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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAGCATTTATCTGCTAAATACTGTCCTCTTGTACCTCCTCCAAGGTCAACGATTGCAGCAGCTTTTAGTTCAGATGGAAGAACTCTTGCTTCTACACAgtaagtatcatgagtcgtatttgttggaattttttttttgtttgctaatgagtttttttttgtatttttaatcttgtag

Basic information

species Arabidopsis thaliana
transcript AT1G04140.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G04140.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os09g12550.1 (Oryza sativa), 5'ss of exon 4
TGCAGCATTTATCTGCTAAATACTGTCCTCTTGTACCTCCTCCAAGGTCAACGATTGCAGCAGCTTTTAGTTCAGATGGAAGAACTCTTGCTTCTACACAgtaagtatcatgagtcgtatttgttggaattttttttttgtttgctaatgagtttttttttgtatttttaatcttgtag
|||| |  |  ||||| |  || |||| |||  | ||| ||||||||||||| |||||||| || || ||| | ||||| ||||| ||||| || ||||||||||     | |   | || || || |  | | || |     |  ||  | ||    |   ||   ||  |  | |||
TGCATCGGTGGTCTGCCAGGTATTGTCTTCTCCTGCCTGCTCCAAGGTCAACCATTGCAGCTGCATTCAGTCCGGATGGGAGAACACTTGCATCCACACAgtaagc----taaa--ggatatgctgaatatatgttctgaacggaaaaaaacttagactaactacactt--ttctctag

upper sequence: AT1G04140.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G007229_T01 (Zea mays), 5'ss of exon 3
TGCAGCATTTATCTGCTAAATACTGTCCTCTTGTACCTCCTCCAAGGTCAACGATTGCAGCAGCTTTTAGTTCAGATGGAAGAACTCTTGCTTCTACACAgtaagtatcatgagtcg-tatttgttggaattttttttttg-tttgctaatgagtttttttttgtatttttaatcttgtag
||||    |  ||||| || || || |||||| | || ||||| |||||||| |||||||| ||||| ||| ||||||||| ||| ||||| || ||||||||||| |  ||| ||  | | |     | |    |    |   | || |  |  |   | | || || | |         
TGCATAGCTGGTCTGCCAAGTATTGCCCTCTTTTGCCACCTCCTAGGTCAACTATTGCAGCTGCTTTCAGTCCAGATGGAAAAACACTTGCGTCCACACAgtaagtttattgactcactgtataacaaactgaactgaaagacatcctgactaactcaatct-gttttctcag--------

upper sequence: AT1G04140.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G353548_T04 (Zea mays), 5'ss of exon 3
TGCAGCATTTATCTGCTAAATACTGTCCTCTTGTACCTCCTCCAAGGTCAACGATTGCAGCAGCTTTTAGTTCAGATGGAAGAACTCTTGCTTCTACACAgtaagtatcatgagtcg-tatttgttggaattttttttttg-tttgctaatgagtttttttttgtatttttaatcttgtag
|||| |  |  ||||| || || || |||||| | || ||||| |||||||| |||||||| ||||| ||| ||||||||| | | ||||| || ||||||||||| |  ||| ||  | | |     | |    |    |    || ||  |  |   | | || || | |         
TGCATCGCTGGTCTGCCAAGTATTGCCCTCTTTTGCCACCTCCTAGGTCAACTATTGCAGCTGCTTTCAGTCCAGATGGAAAATCACTTGCGTCCACACAgtaagtttattgattcactgtataacaaactgaaatgaaagacacgccaactaactcaatct-gttttctcag--------

upper sequence: AT1G04140.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA19G35370.3 (Glycine max), 5'ss of exon 3
TGCAGCATTTATCTGCTAAATACTGTCCTCTTGTACCTCCTCCAAGGTCAACGATTGCAGCAGCTTTTAGTTCAGATGGAAGAACTCTTGCTTCTACACAgtaagtatca-tgagtcg----------tatttgttggaattttttttttgtttgctaatgagtttttttttgtatttttaatcttgtag
||| |||||| |||||||| || |||||| | || |||||||||||||| || ||||||||||| |||||  ||||||| | |  |||||| || ||||||||||| | |   ||| |          || |  || |||| | |    | ||||  | ||| | || || ||| || |      || ||
TGCGGCATTTGTCTGCTAAGTATTGTCCTTTGGTGCCTCCTCCAAGGTCTACTATTGCAGCAGCATTTAGCCCAGATGGGAAAGTTCTTGCCTCCACACAgtaagttttaactagttgatctcctctttactaatttgaatctatgaact-tttgtgattgaatcttgttatgtgttatg-----tgcag

upper sequence: AT1G04140.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA03G32620.2 (Glycine max), 5'ss of exon 3
TGCAGCATTTATCTGCTAAATACTGTCCTCTTGTACCTCCTCCAAGGTCAACGATTGCAGCAGCTTTTAGTTCAGATGGAAGAACTCTTGCTTCTACACAgtaagtatca-tgagtcg---tatttgttggaattttttttttgtttgctaatgagtttttttttgtatttttaatcttgtag
||| |||||| |||||||| || |||||| |  | |||||||||||||| || ||||||||||| |||||  ||||||| | |  |||||| || ||||||||||| | |   ||| |   |  |  ||   | |||   | | |   ||      |    | ||||  | |      || ||
TGCGGCATTTGTCTGCTAAGTATTGTCCTTTGTTGCCTCCTCCAAGGTCTACTATTGCAGCAGCATTTAGCCCAGATGGGAAAGTTCTTGCCTCCACACAgtaagttttaactagttgatctcctctttactaatttgaatctatgaactttgtgatcggatcttgttatgtgctatgtgcag

upper sequence: AT1G04140.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv07s0005g04630.t01 (Vitis vinifera), 5'ss of exon 3
TGCAGCATTTATCTGCTAAATACTGTCCTCTTGTACCTCCTCCAAGGTCAACGATTGCAGCAGCTTTTAGTTCAGATGGAAGAACTCTTGCTTCTACACAgtaagtatcatgagtcgtatttgttggaattttttttttgtt-tgctaatgagtttttttttgtatttttaatcttgtag------------------------------------------
||||||||||||| || |  || ||||||||  | |||||||| ||||| || ||||||||||| || ||| ||||||||| ||| |||||||| ||||||||| | |  | | | || |||  |    |||| | | | ||    |  ||     | |||| |||   ||||  |||||                                          
TGCAGCATTTATCAGCCAGGTATTGTCCTCTGATGCCTCCTCCGAGGTCTACTATTGCAGCAGCATTCAGTCCAGATGGAAAAACACTTGCTTCCACACAgtaaattt--taacttgtcttttcttttcttttctctattttacatttttgcaccgtcttttttatccgtaattatgtagccaggcttctaactgtactccaatcctatttcatactcacag

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|116443186|gb|EG485778.1|EG485778
EST:     GCGATTGCAGCAGCTTTTAGTTCAGATGGAAGAACTCTTGCTTCTACACA                         TGGTGACCACACTGTAAAAATTATTGATTGTGAGACAGGAAAATGCTTAAA
genomic: ACGATTGCAGCAGCTTTTAGTTCAGATGGAAGAACTCTTGCTTCTACACAgtaagtatca ... aatcttgtagTGGTGACCACACTGTAAAAATTATTGATTGTGAGACAGGAAAATGCTTAAA
EST: gi|86085412|gb|DR381171.1|DR381171
EST:     ACGATTGCAGCAGCTTTTAGTTCAGATGGAAGAACTCTTGCTTCTACACA                         TGGTGACCACACTGTAAAAATTATTGATTGTGAGACAGGAAAATGCTTAAA
genomic: ACGATTGCAGCAGCTTTTAGTTCAGATGGAAGAACTCTTGCTTCTACACAgtaagtatca ... aatcttgtagTGGTGACCACACTGTAAAAATTATTGATTGTGAGACAGGAAAATGCTTAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAGCATTTATCTGCTAAATACTGTCCTCTTGTACCTCCTCCAAGGTCAACGATTGCAGCAGCTTTTAGTTCAGATGGAAGAACTCTTGCTTCTACACAgtaagtatcatgagtcgtatttgttggaattttttttttgtttgctaatgagtttttttttgtatttttaatcttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC