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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgcttctagcatatctacatacacacacacacacacacacacaaagactgatcctttttttacataatcatttctatcttttgactcttaaaaagcagAGAAGGAGATTAATCACACACGCAAATGCAAAGAGCAAGAGCGAGAAGTTTCCGCCACCACACCAAGATGGTGGAGCAATGGGTGTACCATTGGGTGCCT

Basic information

species Arabidopsis thaliana
transcript AT1G54610.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G54610.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os03g22700.1 (Oryza sativa), 3'ss of exon 5
--tctgcttctagcatatctacatacacacacacacacacacacacaaagactgatcctttttttacataatcatttctatcttttgactcttaaaaagcagAGAAGGAGATTAATCACACACGCAAATGCAAAGAGCAAGAGCGAGAAGTTTCCGCCACCACACCAAGATGGTGGAGCAATGGGTGTACCATTGGGTGCCT
  ||| | | |    || |||    |  | |   |  |   ||| |    | ||    ||||   |  |    | ||    |  || | |  ||     |||| |||||||||| | ||||| ||||||||||| |||||||| || |||||||| || || || || |||||||  |        ||  |      |  | 
ggtct-catttgattta-ctatggcccaaaatggagcccggcactctcttaatgtaaattttgcaatgtctctaatttgtcccatttatttatatcttacagAAAAGGAGATTAGTAACACATGCAAATGCAAAAAGCAAGAGTGAAAAGTTTCCTCCTCCGCATCAGGATGGTGCGGTCTCTTTGGTTTCTACAAATCACA

upper sequence: AT1G54610.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G084347_T01 (Zea mays), 3'ss of exon 6
tctgcttctagcatatctacatacacacacacacacacacacacaaagactgatccttt---ttttacataatcatttctatcttttgactcttaaaaagcagAGAAGGAGATTAATCACACACGCAAATGCAAAGAGCAAGAGCGAGAAGTTTCCGCCACCACACCAAGATGGTGGAGCAATGGGTGTACCATTGGGTGCCT---
   |  |||       |    | || |   |  | || ||   || | |   | | ||    | |  |  | |  |    ||| |||   |     ||  |||| ||| || || || || || |||||||| |||||||||||||| ||||| || || ||||| ||||||||||   |  | ||||| || |||| ||| |   
---gagtcttatcagccatggtccaaaaggaagcccatactaccataaagcaaactttgcagtatcgctgatttgtgctaatccttttttttccttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTG---CGGTTGGTGTCCCCTTGGATGCTTCAA

upper sequence: AT1G54610.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA19G42960.1 (Glycine max), 3'ss of exon 5
tctgcttctagcata-tctacatacacacacacacacacacacacaaagactgatcctttt---tttacataatcatttctatcttttgact-cttaaaaagcagAGAAGGAGATTAATCACACACGCAAATGCAAAGAGCAAGAGCGAGAAGTTTCCGCCACCACACCAAGATGGTGGAGCAATGGGTGTACCATTGGGTGCCT---
     |||||    | |||   |  |||     |   | |  ||  || |   ||||  |      || | | | | ||   |  | ||| | |||    | ||||||||  |  ||||||| || |||||||| |||||||||||||| |||||||| |||||||| ||||||||   ||   | ||| | || || ||  | |   
-----ttctaatgaactcttattttacaatagaaagtatatgcatgaatatgcatccagtcaaaagtaaagattaaatttgttactatgatttcttgtgtaacagAGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGCGAAAAGTTTCCTCCACCACATCAAGATGGACAAG---TTGGTTTTCCTTTAGGATCTTCAC

upper sequence: AT1G54610.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G30030.1 (Glycine max), 3'ss of exon 6
------------------------------------------------------------tctgcttc--tagcatatctacatacacacacacacacacac---acacaaagactgatcctttttttacataatcatttctatcttttgactcttaaaaagcagAGAAGGAGATTAATCACACACGCAAATGCAAAGAGCAAGAGCGAGAAGTTTCCGCCACCACACCAAGATGGTGGAGCAATGGGTGTACCATTGGGTGCCT---
                                                            |    |||  || ||| | ||       | |     | |      |   ||||  | |  ||    ||   |||   || ||  |  |    || |    | ||||||||| | |||||||| || |||||||| ||||||||||| || ||||| || ||||||||  |||||||   |||  | ||  | || |||||  | |   
gtatgttaaagaaatttacttctattgttttatgcctttgaactgctgctttccttctaataaaattcattatcatttttattattgaaaatctgtatagttgtgattgaaagtataaaactaacgttgattaaaatttgctg-caatgatttcatgtgtaacagAGAAGGCGTTTAATCACTCATGCAAATGCTAAGAGCAAGAGTGAAAAGTTCCCTCCACCACATGAAGATGG-ACAGC--TTGGCTTTCCTTTGGGATCTTCTA

