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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatagagaaccggacagacactcaaaacctgtttctgttggcaatctgagatcccattgatccaatttgtgtgtttgttttgtagTATGTACCGTATGTTGCGGATAGTAAGCGAGCCATGGACGAGTACACATCAGAGATATTCATGGGAGGGAAGAACACAATTGTGATGCACAATACCTGCG

Basic information

species Arabidopsis thaliana
transcript AT4G39800.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os10g22450.1 (Oryza sativa), 3'ss of exon 7
-gtaaatagaga--accggacagacac-tcaaaacctgtttctgt-tggcaatctgagatcccattg--atccaatttgtgtgtttgtt-----ttgtagTATGTACCGTATGTTGCGGATAGTAAGCGAGCCATGGACGAGTACACATCAGAGATATTCATGGGAGGGAAGAACACAATTGTGATGCACAATACCTGCG
     |||||     || ||| || |  | | | || | |  ||   ||        |||    |||   |     ||| ||  |||||     ||| ||||| | || || |||| ||| || ||| | ||||||||||||||||| || ||||| |||||||||||||||||||| || ||| ||||||| |||||||
ctccgatagaatctgccagaccgaaaaattataccccgctgatgcacggtggctgatgatttggttgctgtttctattgagtaattgttaattgttgcagTATATTCCATACGTTGGGGACAGCAAGAGGGCCATGGACGAGTACACCTCGGAGATCTTCATGGGAGGGAAGAACACCATCGTGCTGCACAACACCTGCG

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 7
----gtaaatagagaaccggacagacactcaaaacctgtttctgttggcaatctgagatccca--ttgatccaatttgtgtgtttgttttgtagTATGTACCGTATGTTGCGGATAGTAAGCGAGCCATGGACGAGTACACATCAGAGATATTCATGGGAGGGAAGAACACAATTGTGATGCACAATACCTGCG
    | || | |   |  |      |      |   ||    |      || || || |      |  | |   |   ||| ||  || || ||||||| ||||||||||  || || ||| | || |||||||||||||| |||||||| |||||||| || |||| ||| || ||  ||||||| ||||| |
gtttgcaatttgtccatggattcttctgcagcagtatgccattaaaaaaaaacttagttttggattaaaacttgtccatgtattc-ttctgcagTATGTGCCGTATGTTGGAGACAGCAAGAGGGCAATGGACGAGTACACCTCAGAGATCTTCATGGGGGGTAAGAGCACCATCGTTCTGCACAACACCTGTG

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 7
-gtaaatagagaaccggacaga-cactcaaaacctgtttctgttggcaatctga-----gatcc-cattgatccaatttgtgtgtttgtt--ttgtagTATGTACCGTATGTTGCGGATAGTAAGCGAGCCATGGACGAGTACACATCAGAGATATTCATGGGAGGGAAGAACACAATTGTGATGCACAATACCTGCG
      |||   | |   ||   |  | |||| |||   |     ||| | | |     |||   ||||||  |          |||| |   || ||||||| |||||||| |  || |||||| | || ||||||||||||||||||||||| |||||||| || |||| ||| || ||| ||||||| |||||||
gtctgttagctgatcttccacctctttaaaaagctggcacgtgcagcagtttaaacgtagatttacattgaaacctgccactcctttgctgcatgcagTATGTGCCGTATGTGGGAGACAGTAAGAGGGCTATGGACGAGTACACATCAGAGATCTTCATGGGCGGCAAGAGCACCATCGTGCTGCACAACACCTGCG

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 5
-gtaaatagagaaccggacaga-cactcaaaacctgtttctgttggcaatctga-----gatcc-cattgatccaatttgtgtgtttgtt--ttgtagTATGTACCGTATGTTGCGGATAGTAAGCGAGCCATGGACGAGTACACATCAGAGATATTCATGGGAGGGAAGAACACAATTGTGATGCACAATACCTGCG
    | |||  || |   ||   |  | |||| |||   |     ||| | | |     |||   |||| |  |          |||| |   || ||||||| ||||| || |  || |||||| | || ||||||||||||||||||||||| |||||||| || |||||||| || ||| ||||||| ||||| |
gtctattagctaatcttccacctctttaaaaagctggcacatgcagcagtttaaacgtagatttacattaaaacttgccactcctttgctgcatgcagTATGTGCCGTACGTGGGAGACAGTAAGAGGGCTATGGACGAGTACACATCAGAGATCTTCATGGGTGGCAAGAACACCATCGTGCTGCACAACACCTGTG

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 7
-gtaaatagagaaccggacagacactcaaaacctgtttctgttggcaatctgagatcccattgatccaatttgt-gtgtttgttttgtagTATGTACCGTATGTTGCGGATAGTAAGCGAGCCATGGACGAGTACACATCAGAGATATTCATGGGAGGGAAGAACACAATTGTGATGCACAATACCTGCG
      |||   | |   ||     | ||||   |||    |  ||||       |  ||||||   || ||||     || | ||| ||||||| ||||| || |  || || ||| | || |||||||||||||| |||||||| |||||||| || |||||||| || ||| ||||||| ||||| |
gtctgttagctgatctttcacctcgttaaaa---gttgacatatgcaaggcagatttacattga---aacttgtcactcttttgttgcagTATGTGCCGTACGTGGGAGACAGCAAGAGGGCTATGGACGAGTACACCTCAGAGATCTTCATGGGCGGCAAGAACACCATCGTGCTGCACAACACCTGTG

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G145638_T02 (Zea mays), 3'ss of exon 3
---------gtaaatagagaaccggacagacactcaaaacctgtttctgttggcaatctgagatcccattgatccaatttgtgtgtttgtt--ttgtagTATGTACCGTATGTTGCGGATAGTAAGCGAGCCATGGACGAGTACACATCAGAGATATTCATGGGAGGGAAGAACACAATTGTGATGCACAATACCTGCG
          | ||     | |     | | |      || ||   | |||   ||  |    |  ||||||  |          ||||||   || ||||||| ||||| || |  ||||||||| | || ||||||||||||||||||||||| || |||||  | |||||||| ||  || ||||||| |||||||
gtctgttagctgaacttccacctctttaaaaagatggcacatgcagcagttta-aacgtagatttacattgaaacttgccactcatttgttgcatgcagTATGTGCCGTACGTGGGAGATAGTAAGAGGGCTATGGACGAGTACACATCAGAGATCTTTATGGGCAGCAAGAACACCATCATGCTGCACAACACCTGCG

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G010768_T01 (Zea mays), 3'ss of exon 1
-gtaaatagagaaccggacagacactcaaaa--cctgt---ttctgttggc--aatctgagatcccattgatccaatttgtgtgtttgtt--ttgtagTATGTACCGTATGTTGCGGATAGTAAGCGAGCCATGGACGAGTACACATCAGAGATATTCATGGGAGGGAAGAACACAATTGTGATGCACAATACCTGCG
  |   |||   | |   ||     | ||||  | ||    | | || |    ||  |    |  ||||||  |          ||||||   || ||||||| | ||| || |  || |||||| | || ||||||||||||||||||||||| ||||||||  | |||||||| || ||| | ||||| ||||  |
atttgttagctgatcttccacctctttaaaaagcttgcaggtgcagtagtttaaacgtagatttacattgaaacttgccactcatttgttgcatgcagTATGTGCTGTACGTGGGAGACAGTAAGAGGGCTATGGACGAGTACACATCAGAGATCTTCATGGGCAGCAAGAACACCATCGTGCTACACAACACCTATG

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G177461_T01 (Zea mays), 3'ss of exon 7
---------gtaaatagagaaccggacagacactcaa---aacctgtttctgttggc---aatctgagatcccattgatccaatttg--tgtgtttgttttgtagTATGTACCGTATGTTGCGGATAGTAAGCGAGCCATGGACGAGTACACATCAGAGATATTCATGGGAGGGAAGAACACAATTGTGATGCACAATACCTGCG
            | | |       |   |  ||| |    | ||  | | || |        | |||       ||  || || |||       || ||||| ||||  | || ||||| |  || || ||| ||||||||||||| || || || ||||| |||||||| || |||||||| || ||| ||||||| ||||| |
gtcggtcggtccacttgttgtttagtttgtgactgagtctatcccatatatgctacttcatgtttgattaattgttactcaaagttgatccctcttcttttgcagTACATCCCCTATGTGGGTGACAGCAAGAGAGCCATGGACGAATATACCTCCGAGATCTTCATGGGCGGCAAGAACACCATCGTGCTGCACAACACCTGTG

