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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcattatctttcaggttctgtgattgagctacatagttaatccttgcttatgatgtgaactttaagtgtgtatctgtttttttcttctctgatgtttagGTAGTGCTGGTGATGTGTTGGAAGATGATCCCGTGGGAAGACTGAAAGTCTTTGTTTATGAGCTTCCAAGTAAATACAACAAGAAGATACTTCAGAAGGA

Basic information

species Arabidopsis thaliana
transcript AT5G61840.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g70200.1 (Oryza sativa), 3'ss of exon 1
agcattatctttcaggttctgtgattgagctacatagttaatccttgctta--tgatgtgaacttta-agtgtgtatctgtttttttcttctctgatgtttagGTAGTGCTGGTGATGTGTTGGAAGATGATCCCGTGGGAAGACTGAAAGTCTTTGTTTATGAGCTTCCAAGTAAATACAACAAGAAGATACTTCAGAAGGA
     |||  |||      |  || |   ||      | | ||  |||       ||    |||  | ||  | |   |  | || |        |  |  ||| |||||||||||||||||||||||||| || || || || || || |||| ||| ||||| || ||||| || |||||||||||| | ||  |||||||
---gctatgcttctaaaatttagaatattcttttccctaattctgtgcaaggtctatagatactccatagcttttgcttaatattgtggcgaaacaaatgcagGAAGTGCTGGTGATGTGTTGGAAGATGACCCTGTTGGGAGGCTTAAGGTCTATGTCTATGATCTCCCAAGCAAGTACAACAAGAAGCTGCTGAAGAAGGA

upper sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G023020_T01 (Zea mays), 3'ss of exon 1
----agcattatctttcaggttctgtgattgagctacatagttaatccttgcttatgatgtgaactttaagtgtgtatctgtttttttcttctctgatgtttagGTAGTGCTGGTGATGTGTTGGAAGATGATCCCGTGGGAAGACTGAAAGTCTTTGTTTATGAGCTTCCAAGTAAATACAACAAGAAGATACTTCAGAAGGA
    || |  ||||         |||  |||   |   || || ||  ||  ||   |||||   |    ||||| |            || |   |  | |||| ||||||||||||||||| |||||| |||| ||||| ||  |||| |||||  |||||||  | ||||| || ||||||||||||||  |    |||||
atgtagaaaaatctccatatgattgtt-ttgctttgtctacttcatattttgttc--atgtgtgttgcttgtgtggactgaaacagcaattatgaaac-tgtagGGAGTGCTGGTGATGTGTTAGAAGATAATCCTGTGGGTAGGTTGAAGGTCTTCATTTATGACTTACCAAGGAAGTACAACAAGAAGATGGTCACCAAGGA

upper sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G059825_T01 (Zea mays), 3'ss of exon 1
---agcattatctttcaggttctgtgattgagctacatagttaatccttgcttatgatgtgaactttaagtgtgtatctgtttttttcttctctgatgtttagGTAGTGCTGGTGATGTGTTGGAAGATGATCCCGTGGGAAGACTGAAAGTCTTTGTTTATGAGCTTCCAAGTAAATACAACAAGAAGATACTTCAGAAGGA
        || | | | | | ||      || || | ||| ||    | | |  |      || |||| |   |      |  | |      |  |  |  ||| || |||||||||||||| |||||||| || || || || || || |||| ||| ||||| || || || ||||||||||||||| | ||  |||||||
tgcctagctagcgtaccgttccttcaggagaact-cttagctaggtat-gttcttttccccaattttatgctagccctaatgctgtggcgaaccaa-atgcagGAAGCGCTGGTGATGTGTTAGAAGATGACCCTGTTGGGAGGCTCAAGGTCTATGTCTATGATCTCCCCAGCAAATACAACAAGAAGCTGCTCAAGAAGGA

upper sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G33420.1 (Glycine max), 3'ss of exon 1
agcattatctttcaggttctgtgattg-agctacatagt--taatccttgcttatgatgtgaactttaagtgtgtatctgtttttttcttctctgatgtttagGTAGTGCTGGTGATGTGTTGGAAGATGATCCCGTGGGAAGACTGAAAGTCTTTGTTTATGAGCTTCCAAGTAAATACAACAAGAAGATACTTCAGAAGGA
    |||  ||     |||| |   || || ||||| ||  | | |    ||| | |  |      | ||  |  ||   | || |  ||   | |  |  |||||||||||||||||| |||||||||||||| ||||||||  |||| || ||||||||||| |||||||||||||| || ||||| || || || |||||
---cttacattagcaattctatttctggagatacattgtagtcaactacactttttaaattctgcgtgaggctaaatgcatgttgtggttgaatcaattgcagGTAGTGCTGGTGATGTATTGGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGTAAATATAATAAGAAAATTCTGCAAAAGGA

upper sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 1
----agcattatctttcaggttctgtgattgagctacatagttaatccttgcttatgatgtgaactttaagtgtgtatctgtttttttcttctctgatgtttagGTAGTGCTGGTGATGTGTTGGAAGATGATCCCGTGGGAAGACTGAAAGTCTTTGTTTATGAGCTTCCAAGTAAATACAACAAGAAGATACTTCAGAAGGA
    |  |  |   |  |  |||||||||| |  | || | |  ||  | | | |  ||   || |   | |   ||    | || |  ||     |  | |||||||||||||||||||||| ||||||||||| ||||||||  |||| || ||||||||||| |||||||| ||||| || ||||| || || || |||||
gtcaaatacaagtctctaaattctgtgatttattt-caaaatatattatagttaa--ataaaaaatgacactac-taagcatgttctggttgaaccaaatgtagGTAGTGCTGGTGATGTGTTAGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGCAAATATAATAAGAAAATTCTGCAAAAGGA

upper sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 1
agcattatctttcaggttctgtgattgagctacatagttaatccttgcttatgatgtgaactttaagtgtgtatctgtttttttcttctctgatgtttagGTAGTGCTGGTGATGTGTTGGAAGATGATCCCGTGGGAAGACTGAAAGTCTTTGTTTATGAGCTTCCAAGTAAATACAACAAGAAGATACTTCAGAAGGA
       ||| | |  ||||||| || |  | || | |  ||  | | | |  ||   ||  | |      ||    | || |  ||     |  | ||||||||||||||||||| || ||||||||||| ||||||||  |||| || ||||||||||| |||||||| ||||| || ||||| || || || |||||
------gtctct-aaattctgtggtttattt-caaaatatattatagttaa--ataaaaaaatgagactactaagcatgttgtggttgaaccaaatgtagGTAGTGCTGGTGATGTATTAGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGCAAATATAATAAGAAAATTCTGCAAAAGGA

upper sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 1
agcattatctttcaggttctgtgattgagctacatagttaatccttgcttatgatgtgaactttaagtgt--gtatctgtttttttcttctctgatg-------tttagGTAGTGCTGGTGATGTGTTGGAAGATGATCCCGTGGGAAGACTGAAAGTCTTTGTTTATGAGCTTCCAAGTAAATACAACAAGAAGATACTTCAGAAGGA
    |   |||| |   ||||      |||  || | ||  ||||  | | | |  ||||||| ||   |  | |||| |          |  | ||       | ||||||| |||||||| || ||||||||  |||| ||||||||  ||||||| ||||||||||| |||||||||||||||||||||||||| || || |||||
----tgtcctttaaaaatctg----ctagcagcaaaattt-tcctaacctgtcaactgaacttaaaaaattaggatctctaaccacgccttgggttgcacctcatgtagGTAGCGCTGGTGACGTCTTGGAAGACAATCCAGTGGGAAGGTTGAAAGTTTTTGTTTATGAACTTCCAAGTAAATACAACAAGAAGATTCTGCAAAAGGA

upper sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 1
----agcattatc---tttcaggttctgtgattgagctacatagttaatccttgcttatgatgtgaactttaagtgtgtatctgtttttttcttctctgatgtttagGTAGTGCTGGTGATGTGTTGGAAGATGATCCCGTGGGAAGACTGAAAGTCTTTGTTTATGAGCTTCCAAGTAAATACAACAAGAAGATACTTCAGAAGGA
    ||  |||     ||  | ||||| |   |||||    |  || |     |  | ||| |     | |||     | ||   |||    |||  |||  |  ||| |||||||||||||| |||||||||||||| || |||||  |||| || ||||| || ||||||||||| ||||||||||| ||||| |||||||||||
cccgagagttaaacaattctaagttctct---tgagcagtttgatttaatggggactctgaagca---tgtaatctgatctccactttgggtttcaatga-atgcagGAAGTGCTGGTGATGTTTTGGAAGATGATCCAGTAGGAAGGTTGAAGGTTTTTGTGTACGAGCTTCCAAGCAAATACAACAAAAAGATCCTTCAGAAGGA

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|47831034|gb|CK120718.1|CK120718
EST:     GATTTCTGCTTTCCGTCTGAGTCGGAGTCAACCAACTGAGCGAATTTCAG                         GTAGTGCTGGTGATGTGTTGGAAGATGATCCCGTGGGAAGACTGAAAGTCT
genomic: GATTTCTGCTTTCCGTCTGAGTCGGAGTCAACCAACTGAGCGAATTTCAGgtgagttcta ... tgatgtttagGTAGTGCTGGTGATGTGTTGGAAGATGATCCCGTGGGAAGACTGAAAGTCT
EST: gi|86040266|gb|DR336021.1|DR336021
EST:     GATTTCTGCTTTCCGTCTGAGTCGGAGTCAACCAACTGAGCGAATTTCAG                         GTAGTGCTGGTGATGTGTTGGAAGATGATCCCGTGGGAAGACTGAAAGTCT
genomic: GATTTCTGCTTTCCGTCTGAGTCGGAGTCAACCAACTGAGCGAATTTCAGgtgagttcta ... tgatgtttagGTAGTGCTGGTGATGTGTTGGAAGATGATCCCGTGGGAAGACTGAAAGTCT
EST: gi|86040268|gb|DR336023.1|DR336023
EST:     GATTTCTGCTTTCCGTCTGAGTCGGAGTCAACCAACTGAGCGAATTTCAG                         GTAGTGCTGGTGATGTGTTGGAAGATGATCCCGTGGGAAGACTGAAAGY-T
genomic: GATTTCTGCTTTCCGTCTGAGTCGGAGTCAACCAACTGAGCGAATTTCAGgtgagttcta ... tgatgtttagGTAGTGCTGGTGATGTGTTGGAAGATGATCCCGTGGGAAGACTGAAAGTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttatgatgtgaactttaagtgtgtatctgtttttttcttctctgatgtttagGTAGTGCTGGTGATGTGTTGGAAGATGATCCCGTGGGAAGACTGAAAGTCTTTGTTTATGAGCTTCCAAGTAAATACAACAAGAAGATACTTCAGAAGGA
                                          ctctgat  putative branch site (score: 4)
                        tgtatctgtttttttc  CT-rich tract
                                tttttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcattatctttcaggttctgtgattgagctacatagttaatccttgcttatgatgtgaactttaagtgtgtatctgtttttttcttctctgatgtttagGTAGTGCTGGTGATGTGTTGGAAGATGATCCCGTGGGAAGACTGAAAGTCTTTGTTTATGAGCTTCCAAGTAAATACAACAAGAAGATACTTCAGAAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - ctttcag
- - - - - - - - - - - - - - -ctacata