upper sequence: AT1G54610.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA20G37360.1 (Glycine max), 3'ss of exon 6
-----------------------------------------------------------------tctgcttctagcatatctacatacacacacacacacacacacacaaagactgatcctttttttacataatcatttctatcttttgactcttaaaaagcagAGAAGGAGATTAATCACACACGCAAATGCAAAGAGCAAGAGCGAGAAGTTTCCGCCACCACACCAAGATGGTGGAGCAATGGGTGTACCATTGGGTGCCT---
                                                                 |    || |    | | ||  |  | |     | |          ||     |   ||  | |  || |  ||||    |  |    || |    | ||||||||| | |||||||| || |||||||| ||||||||||| || ||||| || ||||||||  |||||||   |||  | ||  | || |||||  | |   
gtatgttaaagaaatttacttctattgtttgatgcctttgtactgcttctatccttctaataaaattcatttttgttttttataattgaaaatctgtataattgtgattgaaagtataaaattaatgttgattaaaatttgctgcaatgatttcatgtgtaacagAGAAGGCGTTTAATCACTCATGCAAATGCTAAGAGCAAGAGTGAAAAGTTACCTCCACCACATGAAGATGG-ACAGC--TTGGCTTTCCTTTGGGATCTTCTA

upper sequence: AT1G54610.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA03G40330.1 (Glycine max), 3'ss of exon 6
tctgcttctagcatatc-tacatacacacacacacacacacacacaaagactgatcctttttttacataatcatttctatcttttgact-cttaaaaagcagAGAAGGAGATTAATCACACACGCAAATGCAAAGAGCAAGAGCGAGAAGTTTCCGCCACCACACCAAGATGGTGGAGCAATGGGTGTACCATTGGGTGCCT---
 ||| || ||   ||   |||| |   |    ||     |  ||   || |  | |       || | | | | ||   |  | ||| | |||    | ||||||||  |  ||||||| || |||||||| ||||||||||| || ||||| || |||||||| ||||||||   ||   | ||| | || |||||  | |   
actgatt-tattttacaatacaaa-gtatctgcatgataatgcatccagtcaaaactcaaaagtaaagattaaatttgttactatgatttcttctgtaacagAGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTCCCTCCACCACATCAAGATGGACAAG---TTGGTTTTCCTTTGGGATCTTCAC

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|125104103|gb|EL158278.1|EL158278
EST:     CAAATGTCGAT                         AGAAGGAGATTAATCACACACGCAAATGCAAAGAGCAAGAGCGAGAAGTTT
genomic: CAAATGTCGATgtatgtcctt ... taaaaagcagAGAAGGAGATTAATCACACACGCAAATGCAAAGAGCAAGAGCGAGAAGTTT
EST: gi|164204110|gb|ES192079.1|ES192079
EST:     AGCTCTTCCAGCTCCTGAAGCTAATGCAGAACTTCAGTCAAATGTCGAT                         AGAAGGAGATTAATC
genomic: AGCTCTTCCAGCTCCTGAAGCTAATGCAGAACTTCAGTCAAATGTCGATgtatgtcctt ... taaaaagcagAGAAGGAGATTAATC
EST: gi|125316436|gb|EL330521.1|EL330521
EST:     CAGAACTTCAGTCAAATGTCGAT                         AGAAGGAGATTAATCACACACGCAAATGCAAAGAGCAAGAGCGAGAAGTTT
genomic: CAGAACTTCAGTCAAATGTCGATgtatgtcctt ... taaaaagcagAGAAGGAGATTAATCACACACGCAAATGCAAAGAGCAAGAGCGAGAAGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagactgatcctttttttacataatcatttctatcttttgactcttaaaaagcagAGAAGGAGATTAATCACACACGCAAATGCAAAGAGCAAGAGCGAGAAGTTTCCGCCACCACACCAAGATGGTGGAGCAATGGGTGTACCATTGGGTGCCT
                                   ttttgac  putative branch site (score: 3)
                                         ctctt  CT-rich tract
           tttttttacataatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgcttctagcatatctacatacacacacacacacacacacacaaagactgatcctttttttacataatcatttctatcttttgactcttaaaaagcagAGAAGGAGATTAATCACACACGCAAATGCAAAGAGCAAGAGCGAGAAGTTTCCGCCACCACACCAAGATGGTGGAGCAATGGGTGTACCATTGGGTGCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA