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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaattaggagactgttgtgtagttgctgctaattcgaaattgtatgttattctggatgaaattgagttgtttgataacatttgggaactaattttgcagACATCCAAGGCACATAGCTTGACATGTATGGATCTTTATGTGTTTGCAACGCCATACAGGATCACTTGGGACTACTATTTCTCTGCTAGAGATCATACTT

Basic information

species Arabidopsis thaliana
transcript AT1G70160.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G70160.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os09g22440.1 (Oryza sativa), 3'ss of exon 1
----aaaat---taggagactgttgtgtagttgctgctaattcgaaattgtatgttattctgga--tgaaattgagttgtttgataacatttgggaactaattttgcagACATCCAAGGCACATAGCTTGACATGTATGGATCTTTATGTGTTTGCAACGCCATACAGGATCACTTGGGACTACTATTTCTCTGCTAGAGATCATACTT
    ||| |   ||  | | | |   | | | || | |||   ||  |||| ||||||| ||    ||   || |  | ||| ||    ||| |    ||  | |||||||  |    ||  | || | |||||| |||||||| |||||||||||||| ||||| ||||| || ||||| ||||||||  ||||| |||| || ||||
atgcaaagtgcatatcaaattatca-gcattggcagttaagatga--ttgt-tgttattatgagtttgttcttaacatattttatt---ttttgttgtta--tatgcagACTGCTTCAGCTAAGAGTTGGACATGCATGGATCTCTATGTGTTTGCAACACCATATAGGATAACATGGGATTACTATTTTGCTGCTCGAGAACACACTT

upper sequence: AT1G70160.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os08g32910.1 (Oryza sativa), 3'ss of exon 1
aaaattaggagactgttgtgtagt-tgctgctaattcgaaattgtatgttattctggatg--aaattgagtt---gtttgataacatttgggaactaattttgcagACATCCAAGGCACATAGCTTGACATGTATGGATCTTTATGTGTTTGCAACGCCATACAGGATCACTTGGGACTACTATTTCTCTGCTAGAGATCATACTT
      |    |||||     |||  | |  |  | |  |||  ||| |  | ||  ||    | ||  ||    |    | ||  ||||        || || ||||  |    || || |||| |||||| |||||||| ||||||||||||||||| ||||||||    ||||| |||||  |  | ||    || || || |
------actgtactgtatgaaagtgcgttctttgtactgaatcatatatagtccttcatacttagttttgtctcagcagcaaaatgtttgttgtggggttatgtagACTGCTTCAGCTCAGAGCTGGACATGCATGGATCTGTATGTGTTTGCAACGCCGTACAGGATAGGATGGGATTACTACATTACAGCACAGGAGCACACCT

upper sequence: AT1G70160.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G17350.1 (Glycine max), 3'ss of exon 1
aaaattaggagactgttgtgtagttgctgcta-attcgaaattgtatgttattctggatgaaattgagttgtttgataacatttgggaactaatttt-gcagACATCCAAGGCACATAGCTTGACATGTATGGATCTTTATGTGTTTGCAACGCCATACAGGATCACTTGGGACTACTATTTCTCTGCTAGAGATCATACTT
  |||| | |   | |  |||  || ||| ||      |  |||  || |  | ||||| | |  |  |  |||| | | || |      |  ||||  ||||||      |||||||||| ||| || |||||| | ||||| |||||||| || |||||||| |||||||||||||| |||||| |  |||| |||||  
ttaattggaaatttttaatgtgttttctgttatgccttatgttgcttgatgatatggattatac-gtttcctttgctgaaatataattgttcttttttacaGACAGAGGCTGCACATAGCTGGACCTGCATGGATTTGTATGTTTTTGCAACACCCTACAGGATTACTTGGGACTACTACTTCTCTTCACGAGAACATACC-

upper sequence: AT1G70160.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G03160.1 (Glycine max), 3'ss of exon 1
aaaattagg--agactgttgtgtagttgctgctaattcgaaattgtatgttattctggatgaaattgagttgtttgataacatttgggaactaa--ttttgcagACATCCAAGGCACATAGCTTGACATGTATGGATCTTTATGTGTTTGCAACGCCATACAGGATCACTTGGGACTACTATTTCTCTGCTAGAGATCATACTT
    || ||   || || |   |      |  || |       | |   |    ||   ||        || |    | | |||     | |    |||| ||||||      || || || | ||| || |||||||| ||||| ||||||||||| || ||||| || ||||| ||||||||||||||  |||| |||||||
---ttttggttggattgcttgatgagaaattttagtatctgtctttggttgtccctttctgctccccctttataatgtga-attataatattggccttttacagACAGAAGCTGCTCACAGTTGGACCTGCATGGATCTGTATGTATTTGCAACGCCTTATAGGATTACATGGGATTACTATTTCTCTGCGCGAGAACATACTT

upper sequence: AT1G70160.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G04400.1 (Glycine max), 3'ss of exon 1
aaaattagg--agactgttgtgtagttgctgctaattcgaaattgtatgttattctggatgaaattgagttgtttgataacatttgggaactaa--ttttgcagACATCCAAGGCACATAGCTTGACATGTATGGATCTTTATGTGTTTGCAACGCCATACAGGATCACTTGGGACTACTATTTCTCTGCTAGAGATCATACTT
    || ||   || ||||   |      |   | |         ||| |    ||   ||        || |    | | ||||    | |    |||| ||||||      ||||| || | ||| || |||||||| ||||| |||||||| || || ||||| || ||||||||||||||||||||  |||| |||||||
---ttttggttggattgtttgatgagaaatttaagtatctgtccttatttgtccctttctgctccctctttataatgtga-attttaacattggccttttacagACAGAAGCTGCACACAGTTGGACCTGCATGGATCTGTATGTTTTTGCAACACCTTATAGGATTACATGGGACTACTATTTCTCTGCGCGAGAACATACTT

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|116483746|gb|EG526338.1|EG526338
EST:     GGTGGTGGTGTTCTTCATCTCAAA                         ACATCCAAGGCACATAGCTTGACATGTATGGATCTTTATGTGTTTGCAACG
genomic: GGTGGTGGTGTTCTTCATCTCAAAgttggttaat ... aattttgcagACATCCAAGGCACATAGCTTGACATGTATGGATCTTTATGTGTTTGCAACG
EST: gi|124830308|gb|EH914764.1|EH914764
EST:     GTAGTGATCGTGACGTCCCTGGACTTGGTGGTGGTGTTCTTCATCTCAAA                         ACATCCAAGGCACATAGCTTGACATGT
genomic: GTAGTGATCGTGACGTCCCTGGACTTGGTGGTGGTGTTCTTCATCTCAAAgttggttaat ... aattttgcagACATCCAAGGCACATAGCTTGACATGT
EST: gi|47829214|gb|CK118898.1|CK118898
EST:     GTAGCGATCGTGACGTCCCTGGACTTGGTGGTGGTGTTCTTCATCTCAAA                         ACATCCAAGGCACATAGCTTGACATGTATGGATCTTTATGTGTTTGCAACG
genomic: GTAGTGATCGTGACGTCCCTGGACTTGGTGGTGGTGTTCTTCATCTCAAAgttggttaat ... aattttgcagACATCCAAGGCACATAGCTTGACATGTATGGATCTTTATGTGTTTGCAACG
EST: gi|116483745|gb|EG526337.1|EG526337
EST:     GGTGGTGGTGTTCTTCATCTCAAA                         ACATCCAAGGCACATAGCTTGACATGTATGGATCTTTATGTGTTTGCAACG
genomic: GGTGGTGGTGTTCTTCATCTCAAAgttggttaat ... aattttgcagACATCCAAGGCACATAGCTTGACATGTATGGATCTTTATGTGTTTGCAACG
EST: gi|124900084|gb|EH974702.1|EH974702
EST:     TGATCGTGACGTCCCTGGACTTGGTGGTGGTGTTCTTCATCTCAAA                         ACATCCAAGGCACATAGCTTGACATGTATGGATCTTTATGTGTTTGCAACG
genomic: TGATCGTGACGTCCCTGGACTTGGTGGTGGTGTTCTTCATCTCAAAgttggttaat ... aattttgcagACATCCAAGGCACATAGCTTGACATGTATGGATCTTTATGTGTTTGCAACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttattctggatgaaattgagttgtttgataacatttgggaactaattttgcagACATCCAAGGCACATAGCTTGACATGTATGGATCTTTATGTGTTTGCAACGCCATACAGGATCACTTGGGACTACTATTTCTCTGCTAGAGATCATACTT
                                         aactaat  putative branch site (score: 2)
                                         aactaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaattaggagactgttgtgtagttgctgctaattcgaaattgtatgttattctggatgaaattgagttgtttgataacatttgggaactaattttgcagACATCCAAGGCACATAGCTTGACATGTATGGATCTTTATGTGTTTGCAACGCCATACAGGATCACTTGGGACTACTATTTCTCTGCTAGAGATCATACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - ctgctaa
- - - - - - - - - - - - - - - - - -cgaaatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gataaca