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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAGTAGTTACTCATCAATGGAAGGTGTTTTGTACTGTAAGCCTCATTTTGAGCAGCTCTTTAAGGAGAGTGGTAGTTTCAACAAGAACTTTCAGTCACgtatgtagttttgtttctgcttcgattcatgttttttttccgcttgcccttcttttggttattgatttaatcagtcttgcaactttgtttcctcacag

Basic information

species Arabidopsis thaliana
transcript AT3G55770.6
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G55770.6 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA18G03490.1 (Glycine max), 5'ss of exon 4
-CTGAGTAGTTACTCATCAATGGAAGGTGTTTTGTACTGTAAGCCTCATTTTGAGCAGCTCTTTAAGGAGAGTGGTAGTTTCAACAAGAACTTTCAGTCACgtatgtagttttgtttctgcttcga--ttcatgttttttttccgcttgcccttcttttggttattgatttaatcagtcttgcaactttgtttcctcacag
 |||||||  || || ||||||||||||||| | |||||||||||||| | |||||||||||| |||||||||||    |||| ||||||||| ||||||||||||| ||| | ||||| ||| ||   | | ||| | |||  | | |   ||   |    |     ||||||  | | |   | |||  ||    ||| 
GCTGAGTAACTATTCCTCAATGGAAGGTGTTCTTTACTGTAAGCCTCACTATGAGCAGCTCTTCAAGGAGAGTGGCTCCTTCAGCAAGAACTTCCAGTCAcgtatgt-gttctttttcttctttgaggatgaagttgtgtttgtg-tggtttttgaatcatatgcctctttaattggccat---attttcattttgaaca-

upper sequence: AT3G55770.6 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA11G34830.1 (Glycine max), 5'ss of exon 4
CTGAGTAGTTACTCATCAATGGAAGGTGTTTTGTACTGTAAGCCTCATTTTGAGCAGCTCTTTAAGGAGAGTGGTAGTTTCAACAAGAACTTTCAGTCACgtatgtagttttgtttctgcttcgattcatgttttttttccgcttgcccttcttttgg-ttattgatttaatcagtcttgca-actttgtttcctcacag
||||| |  || || ||||||||||||||| | || ||||||||||| |||||||||||||| |||||||||||    |||| ||||||||| |||||||||||||  | ||  || |  |    || |   |     |  | |||      |||||  | ||     | || | |    || |  ||  ||    ||||
CTGAGCAACTATTCCTCAATGGAAGGTGTTCTTTATTGTAAGCCTCACTTTGAGCAGCTCTTCAAGGAGAGTGGGTCCTTCAGCAAGAACTTCCAGTCACgtatgtgttcttccttttcttct--ttgagaatgaagctgtgtttgtgtggtttttgaatcatatgcctcattaattggccatatattcattttgaacag

upper sequence: AT3G55770.6 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA14G06800.2 (Glycine max), 5'ss of exon 3
CTGAGTAGTTACTCATCAATGGAAGGTGTTTTGTACTGTAAGCCTCATTTTGAGCAGCTCTTTAAGGAGAGTGGTAGTTTCAACAAGAACTTTCAGTCACgtatgtagttttgtttctgcttcgattc-atgttttttttccgcttgcccttcttttggttattgatttaatcagtcttgcaactttgtttcctcacag
|| || |  || || || |||||||||||| | |||||||||||||||| |||||| ||||| |||||||  ||   |||||| |||||||| |||||||||| ||  | || ||| |  |    ||| | |||   |||| | |||   ||  | ||   ||    |||||  ||  ||  | ||   ||    ||||
CTCAGCAACTATTCCTCCATGGAAGGTGTTCTATACTGTAAGCCTCATTATGAGCAACTCTTCAAGGAGACAGGATCTTTCAAGAAGAACTTCCAGTCACgtacgtcttcttctttttcttcttcttctaggttagatttctgtttgtgatt--tctga--atcagattaattggtgatg--atttcaatttga-acag

upper sequence: AT3G55770.6 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA02G42100.1 (Glycine max), 5'ss of exon 2
CTGAGTAGTTACTCATCAATGGAAGGTGTTTTGTACTGTAAGCCTCATTTTGAGCAGCTCTTTAAGGAGAGTGGTAGTTTCAACAAGAACTTTCAGTCACgtatgtagttttgtttctgcttcgatt-catgttttttttccgcttgcccttcttttggttattgatttaatcagtcttgcaactttgtttcctcacag
|| || |  || || || |||||| ||||| | |||||||||||||||  |||||| ||||| |||||||  ||   |||||| |||||||| |||||||||| ||  | || ||  |  |   |||  | | |    ||| | |||   ||  | ||   ||    ||||   ||  ||  | ||   ||    ||||
CTTAGCAACTATTCCTCCATGGAAAGTGTTCTTTACTGTAAGCCTCATAATGAGCAACTCTTCAAGGAGACAGGATCTTTCAAGAAGAACTTCCAGTCACgtacgtcttcttcttcttattattattataggatagagttctgtttgtgatt--tctga--atcagattaactggtgatg--atttcaatttga-acag

upper sequence: AT3G55770.6 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv13s0019g03280.t01 (Vitis vinifera), 5'ss of exon 3
CTGAGTAGTTACTCATCAATGGAAGGTGTTTTGTACTGTAAGCCTCATTTTGAGCAGCTCTTTAAGGAGAGTGGTAGTTTCAACAAGAACTTTCAGTCACgtatgtagttttgtttctgcttcgattcatgttttttttccgcttgcccttc---ttttggttattgatttaatcagtcttgcaactttgtttcctcacag
||||| | ||| || |||||||| |||||| | |||||||||||||| |||||||||||||||||||||  ||| | |||||||||||| ||||||||||||  ||  | |||||||     |   | |  || ||| |  | || | |      || |  |   |  ||||||  ||     |  |||  ||    ||||
CTGAGCAATTATTCCTCAATGGAGGGTGTTCTTTACTGTAAGCCTCACTTTGAGCAGCTCTTTAAGGAGTCTGGAAATTTCAACAAGAATTTTCAGTCACgtgagtcttcttgtttc---accagataagattctttgtttgatttctcaatggtttctattccattgtttaat--gtgcaatatatttcattttcaacag

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|47829977|gb|CK119661.1|CK119661
EST:     TGAGCAGCTCTTTAAGGAGAGTGGTAGTTTCAACAAGAACTTTCAGTCAC                         CTGCAAAATCGGCTGACAAATCAACTCCTGAGCTG
genomic: TGAGCAGCTCTTTAAGGAGAGTGGTAGTTTCAACAAGAACTTTCAGTCACgtatgtagtt ... ttcctcacagCTGCAAAATCGGCTGACAAATCAACTCCTGAGCTG
EST: gi|124757831|gb|EH847961.1|EH847961
EST:     AGCAGCTCTTTAAGGAGAGTGGTAGTTTCAACAAGAACTTTCAGTCAC                         CTGCAAAATCGGCTGACAAATCAACTCCTGAGCTG
genomic: AGCAGCTCTTTAAGGAGAGTGGTAGTTTCAACAAGAACTTTCAGTCACgtatgtagtt ... ttcctcacagCTGCAAAATCGGCTGACAAATCAACTCCTGAGCTG
EST: gi|125078742|gb|EL141010.1|EL141010
EST:     TAAGGAGAGTGGTAGTTTCAACAAGAACTTTCAGTCAC                         CTGCAAAATCGGCTGACAAATCAACTCCTGAGCTG
genomic: TAAGGAGAGTGGTAGTTTCAACAAGAACTTTCAGTCACgtatgtagtt ... ttcctcacagCTGCAAAATCGGCTGACAAATCAACTCCTGAGCTG
EST: gi|301502045|gb|HO207585.1|HO207585
EST:     TGAGCAGCTCTTTAAGGAGAGTGGTAGTTTCAACAAGAACTTTCAGTCAC                         CTGCAAAATCGGCTGACAAATCAACTCCTGAGCTG
genomic: TGAGCAGCTCTTTAAGGAGAGTGGTAGTTTCAACAAGAACTTTCAGTCACgtatgtagtt ... ttcctcacagCTGCAAAATCGGCTGACAAATCAACTCCTGAGCTG
EST: gi|124979033|gb|EL052135.1|EL052135
EST:     CAGCTCTTTAAGGAGAGTGGTAGTTTCAACAAGAACTTTCAGTCAC                         CTGCAAAATCGGCTGACAAATCAACTCCTGAGCTG
genomic: CAGCTCTTTAAGGAGAGTGGTAGTTTCAACAAGAACTTTCAGTCACgtatgtagtt ... ttcctcacagCTGCAAAATCGGCTGACAAATCAACTCCTGAGCTG
EST: gi|125009929|gb|EL082198.1|EL082198
EST:     AGCTCTTTAAGGAGAGTGGTAGTTTCAACAAGAACTTTCAGTCAC                         CTGCAAAATCGGCTGACAAATCAACTCCTGAGCTG
genomic: AGCTCTTTAAGGAGAGTGGTAGTTTCAACAAGAACTTTCAGTCACgtatgtagtt ... ttcctcacagCTGCAAAATCGGCTGACAAATCAACTCCTGAGCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGAGTAGTTACTCATCAATGGAAGGTGTTTTGTACTGTAAGCCTCATTTTGAGCAGCTCTTTAAGGAGAGTGGTAGTTTCAACAAGAACTTTCAGTCACgtatgtagttttgtttctgcttcgattcatgttttttttccgcttgcccttcttttggttattgatttaatcagtcttgcaactttgtttcctcacag

- - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC