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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatagtttgtacttcttgtgcttctgttgataaattgcttcagccttctgaacttgaatggtgacttaaatatttttctttccttttctttccttctagCCATTGCTGTTTCTCGGGATCACAAGCCAGATCAAACTGATGAGAGGCGAAGGATTGAAGATGCAGGTGGCTTTGTTATGTGGGCTG

Basic information

species Glycine max
transcript GLYMA14G12220.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G12220.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G166035_T02 (Zea mays), 3'ss of exon 4
------tcatagtttgtacttcttgtgcttctgttgataaattgcttcagccttctga-acttgaatggtgacttaaatatttttctttccttttctttccttctagCCATTGCTGTTTCTCGGGATCACAAGCCAGATCAAACTGATGAGAGGCGAAGGATTGAAGATGCAGGTGGCTTTGTTATGTGGGCTG
      ||| | |  ||   ||   | | | |||    |      |  |  |   | | |||| ||   |   ||   |||  |  |||||   ||||  | |  ||| ||||| |||||  |||||||||| || ||||| || |||||||||| ||| ||||| |||||||| |||||||||||||||||||
gctgaatcagaatcagtttctcaaat-cgtttgtcaggattccaatctaatcgcattacacttcaacaat---tt---tatgatgttttccccatcttgacctgcagCAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTG

upper sequence: GLYMA14G12220.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G829894_T01 (Zea mays), 3'ss of exon 3
tcatagtttgtacttcttgtgcttctgttgataaattgcttcagccttctgaacttgaatggtgacttaaatatttttctttccttttctttcc-ttctagCCATTGCTGTTTCTCGGGATCACAAGCCAGATCAAACTGATGAGAGGCGAAGGATTGAAGATGCAGGTGGCTTTGTTATGTGGGCTG
|  |      |   |    ||  | |   |||     |||  | |    |  ||||| ||      ||   | || |  |||||   |||      |  ||| ||||| |||||  |||||||||| || ||||| || |||||||| | ||| ||||| || ||||| |||||||||||||||||||
ttgtgacgaatggataaactgaatatcaggattccaagcta-accacgttccacttgtattcgatattttttgttatgttttccccatctcggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG

upper sequence: GLYMA14G12220.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G056572_T02 (Zea mays), 3'ss of exon 4
tcatagtttgtacttcttgtgcttctgttgataaattgcttcagccttc-tgaacttgaatggtgacttaaatatttttctttccttttctt-tccttctagCCATTGCTGTTTCTCGGGATCACAAGCCAGATCAAACTGATGAGAGGCGAAGGATTGAAGATGCAGGTGGCTTTGTTATGTGGGCTG
  |  | |           || ||||   | | |  |  |||| | ||  |||    |  |    ||||   ||  ||  |    | | ||| |  ||  ||| |||||||||||   |||||||||||| ||||||||||||||| |||   | ||||||||||| || || ||||| |||||||| |
ctactgctaagctaggagttgattctacggctga--tatttcaacattggtgacaccgtttaaccactttcctaacttgatgcattctgcttctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAG

upper sequence: GLYMA14G12220.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 5
tcatagtttgtacttcttgt--gcttctgttgataaa--ttgct-tcagccttctgaacttgaatggtgacttaaatatttttctttccttttctttccttctagCCATTGCTGTTTCTCGGGATCACAAGCCAGATCAAACTGATGAGAGGCGAAGGATTGAAGATGCAGGTGGCTTTGTTATGTGGGCTG
 |||| ||   |   | ||   ||   |||| || ||  ||||  | || |        ||| ||||| ||| |    |||    ||  ||||  ||  |   ||| |||||||| || || ||||||||||| ||||||| ||| ||| | | ||| ||||| |||||||| || ||||| ||||||||||
acatacttataatcacatgatagcccttgttcatgaaatttgcaataagtcgctctgttttgtatggt-actaa----tttgatatttttttttgtttgtcaaagCTATTGCTGTATCCCGAGATCACAAGCCTGATCAAAGTGACGAGCGCCAAAGAATTGAGGATGCAGGAGGATTTGTCATGTGGGCTG

upper sequence: GLYMA14G12220.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 3'ss of exon 5
tcatagtttgtacttcttgtgcttctgttgataaattgcttc----agccttc-tgaacttgaatggtgacttaaatatttttctttccttttctttccttctagCCATTGCTGTTTCTCGGGATCACAAGCCAGATCAAACTGATGAGAGGCGAAGGATTGAAGATGCAGGTGGCTTTGTTATGTGGGCTG
  ||   ||  |  ||||     ||| | || || |||||||    ||  |||      || | || |   | |  |  |        ||| |  || | || |||||||||||||||||| |||||||||||||| |||||||||||| |||   | ||||| ||||| || || ||||| ||||||||||
-gatgaattaaagatctt----ctctatggagaatttgcttcgtctagtgttcactggtttcagtgtttgatcatctgatgaaaacatcttgtaatttcctccagCCATTGCTGTTTCTCGAGATCACAAGCCAGACCAAACTGATGAGCGGCAGCGTATTGAGGATGCTGGAGGGTTTGTGATGTGGGCTG

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|58016294|gb|CX703036.1|CX703036
EST:     G-TGCAAATTG-TGGGGACTCCAGAGCTGTTATATGCAGGGGTGG-AATG                         CCATTGCTG-TTCTTCGGGATCACAAGCCAGATCAAACTGATGAGAGGCGA
genomic: GTTGCAAA-TGTTGGGGACTCCAGAGCTGTTATATGCAGGGGTGGAAATGgtaaggcttg ... ttccttctagCCATTGCTGTTTC-TCGGGATCACAAGCCAGATCAAACTGATGAGAGGCGA
EST: gi|58019366|gb|CX706108.1|CX706108
EST:     TGCAGGGGGT-GAAATG                         CCATTGCTGTTTCTCGGGATCACAAGCCAGATCAAACTGATGAGAGGCGAA
genomic: TGCA-GGGGTGGAAATGgtaaggcttg ... ttccttctagCCATTGCTGTTTCTCGGGATCACAAGCCAGATCAAACTGATGAGAGGCGAA
EST: gi|6502191|gb|AW203564.1|AW203564
EST:     TGTTGCAAATGTTGGGGACTNCAGAGCTGTTATATGCANGGGTGGAAATG                         CCATTGCTGTTTCTTCGG-ATCACAAAGC-AGATCAAACTGATGAGAGGCC
genomic: TGTTGCAAATGTTGGGGACTCCAGAGCTGTTATATGCAGGGGTGGAAATGgtaaggcttg ... ttccttctagCCATTGCTGTTTCT-CGGGATCACAA-GCCAGATCAAACTGATGAGAGGC-
EST: gi|120496388|gb|EH224555.1|EH224555
EST:     TGTTGCAAATGTTGGGGACTCCAGAGCTGTTATATGCAGGGGTGGAAATG                         CCATTGCTGTTTCTCGGGATCACAAGCCAGATCAAACTGATGAGAGGCGAA
genomic: TGTTGCAAATGTTGGGGACTCCAGAGCTGTTATATGCAGGGGTGGAAATGgtaaggcttg ... ttccttctagCCATTGCTGTTTCTCGGGATCACAAGCCAGATCAAACTGATGAGAGGCGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctgaacttgaatggtgacttaaatatttttctttccttttctttccttctagCCATTGCTGTTTCTCGGGATCACAAGCCAGATCAAACTGATGAGAGGCGAAGGATTGAAGATGCAGGTGGCTTTGTTATGTGGGCTG
                    cttaaatatttttctt  CT-rich tract
                     ttaaatatttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatagtttgtacttcttgtgcttctgttgataaattgcttcagccttctgaacttgaatggtgacttaaatatttttctttccttttctttccttctagCCATTGCTGTTTCTCGGGATCACAAGCCAGATCAAACTGATGAGAGGCGAAGGATTGAAGATGCAGGTGGCTTTGTTATGTGGGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG