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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTGTTATCCATGCCTCGAGGGCCATGAGTGGCGCATCGTTACTGGCTGTGACCCCAAGAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAGgtcttttttctttccctggagactgattgcatgagacatttcttatctcgcttaactgagattttcgctagacctagccattagggtttttttcggtttg...

Basic information

species Arabidopsis thaliana
transcript AT1G35580.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G35580.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os04g35280.1 (Oryza sativa), 5'ss of exon 3
ATTTGTTATCCATGCCTCGAGGGCCATGAGTGGCGCATCGTTACTGGCTGTGACCCCAAGAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAGgtc-----ttttttctttccctggagactgattgcatgagacatttcttatctcgcttaactgagattttcgctagacctagccattagggtttttttcggtttg
||  | |  ||     ||||    || ||||||    |||| || || || |||||||||||||| |||||||||||||||||||| ||||| |||||||||      |||| |  |||  | |   ||      |  | | ||      |  || |    |   |     | || |  ||     ||    |   | |      
ATCAGCTTCCCGGCGATCGAATCACACGAGTGGGAGTTCGTCACCGGGTGCGACCCCAAGAACACCCGGTGGAGCTACCACAATGGCGGATCCTGGCCAGgttagttattttgtacttcgattgtttctatccttagaaaatataataccttccgataccttattaagaatgataaaattacatcctacaaatccctccc-----

upper sequence: AT1G35580.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os02g34560.1 (Oryza sativa), 5'ss of exon 3
ATTTGTTATCCATGCCTCGAGGGCCATGAGTGGCGCATCGTTACTGGCTGTGACCCCAAGAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAGgtc------ttttttctttccctggagactgattgcatgagacatttcttatctcgcttaactgagattttcgctagacctagccattagggtttttttcggtttg
|| || || ||     | |||   || || ||||| || || || |||||||| || ||||| ||  | ||||| ||||||||||| |||||||||||||||       |||| |  ||   |  |      ||  ||   ||| || |||  ||||  || ||  ||  |   |     |   ||||| |  |  ||| |     
ATATGCTACCCTGCTATTGAGAATCACGAATGGCGTATTGTGACAGGCTGTGATCCGAAGAATACTAGATGGAGTTACCACAATGGAGGATCTTGGCCAGgttagaaggttttcttattatttaaatctctcttaaatattacagtttttag-tcgcaaaaatgttatcatgcttcccttttatcattatg--tgatttggac---

upper sequence: AT1G35580.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G115451_T02 (Zea mays), 5'ss of exon 4
ATTTGTTATCCATGCCTCGAGGGCCATGAGTGGCGCATCGTTACTGGCTGTGACCCCAAGAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAGgtcttttttctttccctggagactgattgcatgagacatttcttatctcgcttaactgagattttcgctagacctagcc-attagggtttttttcggtttg---
|| || |||||    ||||||   ||||||||| | ||  ||||||| ||||||||||| ||||| |||||||| ||||||||||| ||||||||||||||| |  | |||  |  || |   ||| |  ||        | ||   | | |    |   | | | ||     ||| |   || |||| |   |   |||    
ATATGCTATCCTGCTCTCGAGAATCATGAGTGGAGAATTATTACTGGATGTGACCCCAAAAACACCCGGTGGAGTTACCACAATGGAGGATCTTGGCCAGgtatcgtctct--cgttgcaatgtgactaaattt--tgacttttggtttgttaggtttcaactctagcctactctaacttgtttgggtctaaatgtctttattg

upper sequence: AT1G35580.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G007277_T01 (Zea mays), 5'ss of exon 4
ATTTGTTATCCATGCCTCGAGGGCCATGAGTGGCGCATCGTTACTGGCTGTGACCCCAAGAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAGgtcttttttctttccctggagactgattgcatgagacatttcttatctcgcttaactgagattttcgctagacctagc-cattagggtttttttcggtttg-----
|| || |||||    ||||||   ||||||||| | ||  | ||||| ||||||||||||||||| |||||||| ||||||||||| ||||| ||||||||| |  | ||  |      | | |  |||  |      |||  |        || ||   ||||       |  |    || ||| | ||   |   |        
ATATGCTATCCTGCTCTCGAGAATCATGAGTGGAGAATAATCACTGGATGTGACCCCAAGAACACCCGGTGGAGTTACCACAATGGAGGATCGTGGCCAGgtatcatctccctttgca-atattttttgtttt-----ttttctggaaaaagtagctctaatttctatatcatgtgttgcagtagtggttagatgaatgcccgaga

upper sequence: AT1G35580.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G136139_T01 (Zea mays), 5'ss of exon 3
ATTTGTTATCCATGCCTCGAGGGCCATGAGTGGCGCATCGTTACTGGCTGTGACCCCAAGAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAGgtcttt---tttctttccctggag---actgattgcatgagacatttc----ttatctcgcttaactgagattttcgctagacctagccattagggtttttttcggtttg------------
|| || || ||   | ||||||| || |||||||  || || || ||||| ||||||||||||||| | |||||||||||||| || ||||||||||||||||  |   |   |    ||| ||    |||  |||   |    ||||      | ||  |  ||   || |   |  | || ||  |   |         |     |              
ATATGCTACCCGGCCATCGAGGGGCACGAGTGGCAGATAGTCACGGGCTGCGACCCCAAGAACACAAGATGGAGCTACCACAACGGGGGATCTTGGCCAGgtcagtagatcgatcaaactgcagcgttctgcctgccccatggttttcagaaacaactgccgcaaacaagttcagcagttgagctcacatctgaatgcacctctcactcacctttcctgcag

upper sequence: AT1G35580.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA20G31730.1 (Glycine max), 5'ss of exon 4
ATTTGTTATCCATGCCTCGAGGGCCATGAGTGGCGCATCGTTACTGGCTGTGACCCCAAGAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAGgtcttttttctttccctggagact--gattgcatgagacatttcttat----ctcgcttaactgagattttcgctagacctagccattagggtttttttcggtttg
|| | ||||||     | ||| ||||||||||||| || |||||||| ||||| ||||| || ||  | ||||| ||||| ||||| |||||||||||||||  ||  | | | |    | | |   | |  |  |  |||||  | |     | | |||| || ||||||  |  |     |   ||||    || | |      
ATATCTTATCCTGCAATAGAGAGCCATGAGTGGCGAATTGTTACTGGTTGTGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAGgttcttcctttctgctcatatattcaaactttaaaatgcatttaatgtgggatttggttaattgggattttgaccggtaggtgtgcttag----ttgtgcaaac--

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|125189190|gb|EL204144.1|EL204144
EST:     TGACCCCAAGAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAG                         TTTTGCTGTGGCAGCTAACAGCAGCGTGCATTAAGACAGGG
genomic: TGACCCCAAGAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAGgtcttttttc ... caatgtacagTTTTGCTGTGGCAGCTAACAGCAGCGTGCATTAAGACAGGG
EST: gi|125163298|gb|EL190068.1|EL190068
EST:     CCAAGAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAG                         TTTTGCTGTGGCAGCTAACAGCAGCGTGCATTAAGACAGGGAGACCGCAG
genomic: CCAAGAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAGgtcttttttc ... caatgtacagTTTTGCTGTGGCAGCTAACAGCAGCGTGCATTAAGACAGGGAGACCGCAG
EST: gi|125236342|gb|EL250427.1|EL250427
EST:     CAATGGTGGATCTTGGCCAG                         TTTTGCTGTGGCAGCTAACAGCAGCGTGCATTAAGACAGGGAGACCGCAGA
genomic: CAATGGTGGATCTTGGCCAGgtcttttttc ... caatgtacagTTTTGCTGTGGCAGCTAACAGCAGCGTGCATTAAGACAGGGAGACCGCAGA
EST: gi|124836823|gb|EH921262.1|EH921262
EST:     GAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAG                         TTTTGCTGTGGCAGCTAACAGCAGCGTGCATTAAGACAGGGAGACCGCAGA
genomic: GAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAGgtcttttttc ... caatgtacagTTTTGCTGTGGCAGCTAACAGCAGCGTGCATTAAGACAGGGAGACCGCAGA
EST: gi|47827862|gb|CK117546.1|CK117546
EST:     TGACCCCAAGAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAG                         TTTTGCTGTGGCAGCTAACAGCAGCGTGCATTAAGACAGGGAGACCGCAGA
genomic: TGACCCCAAGAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAGgtcttttttc ... caatgtacagTTTTGCTGTGGCAGCTAACAGCAGCGTGCATTAAGACAGGGAGACCGCAGA
EST: gi|164105904|gb|ES157231.1|ES157231
EST:     TGACCCCAAGAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAG                         TTTTGTCTGTGGCAGCTAACAGCAGCGTGCATTAAGACAGGGA
genomic: TGACCCCAAGAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAGgtcttttttc ... caatgtacagTTTTG-CTGTGGCAGCTAACAGCAGCGTGCATTAAGACAGGGA
EST: gi|124841976|gb|EH926413.1|EH926413
EST:     ACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAG                         TTTTGCTGTGGCAGCTAACAGCAGCGTGCATTAAGACAGGGAGACCGCAGA
genomic: ACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAGgtcttttttc ... caatgtacagTTTTGCTGTGGCAGCTAACAGCAGCGTGCATTAAGACAGGGAGACCGCAGA
EST: gi|125279451|gb|EL293536.1|EL293536
EST:     CTACCACAATGGTGGATCTTGGCCAG                         TTTTGCTGTGGCAGCTAACAGCAGCGTGCATTAAGACAGGGAGACCGCAGA
genomic: CTACCACAATGGTGGATCTTGGCCAGgtcttttttc ... caatgtacagTTTTGCTGTGGCAGCTAACAGCAGCGTGCATTAAGACAGGGAGACCGCAGA
EST: gi|125034283|gb|EL106552.1|EL106552
EST:     CCCAAGAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAG                         TTTTGCTGTGGCAGCTAACAGCAGCGTGCATTAAGACAGGGAGACCGCAG
genomic: CCCAAGAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAGgtcttttttc ... caatgtacagTTTTGCTGTGGCAGCTAACAGCAGCGTGCATTAAGACAGGGAGACCGCAG
EST: gi|116437907|gb|EG480499.1|EG480499
EST:     TGACCCCAAGAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAG                         TTTTGCTGTGGCAGCTAACAGCAGCGTGCATTAAGACAGGGAGACCGCAGA
genomic: TGACCCCAAGAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAGgtcttttttc ... caatgtacagTTTTGCTGTGGCAGCTAACAGCAGCGTGCATTAAGACAGGGAGACCGCAGA
EST: gi|125217278|gb|EL231361.1|EL231361
EST:     ACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAG                         TTTTGCTGTGGCAGCTAACAGCAGCGTGCATT
genomic: ACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAGgtcttttttc ... caatgtacagTTTTGCTGTGGCAGCTAACAGCAGCGTGCATT
EST: gi|124750479|gb|EH840609.1|EH840609
EST:     TGACCCCAAGAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAG                         TTTTGCTGTGGCAGCT
genomic: TGACCCCAAGAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAGgtcttttttc ... caatgtacagTTTTGCTGTGGCAGCT
EST: gi|124796013|gb|EH885692.1|EH885692
EST:     TGACCCCAAGAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAG                         TTTTGCTGTGGC
genomic: TGACCCCAAGAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAGgtcttttttc ... caatgtacagTTTTGCTGTGGC
EST: gi|124909274|gb|EH983354.1|EH983354
EST:     TGACCCCAAGAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAG                         TTTTGCTGTGGCAGCTAACAGCAGCGTGCATTAAGACAGGGAG
genomic: TGACCCCAAGAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAGgtcttttttc ... caatgtacagTTTTGCTGTGGCAGCTAACAGCAGCGTGCATTAAGACAGGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTGTTATCCATGCCTCGAGGGCCATGAGTGGCGCATCGTTACTGGCTGTGACCCCAAGAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAGgtcttttttctttccctggagactgattgcatgagacatttcttatctcgcttaactgagattttcgctagacctagccattagggtttttttcggtttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttctttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatctcgc