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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtaagctagttcaagatactgtaaaatatttcaatgctacatccagatttcagatctcttcctggttattcacacaatttttgcatattgttcctttagGTTGTTACTCTCTGGTACCGAGCACCAGAGATACTCCTAGGATCTCATCATTACTCTACACCTGTTGATATTTGGTCTGTGGGGTGCATATTTGCTGAGA

Basic information

species Arabidopsis thaliana
transcript AT3G48750.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G48750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G08330.1 (Glycine max), 3'ss of exon 4
----agtaagctagttc--aagatactgtaaaatatttcaatgctacatccagatttcagatctcttcctggttattcacacaatttttgcatattgttcctttagGTTGTTACTCTCTGGTACCGAGCACCAGAGATACTCCTAGGATCTCATCATTACTCTACACCTGTTGATATTTGGTCTGTGGGGTGCATATTTGCTGAGA
    |  ||  || |||    || |  ||| |||  |  |  |  |  |  | |  ||| ||    |  |  | | | | | |   ||||   ||||||  | ||||| || || || |||||| |||| ||||| ||  | || ||||| |||||||| ||||| || |||||||||||||| ||||| ||||||||||| ||||
cttaaaaaatataattcttgtgaaaaggtacaatggtagagggaca-gtaaaaacatcaaattatctttttctgagttataga---tttggcgattgtt--tgtagGTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCATTATTCTACCCCAGTTGATATTTGGTCAGTGGGATGCATATTTGCAGAGA

upper sequence: AT3G48750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G03470.1 (Glycine max), 3'ss of exon 4
agtaagctagttcaa-gatactgtaaaatatt--tcaatgctacatccagatttcagatctcttcctggtt--attcacacaatttttgcatattgttcctttagGTTGTTACTCTCTGGTACCGAGCACCAGAGATACTCCTAGGATCTCATCATTACTCTACACCTGTTGATATTTGGTCTGTGGGGTGCATATTTGCTGAGA
   ||  |  |  || | || |||   |   |  |  ||| |   |     ||| | || | ||||   ||   |    | |||  |||   ||||||  | ||||| || ||  | |||||| |||| ||||| ||| | || ||||||| |||||| ||||| || |||||| ||||||| ||||| ||||||||||| ||||
---aatttcatggaaaggtattgtggtaggctggttgatgatttttaacagtttaatatttattcccatttctgtgtttataataattggtgattgtt--tgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCATTATTCTACGCCAGTTGATGTTTGGTCAGTGGGATGCATATTTGCAGAGA

upper sequence: AT3G48750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G25320.1 (Glycine max), 3'ss of exon 3
agtaagctagttcaagatactgtaaa---atatt--tcaatgctacatccagatttcagatctcttcctggttattcacacaatttttgcatattgttcctttagGTTGTTACTCTCTGGTACCGAGCACCAGAGATACTCCTAGGATCTCATCATTACTCTACACCTGTTGATATTTGGTCTGTGGGGTGCATATTTGCTGAGA
  |||   |  | ||  |  ||||||   ||| |  |  |||     |  | |  ||| ||    |  |  | | | | | |   ||||   ||||||  | ||||| || || || |||||| |||| || || ||  | || ||||| | ||| || ||||| || |||||||||||||| ||||| ||||||||||| ||||
cttaaaaaatataaatcttttgtaaaggtataatggtagatggacagtaaaaacatcaaattatctttttctgagttataaa---tttggcgattgtt--tgtagGTGGTAACACTGTGGTACAGAGCTCCGGAAATTTTGCTTGGATCCCGTCAGTATTCTACCCCAGTTGATATTTGGTCAGTGGGATGCATATTTGCAGAGA

