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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttgatcgtctctatgttttctcataatgtttttgtaaagttgtgcattggggagatttcatatgaatgtgtgtgttttgtagGATGCTGCGGCTGATGAAGAAGATGATGATGATGTTGACCTTTTCGGAGAGGAGACCGAAGAGGAAAAGAAAGCTGCTGAAGAGAGAGCAGCTTCTGTCA

Basic information

species Arabidopsis thaliana
transcript AT1G30230.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G30230.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g29260.1 (Oryza sativa), 3'ss of exon 4
---------gtatgcttgatcgtctc-tatgttttctcataatgtttttgtaaagttgtgcattggggagatttcatatga-atgtgtgtgttttg----tagGATGCTGCGGCTGATGAAGAAGATGATGATGATGTTGACCTTTTCGGAGAGGAGACCGAAGAGGAAAAGAAAGCTGCTGAAGAGAGAGCAGCTTCTGTCA
         |||| |    | || |   ||||||| | || |   |   | ||  ||    ||||   |  ||  || ||  | || |  | |||      |||   | || |||||||||||||||||||| |||||||| || || || |||||||| |||||||| |||||||| || |||||  | || ||  ||||||
atatcagtcgtat-ccaatttgtgtgacatgttttgt-atcacactgaagaaagtttaaatattgct-atcttgaatgtgctaagtataagatttaataccagGCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAGGAGACTGAAGAGGAGAAGAAAGCAGCAGAAGAACGGGCCGCAGCTGTCA

upper sequence: AT1G30230.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os07g42300.2 (Oryza sativa), 3'ss of exon 4
---------------------------------------------------------gtatgcttgatcgtctct-----atgttttctcataatgtttttgtaaagttgtg-cattggggag-atttc----atatgaatgtgtgtgtt--ttgtagGATGCTGCGGCTGATGAAGAAGATGATGATGATGTTGACCTTTTCGGAGAGGAGACCGAAGAGGAAAAGAAAGCTGCTGAAGAGAGAGCAGCTTCTGTCA
                                                         |||   |  || ||   |      ||||| |  || | ||||||||       ||    |||  |  || ||    |||| |   | | |  |  ||  ||| | |||| |||||||| || |||||||| |||||||||||||| || |||||||| |||||||| ||||| || ||||| ||| | || ||| ||||||
gtcatacaaccctagccttgtcttgtttgcctgaaatctgtgaagtgttctagcatagtactgtgaattgtgatttgatgctgtttgcaaattacgtttttgtggttcaatggtgctggttaccatctctaatatatcatcatatcttctaatttcagGCTCCTGCAGCTGATGATGACGATGATGACGATGTTGACCTTTTTGGTGAGGAGACTGAAGAGGAGAAGAAGGCAGCTGAGGAGCGTGCTGCTGCTGTCA

upper sequence: AT1G30230.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G153569_T02 (Zea mays), 3'ss of exon 4
----gtatgcttgatcgtct--ctatgttttctcataatgtttttgtaaagttgtgcattggggagatttcatatgaatgtgtgtgttttgta------gGATGCTGCGGCTGATGAAGAAGATGATGATGATGTTGACCTTTTCGGAGAGGAGACCGAAGAGGAAAAGAAAGCTGCTGAAGAGAGAGCAGCTTCTGTCA
    || | ||  | |      | ||||  |   |||       | | ||  | ||  ||    || ||    |   | |||  | | |  ||      ||   | || ||||| || || || |||||||||||||||||||| || |||||||| |||||||| ||||| |||||||||||  | || ||  ||| ||
tattgtttactaaagctatcaaccatgtggttcaatatctgagatatgaatctctgacttacccagtttagtcactgaagtgcatttctaataaccacagGCCCCAGCTGCTGACGAGGATGACGATGATGATGTTGACCTTTTTGGCGAGGAGACTGAAGAGGAGAAGAAGGCTGCTGAAGAACGTGCTGCGGCTGCCA

upper sequence: AT1G30230.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G031545_T03 (Zea mays), 3'ss of exon 4
-----gtatgcttgatcgtc-------tctatgttttctcataatgtttttgtaaagttgtgcattggggagatttcatatgaatgtgtgtgttttgtagGATGCTGCGGCTGATGAAGAAGATGATGATGATGTTGACCTTTTCGGAGAGGAGACCGAAGAGGAAAAGAAAGCTGCTGAAGAGAGAGCAGCTTCTGTCA
     ||||| || |   ||       |  |  || |    |  |    |  |  ||||    | |   |  | |  |    | | | |         |||   | |  ||||| || || || || ||||||||||||||||| || |||||||||||||| || ||||| |||||||||||| | || ||  ||| ||
caaccgtatggttcaatatcagaaaaatgaaacttgtacagttgtacactacttgagttacatagtttagtcactgaaatccattttctaataaccacagGCCCCAGTTGCTGAGGAGGACGACGACGATGATGTTGACCTTTTTGGTGAGGAGACCGAAGATGAGAAGAAGGCTGCTGAAGAGCGTGCTGCAGCTGCCA

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|47831915|gb|CK121599.1|CK121599
EST:     CTCCTATCACTGAGGAGGCTGTTGCTACTCCCCCTGCAGCTGATTCTAAG                         GATGCTGCGGCTGATGAAGAAGATGATGATGATGTTGACCTTTTCGGAGAG
genomic: CTCCTATCACTGAGGAGGCTGTTGCTACTCCCCCTGCAGCTGATTCTAAGgtatgcttga ... tgttttgtagGATGCTGCGGCTGATGAAGAAGATGATGATGATGTTGACCTTTTCGGAGAG
EST: gi|125204343|gb|EL219297.1|EL219297
EST:     TCCTATCACTGAGGAGGCTGTTGCTACTCCCCCTGCAGCTAGATTCTAAG                         GATGCTGCGGCTGA
genomic: TCCTATCACTGAGGAGGCTGTTGCTACTCCCCCTGCAGCT-GATTCTAAGgtatgcttga ... tgttttgtagGATGCTGCGGCTGA
EST: gi|152034196|gb|BP821871.2|BP821871
EST:     CTCCTATCACTGAGGAGGCTGTTGCTACTCCCCCTGCAGCTGATTCTAAG                         GATGCTGCGGCTGATGAAGAAGATGATGATGATGTTGACCTTTTCGGAGAG
genomic: CTCCTATCACTGAGGAGGCTGTTGCTACTCCCCCTGCAGCTGATTCTAAGgtatgcttga ... tgttttgtagGATGCTGCGGCTGATGAAGAAGATGATGATGATGTTGACCTTTTCGGAGAG
EST: gi|125227063|gb|EL241148.1|EL241148
EST:     TGAGGAGGCTGTTGCTACTCCCCCTGCAGCTGATTCTAAG                         GATGCTGCGGCTGATGAAGAAG
genomic: TGAGGAGGCTGTTGCTACTCCCCCTGCAGCTGATTCTAAGgtatgcttga ... tgttttgtagGATGCTGCGGCTGATGAAGAAG
EST: gi|86085521|gb|DR381280.1|DR381280
EST:     TGCAGCTGATTCTAAG                         GATGCTGCGGCTGATGAAGAAGATGATGATGATGTTGACCTTTTCGGAGAG
genomic: TGCAGCTGATTCTAAGgtatgcttga ... tgttttgtagGATGCTGCGGCTGATGAAGAAGATGATGATGATGTTGACCTTTTCGGAGAG
EST: gi|164236474|gb|EL995246.1|EL995246
EST:     TTGCTACTCCCCCTGCAGCTGATTCTAAG                         GATGCTGCGGCTGATGAAGAAGATGATGATGATGTTGACCTTTTCGGAGAG
genomic: TTGCTACTCCCCCTGCAGCTGATTCTAAGgtatgcttga ... tgttttgtagGATGCTGCGGCTGATGAAGAAGATGATGATGATGTTGACCTTTTCGGAGAG
EST: gi|124942336|gb|EL018611.1|EL018611
EST:     CTCCTATCACTGAGGAGGCTGTTGCTACTCCCCCTGCAGCTGATTCTAAG                         GATGCTGCGGCTGATGAAGAAG
genomic: CTCCTATCACTGAGGAGGCTGTTGCTACTCCCCCTGCAGCTGATTCTAAGgtatgcttga ... tgttttgtagGATGCTGCGGCTGATGAAGAAG
EST: gi|125259158|gb|EL273243.1|EL273243
EST:     TGCAGCTGATTCTAAG                         GATGCTGCGGCTGATGAAGAAGATGATGATGATGTTGACCTTTTCGGAGAG
genomic: TGCAGCTGATTCTAAGgtatgcttga ... tgttttgtagGATGCTGCGGCTGATGAAGAAGATGATGATGATGTTGACCTTTTCGGAGAG
EST: gi|152033786|gb|BP815997.2|BP815997
EST:     TCCTATCACTGAGGAGGCTGTTGCCTACTCCCCCTGCAGCTGATTCTAAG                         GATGCTGCGGCTGATGAAGAAGATGATGATGATGTTGACCTTTTCGGAGAG
genomic: TCCTATCACTGAGGAGGCTGTTG-CTACTCCCCCTGCAGCTGATTCTAAGgtatgcttga ... tgttttgtagGATGCTGCGGCTGATGAAGAAGATGATGATGATGTTGACCTTTTCGGAGAG
EST: gi|152037744|gb|BP796307.2|BP796307
EST:     CTCCTATCACTGAGGAGGCTGTTGCTACTCCCCCTGCAGCTGATTCTAAG                         GATGCTGCGGCTGATGAAGAAGATGATGATGATGTTGACCTTTTCGGAGAG
genomic: CTCCTATCACTGAGGAGGCTGTTGCTACTCCCCCTGCAGCTGATTCTAAGgtatgcttga ... tgttttgtagGATGCTGCGGCTGATGAAGAAGATGATGATGATGTTGACCTTTTCGGAGAG
EST: gi|116416034|gb|EG458626.1|EG458626
EST:     CTCCTATCACTGAGGAGGCTGTTGCTACTCCCCCTGCAGCTGATTCTAAG                         GATGCTGCGGCTGATGAAGAAGATGATGATGATGTTGACCTTTTCGGAGAG
genomic: CTCCTATCACTGAGGAGGCTGTTGCTACTCCCCCTGCAGCTGATTCTAAGgtatgcttga ... tgttttgtagGATGCTGCGGCTGATGAAGAAGATGATGATGATGTTGACCTTTTCGGAGAG
EST: gi|152037721|gb|BP796075.2|BP796075
EST:     CTCCTATCACTGAGGAGGCTGTTGCTACTCCCCCTGCAGCTGATTCTAAG                         GATGCTGCGGCTGATGAAGAAGATGATGATGATGTTGACCTTTTCGGAGAG
genomic: CTCCTATCACTGAGGAGGCTGTTGCTACTCCCCCTGCAGCTGATTCTAAGgtatgcttga ... tgttttgtagGATGCTGCGGCTGATGAAGAAGATGATGATGATGTTGACCTTTTCGGAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttgtaaagttgtgcattggggagatttcatatgaatgtgtgtgttttgtagGATGCTGCGGCTGATGAAGAAGATGATGATGATGTTGACCTTTTCGGAGAGGAGACCGAAGAGGAAAAGAAAGCTGCTGAAGAGAGAGCAGCTTCTGTCA
                           atttcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcttgatcgtctctatgttttctcataatgtttttgtaaagttgtgcattggggagatttcatatgaatgtgtgtgttttgtagGATGCTGCGGCTGATGAAGAAGATGATGATGATGTTGACCTTTTCGGAGAGGAGACCGAAGAGGAAAAGAAAGCTGCTGAAGAGAGAGCAGCTTCTGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT