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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtaaacctctttccttttctatcattttagcccataaatatattcatgtgttgttgttttgttccggatcttacacttatcgtctgttgctttgtttttctcccgaatgtaaattctttgaacagATACCAACAAATCATGCTGGTCTTATTGAATATAGGGCACATCCTTTTTGGGTTCAGAAGTATTGTCCTTCTCACGAACACGATGCTACCCCGAGATGTT

Basic information

species Arabidopsis thaliana
transcript AT1G19270.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G19270.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g42820.2 (Oryza sativa), 3'ss of exon 8
gtacgtaaacctctttccttttctatcattttagcccataaatatattcatgtgttgttgttttgttccggatcttacacttatcgtctgttgctttgtttttctcccgaatgtaaattctttgaacagATACCAACAAATCATGCTGGTCTTATTGAATATAGGGCACATCCTTTTTGGGTTCAGAAGTATTGTCCTTCTCACGAACACGATGCTACCCCGAGATGTT
                  |      |||| || |   || |  ||    || |  |  |   |  ||    |  |||         |||||||  ||||  |       |||| | |||   ||| ||||| ||||||||  | | ||| |  ||||||||| |||| |||||||| ||| | ||||||||||||||| | || |||   |||  ||| || || || |
-----------------gtaagaattcatgttgg---atgagcatgagaatttagtaatagctactttttaacttta---------tctgttgagttgtgct-------aatg-acatttgatgatcagATTCCAACAAACAAAGATGGCCACATTGAATATCGGGCCCATCCTTTCTGGATGCAGAAGTATTGTCCTGCCCATGAAACTGATCGTACTCCTAGGTGCT

upper sequence: AT1G19270.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 6
--------------------------------------------------gtacgtaaacctctttccttttctatcattttagcccataaatatattca-tgtgttgttgttttgttccggatcttacacttatcgtctgttgctttgtttttctcccgaatgt--aaattctt-tgaacagATACCAACAAATCATGCTGGTCTTATTGAATATAGGGCACATCCTTTTTGGGTTCAGAAGTATTGTCCTTCTCACGAACACGATGCTACCCCGAGATGTT
                                                   |  ||  | |  ||| |||  || |   |       | |  ||| | || | | |||  |  | || |    ||| ||| || || |   |  | |  ||  |||  | ||| |   | | ||| |   ||||| || ||||||     ||| |||||||||||||||||||||||||| ||||| || || || |||||||| || |||   |||| ||| ||||| || |
gtaaggatcactttatttaccctgaccgatctgtttatgctataagttttttctgttgaacattttacttgcctgtttgtgctaataaaatctatctccaatatcttggagaat-gtgctttctct-acatttttcatgattgacatgtttactcttgctaatatctgattacttcttttcagATTCCTACAAATATGAATGGCCTTATTGAATATAGGGCACATCCTTTCTGGGTACAAAAATACTGTCCTTCACATGAAATGGATGGTACTCCGAGGTGCT

upper sequence: AT1G19270.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G342105_T02 (Zea mays), 3'ss of exon 3
gtacgtaaacctctttccttttctatcattttagcccataaatatattcatgtgttgttgttttgttccggatcttacacttatcgtctgttgctttgtttttctcccgaatgtaaattctttgaacagATACCAACAAATCATGCTGGTCTTATTGAATATAGGGCACATCCTTTTTGGGTTCAGAAGTATTGTCCTTCTCACGAACACGATGCTACCCCGAGATGTT
                        | || | |   |  | | |  ||  ||| | |      ||     | |  | |   | ||  ||  ||   || || || |  |  ||| || ||   | | ||||| || ||| || |   ||| || ||||||||  |||| |||||||||||| | ||||||||||||||||| || ||| | |||| ||| || || || |
---------------------gtaagcactcttcactttgatttgatagatgagcttgaaaatttagtagtaaataatcttgattatccatttggttattcttatttctgatggaattttggtaaccagATTCCCACAGATAAAAATGGCCTCATTGAATACCGGGCCCATCCTTTTTGGATGCAGAAGTATTGTCCTTCCCATGAAAATGATGGTACACCTAGGTGCT

upper sequence: AT1G19270.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA14G08450.1 (Glycine max), 3'ss of exon 6
gtacgtaaacctctttccttttctatcattttagcccataaatatattcatgtgttgttgttttgttccggatcttaca-cttatcgtctgttgctttgtttttctcccgaatgtaaattctttgaacagATACCAACAAATCATGCTGGTCTTATTGAATATAGGGCACATCCTTTTTGGGTTCAGAAGTATTGTCCTTCTCACGAACACGATGCTACCCCGAGATGTT
                       |   |||||     | | | ||  |  |  ||| |    |||      | |||| | || || | |||||| || ||||||      ||| || ||| ||| | ||||| |||||||||| |||||||||||||||||||||||||||||| || ||| | ||||| ||||| ||| |||||||||| |||| |||  |  | ||||
-----------------------ttagattttgaa--aaagacatgcttttaagttttcaccttgacttcaaccttatatctcattgcctgttg-ttggtttttggt---aatatatattttttca-cagATTCCAACAAATCCTGCTGGTCTTATTGAATATAGGGCACATCCATTCTGGATCCAGAAATATTGCCCTACTCACGAACATGATGGTACTACACGCTGTT

upper sequence: AT1G19270.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G36620.1 (Glycine max), 3'ss of exon 5
gtacgtaaacctctttccttttctatcattttagcccataaatatattcatgtgttgttgttttgttccggatcttacacttatcgtctgttgctttgtttttctcccgaatgtaaattctttgaacagATACCAACAAATCATGCTGGTCTTATTGAATATAGGGCACATCCTTTTTGGGTTCAGAAGTATTGTCCTTCTCACGAACACGATGCTACCCCGAGATGTT-
             | |  ||  || |||| ||||    |||| | |  ||||  ||||   |||       | |||| || | | ||  |||  |||| |         ||| || ||| ||| | ||||| |||||||||| |||||||||||||||||||||||||||||| || ||| | ||||| ||||| ||| |||| ||||| |||| ||| ||  | |||| 
---------taattgtttttaactctcatgttagattttaaaaaga--catgc-ttgtaagttttc-----acctta-acctgttgttggtt--tttggt---------aatatatattttttca-cagaTTCCAACAAATCCTGCTGGTCTTATTGAATATAGGGCACATCCATTCTGGATCCAGAAATATTGCCCTACTCATGAACATGATGGTACTCCACGCTGTTG

upper sequence: AT1G19270.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv18s0001g11820.t01 (Vitis vinifera), 3'ss of exon 6
gtacgtaaacctctttccttttctatcattttagcccataa-atatattcatgtgttgttgtt-ttgttccggatcttacacttatcgtctgttgctttgtttttctcccgaatgtaaat-tctttgaacagATACCAACAAATCATGCTGGTCTTATTGAATATAGGGCACATCCTTTTTGGGTTCAGAAGTATTGTCCTTCTCACGAACACGATGCTACCCCGAGATGTT
                                ||   || | ||||     | |  |  | || ||  |  ||||  | |||| ||  || |||  | |   |||||   |||  ||||| | |||  |||||| ||||| || | |||||||||||||||||||||||| ||||||||||||||||||||||| || |||||||| || || ||    || || ||||| |
-------------------------------aagaaaatgagatatgcaattttactactattcttcctttggatacttcactcattttcagtttgtgttggtttcttg-gaacataaatatatttttacagATTCCAACGAACCCTGCTGGTCTTATTGAATATAGGGCGCATCCTTTTTGGGTTCAGAAGTACTGCCCTTCTCATGAGCATGACAGAACACCTAGATGCT

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|116457268|gb|EG499860.1|EG499860
EST:     CTTGTTACAGGGAGAGATATCATCCTAAATGTGATGTCTGCAGCCACTTT                         ATACCAACAAATCATGCTGGTCTTATTGAATATAGGGCACATCCTTTTTGG
genomic: CTTGTTACAGGGAGAGATATCATCCTAAATGTGATGTCTGCAGCCACTTTgtacgtaaac ... ctttgaacagATACCAACAAATCATGCTGGTCTTATTGAATATAGGGCACATCCTTTTTGG
EST: gi|86057437|gb|DR353194.1|DR353194
EST:     CTTGTTACAGGGAGAGATATCATCCTAAATGTGATGTCTGCAGCCACTTT                         ATACCAACAAATCATGCTGGTCTTATTGAATATAGGGCACATCCTTTTTGG
genomic: CTTGTTACAGGGAGAGATATCATCCTAAATGTGATGTCTGCAGCCACTTTgtacgtaaac ... ctttgaacagATACCAACAAATCATGCTGGTCTTATTGAATATAGGGCACATCCTTTTTGG
EST: gi|116457269|gb|EG499861.1|EG499861
EST:     TGTGATGTCTGCAGCCACTTT                         ATACCCAACAAAATCATGCTGGTCTTATTGAATATAGGGCACATCCTTTTT
genomic: TGTGATGTCTGCAGCCACTTTgtacgtaaac ... ctttgaacagATA-CCAAC-AAATCATGCTGGTCTTATTGAATATAGGGCACATCCTTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacacttatcgtctgttgctttgtttttctcccgaatgtaaattctttgaacagATACCAACAAATCATGCTGGTCTTATTGAATATAGGGCACATCCTTTTTGGGTTCAGAAGTATTGTCCTTCTCACGAACACGATGCTACCCCGAGATGTT
 atcttac  putative branch site (score: 3)
                                           ttcttt  putative PPT
                                   aatgtaaattcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtaaacctctttccttttctatcattttagcccataaatatattcatgtgttgttgttttgttccggatcttacacttatcgtctgttgctttgtttttctcccgaatgtaaattctttgaacagATACCAACAAATCATGCTGGTCTTATTGAATATAGGGCACATCCTTTTTGGGTTCAGAAGTATTGTCCTTCTCACGAACACGATGCTACCCCGAGATGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG