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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttcattactgttcacttggccgtttggaaaaatcaaatatgtgtcttttgttatctttatgacaagaaattatcttgacagTAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAG

Basic information

species Arabidopsis thaliana
transcript AT3G15980.3
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 20
--gtatttcattactgttcacttggccgtttggaaaaatcaaatatgtgtcttttgttatctttatgacaagaaattatcttgacagTAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAG
    || |   | |||||  ||     |        | |  | ||  |   ||||   | ||  |   ||   |  |||  | |||| || || ||||| ||||||||  | |||||||||||||||||||| ||||||||||| |||||||||||  |||||||  | || ||||| || 
gtacatgtacatcctgtttgctgttatgaactccccattgtagtaaatcatttttcaaagctaaacctcatctatgtattat-acagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAA

upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os06g05180.4 (Oryza sativa), 3'ss of exon 4
--gtatttcattactgttcacttggccgtttggaaaaatcaaatatgtgtcttttgttatctttatgacaagaaattatcttgacagTAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAG------
    || |   | |||||  ||     |        | |  | ||  |   ||||   | ||  |   ||   |  |||  | |||| || || ||||| ||||||||  | |||||||||||||||||||| ||||||||||| |||||||||||  |||||||  | || ||||| ||       
gtacatgtacatcctgtttgctgttatgaactccccattgtagtaaatcatttttcaaagctaaacctcatctatgtattat-acagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAAGTAATT

upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G443953_T01 (Zea mays), 3'ss of exon 21
---gtatttcattactg--ttcacttggccgt--ttggaaaaatcaaatatgtgtcttttgttatctttatgacaagaaattatcttgacagTAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAG
   |  ||     | ||  | ||  | ||| |  |  | || |||   |||  | | ||   ||| || |  |   |   ||  ||  ||||||| || || |||||||| || ||||||||||| ||||| ||||||||||||||||| || || ||  |  ||||||   | || |||   |||
gtaggcttctgcaattgaatgcatcttgccctactcagtaacatcttgtatcggacattg--tatgttgacaattggtcctttgctgtacagTAATCGTATTCCAGAAGCAGCACTGATGGCACGATCTTACCTTCCAAGCAAAGTTTCTGATATTGTCTCAATATGGAAAAAGGACCTCCAAAAG

upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G443953_T02 (Zea mays), 3'ss of exon 20
-------------gtatttcattactg--ttcacttggccgt--ttggaaaaatcaaatatgtgtcttttgttatctttatgacaagaaattatcttgacagTAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAG
             |  ||     | ||  | ||  | ||| |  |  | || |||   |||  | | ||   ||| || |  |   |   ||  ||  ||||||| || || |||||||| || ||||||||||| ||||| ||||||||||||||||| || || ||  |  ||||||   | || |||   |||
tggttgataggtaggcttctgcaattgaatgcatcttgccctactcagtaacatcttgtatcggacattg--tatgttgacaattggtcctttgctgtacagTAATCGTATTCCAGAAGCAGCACTGATGGCACGATCTTACCTTCCAAGCAAAGTTTCTGATATTGTCTCAATATGGAAAAAGGACCTCCAAAAG

upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 20
-------------------------------------------------------------------gtatttcatt--actgttcacttggccgt---ttggaaaaatcaaatatgtgtcttttgttatctttatgacaa---gaaattatct-tgacagTAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAG
                                                                    |||||||||  || |   |  |||  ||   ||  |  |  ||   |  ||   ||   | |  | || | |    || ||  ||| |  |||||| |||||||| ||||||||| | |||||||| ||||| ||||||||||| ||| | |||||| |  |  | |||||  | || |||| ||||
gtaatcattttccttaccatataaccatagaaaatcaactgctgatactaatttattacacatttacttatttcatttaacagacaatatggtggtagtttatatgacccaggaagttgagattgagtttactgattagactctgatatggtctgttgcagTAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAG

upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 20
----gtatt-tcattactgttcacttggccgtttggaaaaat-caaatatgtgtcttttgttatctttatgacaagaaattatcttgacagTAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAG
     | || |  ||||||   || |||       || |  |    | || | ||   | ||    | ||    |   ||| ||||  ||| || ||||| || || |||||| |||||||||| ||||||||||||||||| || || |||||||| ||||| |||||| |||| || |  |||
gtaattgttgttgttactgcaaacatgggaacaaagatagttgtggagatat-tccacttttgggatgatactgaagcattctctttgcagCAATCGGATCCCTGAGGCTGCTTTGATGGCACGGTCTTATCTTCCAAGCAAGGTCTCAGAGATAGTCGCTCTGTGGAGGAAAGACCTTAATAAG

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|125289748|gb|EL303833.1|EL303833
EST:     TTATTTACGCTGGGTAGATTGGAAGATTGTCTGCAGTTATTGGTGGAGAG                         TAACCGGATACCAGAAGCTGCT
genomic: TTATTTACGCTGGGTAGATTGGAAGATTGTCTGCAGTTATTGGTGGAGAGgtatttcatt ... atcttgacagTAACCGGATACCAGAAGCTGCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaaatcaaatatgtgtcttttgttatctttatgacaagaaattatcttgacagTAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAG
                                           ttatctt  CT-rich tract
                   ttttgttatctttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttcattactgttcacttggccgtttggaaaaatcaaatatgtgtcttttgttatctttatgacaagaaattatcttgacagTAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG