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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttttattttcttgtttgtattttcttgcaacaatttttgagttatgtttttatggatttgaagaaacgtgtgggatgtttgtttgttgtcctgaattttttgaacagGATTGGTTTAGATTCAGTGTTGCGTTTTGGCATACTTTCCGTGGGACTGGAGGTGATCCATTTGGTGCTGCTACTAAGTATTGGCCTTGGGAAGATGGTA

Basic information

species Arabidopsis thaliana
transcript AT5G57655.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G57655.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 4
gtacttttattttcttgtttgtattttcttgcaacaatttttgagttatgtttttatggatttgaagaaacgtgtgggatgtttgtttgttgtcctgaattttttgaacagGATTGGTTTAGATTCAGTGTTGCGTTTTGGCATACTTTCCGTGGGACTGGAGGTGATCCATTTGGTGCTGCTACTAAGTATTGGCCTTGGGAAGATGGTA
     |    ||| |   || | | || ||| |   ||  ||   ||||    || ||  |      | || | || | | | | |||  | | ||    |||      |||||||| |  | ||||| || || ||||||||||| |||||||| |||||||| ||||| ||||||||  |||| |||| |||||||||||| ||||| |
----gtagggtttatgaattatgtcttgttgaacagatcctt---ttattcccttttgcgtcatggaatacatctgagttttgtattttatctgcttgcgttt------agGATTGGATGCGGTTCAGCGTGGCCTTTTGGCATACGTTCCGTGGTACTGGAGGAGATCCTTTTGGTGCCCCTACAAAGTCTTGGCCTTGGGAGGATGGCA

upper sequence: AT5G57655.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G005493_T01 (Zea mays), 3'ss of exon 4
-----------------gtacttttattttctt-gtttgtattttcttgcaacaatttttgagttatgtttttatggatttgaagaaacgtgtgggatgtt-----tgtttgttgtcctgaattttttgaacagGATTGGTTTAGATTCAGTGTTGCGTTTTGGCATACTTTCCGTGGGACTGGAGGTGATCCATTTGGTGCTGCTACTAAGTATTGGCCTTGGGAAGATGGTA
                    | | |  |  ||| ||||   |||   || | |   | ||      |||     |  |      | |   ||| |||||         ||| |  |  |   || |   |  |||| ||| |  | |||||||||||||| ||||| || |||||||| ||||| | |||||| ||||||||  |||| |||  |||||||||||| || || |
gtatgatcagtagtgaaccccatctgctggctttgtttagttttcactgtaccccctcttttacactgtaaaggtaaaacctttgcacgctgtaggatgaagtcaacatttatgcttatttgttctgctactagGACTGGATGCGCTTCAGTGTTGCGTTCTGGCACACGTTCCGTGGTACTGGTGCTGATCCTTTTGGTGCGCCTACAAAGGTTTGGCCTTGGGAGGACGGCA

upper sequence: AT5G57655.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G081682_T02 (Zea mays), 3'ss of exon 4
gtacttttattttcttgtttgtattttcttgcaacaatttttgagttatgtttttatggatttgaagaaacgtgtgggatgtttg--tttgttgtcctgaattttttgaacagGATTGGTTTAGATTCAGTGTTGCGTTTTGGCATACTTTCCGTGGGACTGGAGGTGATCCATTTGGTGCTGCTACTAAGTATTGGCCTTGGGAAGATGGTA
       |||      ||   |       |||  |     |  |       |||||          |||    ||      ||||  | | |  |  |    |||   |  |||||||| |  | ||||||||||| || ||||| || |||||||| ||||| | |||||| || |||||| |||| |||  |||||||||||| || || |
------gtatcgatcagtgaatccccatctgctgcttcactataccccctcttttacactcactgtgaagtacgtcaaccctttgcatctatgcttatttgctttgctattagGATTGGATGCGCTTCAGTGTTGCATTCTGGCACACGTTCCGTGGTACTGGCGCTGATCCTTTCGGTGCTCCTACAAAGACTTGGCCTTGGGAGGACGGCA

upper sequence: AT5G57655.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: AC190975.3_FGT004 (Zea mays), 3'ss of exon 1
gtacttttattttcttgtttgtattttcttgcaacaatttttgagttatgtttttatggatttgaagaaacgtgtgggatgtttg--tttgttgtcctgaattttttgaacagGATTGGTTTAGATTCAGTGTTGCGTTTTGGCATACTTTCCGTGGGACTGGAGGTGATCCATTTGGTGCTGCTACTAAGTATTGGCCTTGGGAAGATGGTA
       |||      ||           |||  |  |   |        | ||||          |||     |      ||||  | | |  |  |    |||   |  |||||||| |    ||||||||||| || ||||| || ||| |||| |||||   |||||| ||||||||| |||| |||  |||||||||||| ||||| |
------gtatcaatcagtgaacccccatctgctgct-tcactataccccctctttacactcactgtgaagtacatcaaccctttgcatctatgcttatttgctttgctattagGATTGGATGCACTTCAGTGTTGCCTTCTGGCACACGTTCTGTGGTACTGGCACTGATCCTTTTGGTGCTCCTACAAAGACTTGGCCTTGGGAGGATGGCA

upper sequence: AT5G57655.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G07380.1 (Glycine max), 3'ss of exon 4
gtacttttattttcttgtttgtattt-tcttgcaacaatttttgagttatgtttttatg----gatttgaagaaacgtgtgggatgtttgtttg---ttgtcctgaattttttgaacagGATTGGTTTAGATTCAGTGTTGCGTTTTGGCATACTTTCCGTGGGACTGGAGGTGATCCATTTGGTGCTGCTACTAAGTATTGGCCTTGGGAAGATGGTA
              | ||||  |||| | || ||| || || | |||| | | | ||       ||      | ||   | || | ||   |||   || | ||  ||  |     ||||||||||| ||||| |||||||| ||||||||||| |||||||| || || | ||| |||||||||||  |||| || || ||||  |||||||||||||
------------gttggttttcatttatattccaagaagttgtcagttttatctatacttcatcatccaccaacacccattggcttttgacttgaatttattctatataatacctgcagGATTGGTTAAGATTTAGTGTTGCATTTTGGCATACATTCCGTGGAACAGGTGCTGACCCATTTGGTGCACCTACCAAATACTGGCTATGGGAAGATGGTA

upper sequence: AT5G57655.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv11s0052g01710.t01 (Vitis vinifera), 3'ss of exon 5
-gtacttttattttcttgtttgtattttcttgcaacaatttttgagttatgtttttatggatttgaagaaacgtgtgggatgtttgtttgttgtcc-tgaattttttga-----acagGATTGGTTTAGATTCAGTGTTGCGTTTTGGCATACTTTCCGTGGGACTGGAGGTGATCCATTTGGTGCTGCTACTAAGTATTGGCCTTGGGAAGATGGTA
  |  |||  |||  ||  || | |||||||       |||||   || | ||||| ||  |  ||   |   | |    |   |     ||  |  | || || || |     | |||||||| | |||||||||||||| |||||||| || |||||||| || ||||||||||||||||||||  |||| |||| |||||| |||||||||||||
gttggtttcttttcttttcttttcttttcttttctttttttttttcttttttttttttgcctcagatttattttatcaactaaattgcaattaccaataaagttgttaatgtcaatagGATTGGATGAGATTCAGTGTTGCATTTTGGCACACATTCCGTGGAACCGGAGGTGATCCATTTGGTGCACCTACAAAGTTTTGGCCATGGGAAGATGGTA

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|125154860|gb|EL185269.1|EL185269
EST:     CTTACAGGTGGTATAACGCTGAAGAAGAGATTCTTGGGAAGAAAATGAAG                         GATTGGTTTAGATTCAGTGTTGCGTTTTGGTATACTTTCCGTGGGACTGGA
genomic: CTTACAGGTGGTATAACGCTGAAGAAGAGATTCTTGGGAAGAAAATGAAGgtacttttat ... ttttgaacagGATTGGTTTAGATTCAGTGTTGCGTTTTGGCATACTTTCCGTGGGACTGGA
EST: gi|86055233|gb|DR350990.1|DR350990
EST:     CTTACAGGKGGTATAACGCTGAAGAAGAGATTCTTGGGAAGAAAATGAAG                         GATTGGTTTAGATTCAGTGTTGCGTTTTGGCATACTTTCCGTGGGACTGGA
genomic: CTTACAGGTGGTATAACGCTGAAGAAGAGATTCTTGGGAAGAAAATGAAGgtacttttat ... ttttgaacagGATTGGTTTAGATTCAGTGTTGCGTTTTGGCATACTTTCCGTGGGACTGGA
EST: gi|116424348|gb|EG466940.1|EG466940
EST:     CTTACAGGTGGTATAACGCTGAAGAAGAGATTCTTGGGAAGAAAATGAAG                         GATTGGTTTAGATTCAGTGTTGCGTTTTGGCATACTTTCCGTGGGACTGGA
genomic: CTTACAGGTGGTATAACGCTGAAGAAGAGATTCTTGGGAAGAAAATGAAGgtacttttat ... ttttgaacagGATTGGTTTAGATTCAGTGTTGCGTTTTGGCATACTTTCCGTGGGACTGGA
EST: gi|301501388|gb|HO206928.1|HO206928
EST:     CTTACAGGTGGTATAACGCTGAAGAAGAGATTCTTGGGAAGAAAATGAAG                         GATTGGTTTAGATTCAGTGTTGCGTTTTGGCATACTTTCCGTGGGACTGGA
genomic: CTTACAGGTGGTATAACGCTGAAGAAGAGATTCTTGGGAAGAAAATGAAGgtacttttat ... ttttgaacagGATTGGTTTAGATTCAGTGTTGCGTTTTGGCATACTTTCCGTGGGACTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggatttgaagaaacgtgtgggatgtttgtttgttgtcctgaattttttgaacagGATTGGTTTAGATTCAGTGTTGCGTTTTGGCATACTTTCCGTGGGACTGGAGGTGATCCATTTGGTGCTGCTACTAAGTATTGGCCTTGGGAAGATGGTA
                                           tttttt  CT-rich tract
                                         aattttttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttttattttcttgtttgtattttcttgcaacaatttttgagttatgtttttatggatttgaagaaacgtgtgggatgtttgtttgttgtcctgaattttttgaacagGATTGGTTTAGATTCAGTGTTGCGTTTTGGCATACTTTCCGTGGGACTGGAGGTGATCCATTTGGTGCTGCTACTAAGTATTGGCCTTGGGAAGATGGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG