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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttaagctcctaataatatgtgaaccatgcttgcttatcgtcattttacagaatgttcttccttttctaagtagtttttatgttgtttcataatcatcagGCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTG

Basic information

species Arabidopsis thaliana
transcript AT2G44610.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G44610.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 1
------tttaagctcctaataatatgtgaaccatgcttgcttatcgtcattttacagaatgttcttccttttctaagtagtttttatgttgtttcataatcatcagGCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTG
      ||| || |   |    ||| | ||      |   || |  |  || |      || || |  | |||| |  |   |||||  | |||    | ||   ||| ||||| |||||||| || || |||||||||||||||||||||||| | || |||||||| ||  | ||
gcaatgtttcagttttaatacttatcttaaaatgtttcagttttaatacttatcttatctggtcgttatgttctcatga---tttattctattttgcgaaca---gGCTACAATCGGTATTGACTTCCTGTCAAAGACAATGTACCTTGAAGATAGGACTGTCAGACTGCAACTTTG

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G075719_T01 (Zea mays), 3'ss of exon 1
--tttaagctcctaataatatgtgaaccatgcttgcttatcgtcattttacagaatgttcttccttttctaagtagtttttatgttgtttca--taatcatcagGCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTG
  | | |  |     |||| | || |   |  | |||| | || |   ||  |   |||  ||  ||   | ||    |  | |||||||    |  |   ||||| ||||||||||||||||| || |||||||||||||||||||||||| |||| || ||||| ||  | ||
agtattattttgagttaatttatgtaattt-ttggcttgttgt-acagtaatgctggttagtctattc--aggtttgctcaaagttgttttctctggtatgcagGCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G169694_T01 (Zea mays), 3'ss of exon 1
-----tttaagctcctaataatatgtgaaccatgcttgcttatcgt-cattttacagaatgttcttccttttctaagtagtttttatgttgtttcataatcatcagGCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTG
      | ||| |  |  | |||  || |   |  | ||||||| | || | | | |  | ||||        |   |     || | || | ||  |||   ||||| || |||||||||||||| || |||||||||||||||||||||||| |||| || ||||| ||  | ||
cgtaggtcaagttttt--ttatacctgtatttt-ttggcttatcatacagtctgctggttattctattcaggtttgctcaaagttgttttctctcg-aatg--cagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G41100.1 (Glycine max), 3'ss of exon 1
-tttaagctcctaataatatgtgaaccatgcttgcttatcgtcattttacaga-atgttcttccttt-tctaagtagtttttatgttgtttcataatcatcagGCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTG
  ||   ||        | ||| |    |  || |||| | |  | ||||  | || |  ||  |   |  || ||| ||||   || |||| | ||   ||||| |||||||||||||||||||||||||| || ||||| |||||||||||||| ||  |||| ||||||||
tctttgactgtggcctgtgtgt-atttttatttccttagcttgttcttactaacatatatttgttgaattcaaatagattttgatttttttcctcatg--cagGCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTG

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G04330.1 (Glycine max), 3'ss of exon 1
----tttaagctcctaataatatgtgaaccatgcttgcttatcgtcattttac-agaatgttcttccttt-tctaagtagtttttatgttgtttcataatcatcagGCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTG
     ||   ||        | ||| |    |  ||  ||| | ||||||||| || |  || ||  |   |  |||| | | ||   || | ||||      ||||| |||||||||||||||||||||||||| || ||||| || ||||||||||| ||  |||| ||||||||
gcttctttgactgtggcctgtgtgt-atttttatttctttagcttcattttactagcacatttttgttgaattcaagttgatattgatttttctcatg-----cagGCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTCGAAGATCGAACTGTTCGACTGCAGTTGTG

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G41090.1 (Glycine max), 3'ss of exon 1
-----tttaagctcctaataatatgtgaaccatgcttgctt-atcgtcattttacagaatgttcttccttttctaagtagtttttatgttgtttcataatcatcagGCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTG
      |||    | ||||  | |  |||  ||  |||||  ||   ||||||      |  |||| | | |      | || ||||    |||   ||    |||||||| ||||||||||||||| ||||||| || ||||| |||||||||||||| ||  | || ||| |   
gttgtcttataagcataatgctcttggaa--atttttgctccatatccattttgtcattttctcttgcctgttcttaaacttattattaatttttcgaa----cagGCCACGATTGGTATTGATTTTTTATCAAAAACTATGTATCTTGAAGATCGAACTGTTCGGCTGCAGCT---

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G05860.1 (Glycine max), 3'ss of exon 1
tttaagctcct-aataatatgtgaaccatgcttgcttatcgtcattttacagaatgttcttccttttctaagtagtttttatgttgtttcataatcatcagGCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTG
|  |   || | ||| | |||     |    || || |      || |  | ||| ||   | |  || ||    | |||   ||   |  |  | | ||||| ||||| ||||| |||||||| ||||| || ||||| |||||||||||||| ||  |||| ||||||||
tgcatattcttgaattacatgcatttccattttcctaaattgagttgtttacaat-tttaccgtactcaaaactttgttttcttttccttttgctaaacagGCTACAATCGGTATCGATTTTCTGTCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTG

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G16200.1 (Glycine max), 3'ss of exon 1
tttaagctcctaataatatgtgaaccatgcttgcttatcgtcattttacaga--atgttcttccttttctaagtagttt---ttatgttgtttcataatcatcagGCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTG
      |  |  || || ||  ||  ||  ||    |    |||||    |   |  || |  |  | || |  | |||   || | ||   |  |  | | ||||| ||||| ||||| |||||||| ||||| || ||||| |||||||||||||| ||  |||| || |||||
----gacaacacattatgtgcaaat-ataattctacacatgcatttagttgtttacattttgaccgtactcaaaactttccttttttttcccttttgctaaacagGCTACAATCGGTATCGATTTTCTGTCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAATTGTG

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv15s0021g00640.t01 (Vitis vinifera), 3'ss of exon 1
-----tttaagctcctaataatatgtgaaccatgcttgcttatcgtcattttacagaatgttcttccttttctaagtagtttttatgttgtttcataatcatcagGCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTG
     | || |   ||    | |  |     || |||    ||       ||      | || |   ||| |||||      || |||| ||   | |    ||||| || |||||||| ||||||||||||||||| ||||||||||||||||| |||||| |  | ||  | ||
ctaaatataggtagctgtatacacctagcttattcttctccataaggtgcttttgttttattttctttttcctaagc-----ttgtgttattaattgacatccagGCTACTATTGGTATCGATTTTCTATCAAAGACGATGTACCTTGAAGATCGGACGGTCCGTTTGCAACTCTG

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S39_147V6.2 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------------------------tttaagctcctaataatatgtgaaccatgcttgcttatcgtcattttacagaatgttcttcctt-----ttctaagtagtttttat------gttgtttcataatcat-----cagGCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTG
                                                                       | ||   |   ||| | ||       |  ||  || |  |  || ||   |       ||||      ||| | || | |  |||      ||| |  | | || |      ||||| || ||||||||||||||||| || ||||| ||||| ||||| ||||| || || ||||| ||| | ||
gttagcttctttccctcctagtcttcttgcataaaaattgtgtgctgctgacatttctggtttgccgtacatcaataactccatactctggatggtttcattctttttgttttttctagtaagaacctgtcctggcaggttcaaggttggtgctattgatgagttttcccttgataactttggcagGCAACTATTGGTATTGATTTTCTCTCCAAGACCATGTATCTTGAGGATCGCACTGTTAGACTACAGCTCTG

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S346_29V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------------------------------------------------ttta--agctcctaataatatgtgaaccatgcttgcttatcgtcattttacagaatgttcttcct--tttctaagtagtttttatgttgtttcataatcatcagGCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTG
                                                                             || |  | ||   ||  | || |  |  ||      |  |  |  ||| | |  |   |   | |  |||  ||| | |  ||||||  | |   | ||  ||||| || || |||||||||||||| || ||||| ||||||||||| ||||| || ||  |||| ||| | ||
gtgagattcttttttatcctctcatctgtgtataatagacttttactcgtaatccctgcagcttctgtgtgatttcattcaccatctttcaaagagatatagaaaatatacattggtaat--tttgagaatacactagacttgattttgaagaattaattatgtcttgtttgattcgacagGCAACCATCGGTATTGATTTTCTCTCTAAGACCATGTACCTTGAGGATCGTACCGTGCGACTACAGCTCTG

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S12_267V6.1 (Physcomitrella patens), 3'ss of exon 2
tttaagctcctaataatatgtgaaccatgcttgcttatcgtcattttacagaatgttcttccttttctaag----tagtttttatgttgtttcataatcatcagGCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTG
  |   |   |   || || |||  || |      |      ||||| || ||  |||    | ||||  |    | ||  | |     ||| ||  |   ||||| || ||||| ||||||||||| ||||| ||||||||||||||||| || || ||  | || ||| | ||
--tgttcatgtgcgaaaatctgatgcacgaaaatattgttcaatttttcaaaac-ttcgaagtgttctgtggttatggtgataaccaaattttatgtttg-cagGCGACTATTGGCATTGATTTTCTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTG

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|124735129|gb|EH826531.1|EH826531
EST:     TTCATGTACGACAAATTCGACAACACTTACCAG                         GCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGA
genomic: TTCATGTACGACAAATTCGACAACACTTACCAGgtaaatttcc ... taatcatcagGCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGA
EST: gi|125036385|gb|EL108654.1|EL108654
EST:     AAATTCGACAACACTTACCAG                         GCCACAATTGGTTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCG
genomic: AAATTCGACAACACTTACCAGgtaaatttcc ... taatcatcagGCCACAATTGG-TATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCG
EST: gi|116467570|gb|EG510162.1|EG510162
EST:     CCAGTATCATTACTCGATTCATGTACGACAAATTCGACAACACTTACCAG                         GCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGA
genomic: CCAGTATCATTACTCGATTCATGTACGACAAATTCGACAACACTTACCAGgtaaatttcc ... taatcatcagGCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGA
EST: gi|125052321|gb|EL124149.1|EL124149
EST:     ATTCATGTACGACAAATTCGACAACACTTACCAG                         GCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGA
genomic: ATTCATGTACGACAAATTCGACAACACTTACCAGgtaaatttcc ... taatcatcagGCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGA
EST: gi|164149879|gb|ES044049.1|ES044049
EST:     TCGATTCATGTACGACAAATTCGACAACACTTACCAG                         GCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGA
genomic: TCGATTCATGTACGACAAATTCGACAACACTTACCAGgtaaatttcc ... taatcatcagGCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGA
EST: gi|124816599|gb|EH901465.1|EH901465
EST:     ATGTACGACAAATTCGACAACACTTACCAG                         GCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGA
genomic: ATGTACGACAAATTCGACAACACTTACCAGgtaaatttcc ... taatcatcagGCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacagaatgttcttccttttctaagtagtttttatgttgtttcataatcatcagGCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTG
                      taagtagtttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttaagctcctaataatatgtgaaccatgcttgcttatcgtcattttacagaatgttcttccttttctaagtagtttttatgttgtttcataatcatcagGCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - ctcctaa
- - - - - - - - - - -gaaccat
- - - - - - - - - - - - - - - - - - - - - - - tacagaa