upper sequence: AT3G48750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 5
-agtaagctagttcaagatactgtaaaatatttcaatgctacatccagatttcagatctcttcctggttattcacacaatttttgcatattgttc-ctttagGTTGTTACTCTCTGGTACCGAGCACCAGAGATACTCCTAGGATCTCATCATTACTCTACACCTGTTGATATTTGGTCTGTGGGGTGCATATTTGCTGAGA
 |       || |||  |||     || |  ||   ||  || |   |||  ||  |||| |  |  |   |      ||         | |||| |   |||| || || || |||||| ||||||| || ||||| || ||||| |  || || ||||| ||||||||| | ||||||||||| || |||||||||||||
tacctccacagatcac-atatgaggaatttgtttggtga-accttttgataccatctctcattattatgtctgggttcataaacattggtggttctccccagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCACTATTCTACTCCTGTTGATGTGTGGTCTGTGGGCTGTATATTTGCTGAGA

upper sequence: AT3G48750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S25_198V6.6 (Physcomitrella patens), 3'ss of exon 6
agtaagctagttcaagatactgtaaaat-atttcaatgctacatccagatttcagatctcttcc-tggttattcacacaattt-ttgcatattgttcctttagGTTGTTACTCTCTGGTACCGAGCACCAGAGATACTCCTAGGATCTCATCATTACTCTACACCTGTTGATATTTGGTCTGTGGGGTGCATATTTGCTGAGA
  |       ||||| ||  ||| |  | ||  |  |  | ||||   |   ||| ||  ||   | ||  ||||     ||  |||  |    |   |  |||| || ||  | |||||| |||||||||| || ||| |||| ||||  || |||||||||||||| ||| | |||||||| || ||||| || |||||||
gatcttacgattcaa-atgttgttagctgataacttttttgcatcataa--acagctcatttgggtcgtagttcatgggtttcattgtctggcttaaatgcagGTGGTAACATTGTGGTACAGAGCACCAGAAATTCTCTTAGGTTCTCGCCACTACTCTACACCTGTAGATGTGTGGTCTGTAGGATGCATTTTCGCTGAGA

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|301501515|gb|HO207055.1|HO207055
EST:     TTGGACTGGCCAGAGCATTCGGTATCCCTGTCAGGACATTTACTCATGAG                         GTTGTTACTCTCTGGTACCGAGCACCAGAGATACTCCTAGGATCTCATCAT
genomic: TTGGACTGGCCAGAGCATTCGGTATCCCTGTCAGGACATTTACTCATGAGgtaccaaaga ... gttcctttagGTTGTTACTCTCTGGTACCGAGCACCAGAGATACTCCTAGGATCTCATCAT
EST: gi|124761295|gb|EH851425.1|EH851425
EST:     CCAGAGCATTCGGTATCCCTGTCGGGACATTTACTCATGAG                         GTTGTTACTCTCTGGTACCGAGCACCAGAGATACTCCTAGGATCTCATCAT
genomic: CCAGAGCATTCGGTATCCCTGTCAGGACATTTACTCATGAGgtaccaaaga ... gttcctttagGTTGTTACTCTCTGGTACCGAGCACCAGAGATACTCCTAGGATCTCATCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatttcagatctcttcctggttattcacacaatttttgcatattgttcctttagGTTGTTACTCTCTGGTACCGAGCACCAGAGATACTCCTAGGATCTCATCATTACTCTACACCTGTTGATATTTGGTCTGTGGGGTGCATATTTGCTGAGA
                                           ttgttccttt  CT-rich tract
                               aatttttgcatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtaagctagttcaagatactgtaaaatatttcaatgctacatccagatttcagatctcttcctggttattcacacaatttttgcatattgttcctttagGTTGTTACTCTCTGGTACCGAGCACCAGAGATACTCCTAGGATCTCATCATTACTCTACACCTGTTGATATTTGGTCTGTGGGGTGCATATTTGCTGAGA

- - - - - - caagata
- - - - - - - - - - - -aaaatat
- - - - - - - - - - - - - - - - - - -ctacatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acacaat