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G14670.3 (Glycine max), 3'ss of exon 6
gtaaatag-agaaccggacagacactcaaaacctgtttctgttggcaatctgag-atcccattgatccaatttgtgtgtttgttttgtagTATGTACCGTATGTTGCGGATAGTAAGCGAGCCATGGACGAGTACACATCAGAGATATTCATGGGAGGGAAGAACACAATTGTGATGCACAATACCTGCG
|||| |   |      | ||  |||||     |   |||  ||||   | |      | | | | |  ||||  | | || |||||| |||||||||| || |||| ||| || ||| | |||||||| |||||| | || |||||||||||||| || ||||||||||||||| ||||||| || || |
gtaatttttatttttagtcactcactctctttcaaattcaattggttctttatttgactcttcggt--aattaatttattggttttgcagTATGTACCTTACGTTGGGGACAGCAAGAGGGCCATGGATGAGTACTCTTCTGAGATATTCATGGGCGGAAAGAACACAATTGTGTTGCACAACACTTGTG

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA18G02210.4 (Glycine max), 3'ss of exon 7
gtaaatagagaaccggacagacactcaaaacctgtttctgttggcaatctgagatcccattgatccaatttg-tgtgtttgttttgtagTATGTACCGTATGTTGCGGATAGTAAGCGAGCCATGGACGAGTACACATCAGAGATATTCATGGGAGGGAAGAACACAATTGTGATGCACAATACCTGCG
    |||          |      |||  |  | ||||| ||| ||      | ||   ||||| | || || | ||||   |||| ||||||| || || || | |||||| ||| |||||||||| |||||||| ||||||||||||||||| || |||||||| |||||  ||||||| || || |
--gtatatttgtttcacccatttttcactatttctttctcttgtca------ggtct--ttgattctatctgctttgttgcctttgcagTATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCAGAGATATTCATGGGTGGAAAGAACACCATTGTTTTGCACAACACATGTG

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA05G31450.4 (Glycine max), 3'ss of exon 4
gtaaatag----agaaccggacagacactcaaaacctgtttctgttgg--caatctgagatcccattgatccaatttgtgtgtttgttttgtagTATGTACCGTATGTTGCGGATAGTAAGCGAGCCATGGACGAGTACACATCAGAGATATTCATGGGAGGGAAGAACACAATTGTGATGCACAATACCTGCG
|||| |      |       |     | |||  ||    |  |       ||||  |  ||    ||||  |  || || | ||  ||||| |||| || || ||||| | ||| || ||| | |||||||| |||||||| || |||||||||||||| || ||||||||||||||| ||||||| || || |
gtaattttttttatttttttatttttagtcactactccctctttcaaattcaattggttatttttttgacact-ttggtttattgtttttgcagTACGTGCCTTATGTAGGGGACAGCAAGAGGGCCATGGATGAGTACACTTCTGAGATATTCATGGGTGGAAAGAACACAATTGTGTTGCACAACACATGTG

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA18G02210.3 (Glycine max), 3'ss of exon 7
-----------------------gtaaatagagaaccggacagacactcaaaacctgtt-tctgttggcaatctgagatcccattgatccaatttg-tgtgtttgttttgtagTATGTACCGTATGTTGCGGATAGTAAGCGAGCCATGGACGAGTACACATCAGAGATATTCATGGGAGGGAAGAACACAATTGTGATGCACAATACCTGCG
                       || | ||  | |         ||| ||        | | | ||     | | || ||   ||||| | || || | ||||   |||| ||||||| || || || | |||||| ||| |||||||||| |||||||| |||||||||||||||||                                   
gtgaacatcccgaccatgttgttgttattaaggtatatttgtttcacccatttttcactatttctttctcttgtcagGTCT--TTGATTCTATCTGCTTTGTTGCCTTTGCAGTATGTGCCTTACGTAGGGGATAGCAAGAGAGCCATGGATGAGTACACTTCAGAGATATTCATGGGT----------------------------------

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 3'ss of exon 7
gtaaatag-agaaccggac----------agacactcaaaacctgtttctg--ttggcaatctgagatcccattgatccaatttgtg------tgtttgttttgtagTATGTACCGTATGTTGCGGATAGTAAGCGAGCCATGGACGAGTACACATCAGAGATATTCATGGGAGGGAAGAACACAATTGTGATGCACAATACCTGCG
||| || | ||||||   |          |   | |  ||  | | | |||  ||||     |    || || ||    |  || |       ||||  | ||| ||||||| || |||||||  ||||| ||| |||||||||| |||||||| || |||||||||||||| ||||||| ||| |||||| ||||||| |||||||
gtatatcgcagaaccctccttttgtttgtatgtattacaattcagatgctggtttggactcattcattctcactggctaacattatacggtgttgttgatattgcagTATGTGCCATATGTTGGAGATAGCAAGAGAGCCATGGATGAGTACACTTCTGAGATATTCATGGGTGGGAAGAGCACCATTGTGCTGCACAACACCTGCG

upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ37320 (Selaginella moellendorffii), 3'ss of exon 7
gtaaatagagaaccggacagacactcaaaacctgtttctgttggcaatctgagatcccattgatccaatttgtgtgtttgttttgtagTATGTACCGTATGTTGCGGATAGTAAGCGAGCCATGGACGAGTACACATCAGAGATATTCATGGGAGGGAAGAACACAATTGTGATGCACAATACCTGCG
                ||| || ||  |    | ||| | | || ||    |  ||||        | ||||    || ||||| |||||||| || || || |  ||||| ||||| ||||||||||| ||||| || ||||||||||||||||| | || ||| || |  |||||||| || ||||
-----------gtaaaacaaacgcttga----tttttttctagggaa----aactcccg-------agtttgct--ttcgttttctagTATGTTCCTTACGTCGGTGATAGCAAGCGGGCCATGGACGAATACACGTCCGAGATATTCATGGGAGGCAGGAGCACCATCGCCATGCACAACACTTGCG

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|86074513|gb|DR370270.1|DR370270
EST:     TATCCTCTTTGAGCCT-GGGAACACCCGGACCATGTTTGTTGTCATCAAG                         TATGTACCGTATGTTGCGGATAGTAAGCGAGCCATGGACGAGTACACATCA
genomic: TATCCTCTTTGAGCCTGGGGAACACCCGGACCATG-TTGTTGTCATCAAGgtaaatagag ... tgttttgtagTATGTACCGTATGTTGCGGATAGTAAGCGAGCCATGGACGAGTACACATCA
EST: gi|47829945|gb|CK119629.1|CK119629
EST:     GTATCCTCTTTGAGCCTGGGGAACACCCGGACCATGTTGTTGTCATCAAG                         TATGTACCGTATGTTGCGGATAGTAAGCGAGCCATGGACGAGTACACATCA
genomic: GTATCCTCTTTGAGCCTGGGGAACACCCGGACCATGTTGTTGTCATCAAGgtaaatagag ... tgttttgtagTATGTACCGTATGTTGCGGATAGTAAGCGAGCCATGGACGAGTACACATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttctgttggcaatctgagatcccattgatccaatttgtgtgtttgttttgtagTATGTACCGTATGTTGCGGATAGTAAGCGAGCCATGGACGAGTACACATCAGAGATATTCATGGGAGGGAAGAACACAATTGTGATGCACAATACCTGCG
                        cattgat  putative branch site (score: 4)
                                           tttgtttt  putative PPT
                                           tttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatagagaaccggacagacactcaaaacctgtttctgttggcaatctgagatcccattgatccaatttgtgtgtttgttttgtagTATGTACCGTATGTTGCGGATAGTAAGCGAGCCATGGACGAGTACACATCAGAGATATTCATGGGAGGGAAGAACACAATTGTGATGCACAATACCTGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC