattgtcttaactttccagGTTTAGCAAATCCAGCACCCATTATACAGACTTTCTATGCAGAAGATACAGTTTTTAATGATGTCAAGCTGGATGGTGTTGTGACTTTAGTAGATGCAAA

upper sequence: AT1G15730.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G180418_T03 (Zea mays), 3'ss of exon 8
-----------------------------------------------------------gttcaatattttctatcactctggagctacatgattcgttaagaacc-aacta-ctatgttattaaagaat-aaatgaat-atattatgtatatt------------------ttctttcagGATTGGCTAACCCTGCTCCGATTATTCAAACTTTCTATGCTGAGGATGAAATTTTCAATGATGTCAAGCTGGATGGGGTTGTCACTCTGGTTGATGCTAA
                                                           ||  ||  ||    |  |      ||  |  ||| || | || |     | || ||  |||||  | | || | || ||| || |||  |    |                  || |||||||  | || || || || || ||||| ||||| |||||||| ||||||| | |||| ||||||||||||||||| || ||||| ||| | ||||| || ||
gtaaagagcttgttaggttattgttcaaacggcagatctcacattaattttttttataagtataaatttgaacagaaaaactaagtaatgtgaatcatgaaaagtttgattatcttggttatccatggatcacataaatcatgttaactgctctccttttttcttcatccaattttttcagGTCTAGCGAATCCAGCACCCATTATACAAACATTCTATGCAGAGGATGTAGTTTTTAATGATGTCAAGCTGGACGGTGTTGTTACTTTAGTTGACGCAAA

upper sequence: AT1G15730.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G43740.1 (Glycine max), 3'ss of exon 3
------------gttcaatattttctatcactctggagctacatgattcgttaagaaccaactactatgttattaaagaataaatgaatatattatgtatattttctttcagGATTGGCTAACCCTGCTCCGATTATTCAAACTTTCTATGCTGAGGATGAAATTTTCAATGATGTCAAGCTGGATGGGGTTGTCACTCTGGTTGATGCTAA
             || | | || | ||  |       | || |     |  ||||     |    | || |      ||   | |   | | || | | || ||     |||| ||||| || ||||| || || || || || || ||||| |||||  | ||||| |||||||||||  ||||||| ||||| |||||||||||||| ||
gtaactgccagactttattcttgtttaatatagatatgatagacctccctgtaagttgttatggttgtgcttagtgtgaccgacttgttttgttgtttgtacttaa---cagGTTTGGCAAATCCTGCACCAATAATCCAGACCTTTTATGCAGAGGAAAATATTTTTAATGATGTCAAATTGGATGGTGTTGTTACTCTGGTTGATGCGAA

upper sequence: AT1G15730.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv09s0002g08260.t01 (Vitis vinifera), 3'ss of exon 3
gttcaatattttctatcactctggagctacatgattcgttaag-aaccaactactatg----ttattaaagaataaatgaatatattatgtatattttctttcagGATTGGCTAACCCTGCTCCGATTATTCAAACTTTCTATGCTGAGGATGAAATTTTCAATGATGTCAAGCTGGATGGGGTTGTCACTCTGGTTGATGCTAA
      ||| | |  |  || |  || ||  |      |  |  | | || |    ||    |   |      || ||  ||  ||  ||| |      |  |||||||||| || || || || || ||||| || || |||||||||||| | ||||||||||||||||| |||||||| ||||| ||| |||||||||||||
-----gtatatacacttcctttacagatatgtagcatttcgactagctaaatgtgttggatttctctgggttttatattcatgaatcttgtttgcaacttcacagGATTGGCAAATCCAGCACCAATCATTCAGACATTTTATGCTGAGGATCAGATTTTCAATGATGTCAAACTGGATGGCGTTGTTACTTTGGTTGATGCTAA

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|116433950|gb|EG476542.1|EG476542
EST:     GGTCCAGACCAAGAAAGGAAGGTTCGACCATATCGTTATTGAGACGACAG                         GATTGGCTAACCCTGCTCCGATTATTCAAACTTTCTATGCTGAGGATGAAA
genomic: GGTCCAGACCAAGAAAGGAAGGTTCGACCATATCGTTATTGAGACGACAGgttcaatatt ... tttctttcagGATTGGCTAACCCTGCTCCGATTATTCAAACTTTCTATGCTGAGGATGAAA
EST: gi|116474224|gb|EG516816.1|EG516816
EST:     GGTCCAGACCAAGAAAGGAAGGTTCGACCATATCGTTATTGAGACGACAG                         GATTGGCTAACCCTGCTCCGATTATTCAAACTTTCTATGCTGAGGATGAAA
genomic: GGTCCAGACCAAGAAAGGAAGGTTCGACCATATCGTTATTGAGACGACAGgttcaatatt ... tttctttcagGATTGGCTAACCCTGCTCCGATTATTCAAACTTTCTATGCTGAGGATGAAA
EST: gi|116474225|gb|EG516817.1|EG516817
EST:     GGTCCAGACCAAGAAAGGAAGGTTCGACCATATCGTTATTGAGACGACAG                         GATTGGCTAACCCTGCTCCGATTATTCAAACTTTCTATGCTGAGGATGAAA
genomic: GGTCCAGACCAAGAAAGGAAGGTTCGACCATATCGTTATTGAGACGACAGgttcaatatt ... tttctttcagGATTGGCTAACCCTGCTCCGATTATTCAAACTTTCTATGCTGAGGATGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaactactatgttattaaagaataaatgaatatattatgtatattttctttcagGATTGGCTAACCCTGCTCCGATTATTCAAACTTTCTATGCTGAGGATGAAATTTTCAATGATGTCAAGCTGGATGGGGTTGTCACTCTGGTTGATGCTAA
                                          tattttctttc  CT-rich tract
        tatgttattaaagaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcaatattttctatcactctggagctacatgattcgttaagaaccaactactatgttattaaagaataaatgaatatattatgtatattttctttcagGATTGGCTAACCCTGCTCCGATTATTCAAACTTTCTATGCTGAGGATGAAATTTTCAATGATGTCAAGCTGGATGGGGTTGTCACTCTGGTTGATGCTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA