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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacactgattttttaaatccttatggaaatgaaagtttagagaaaaatcctctgcctgtgtttttgatttctaacttcaatcattattgcttgatatcagGTTGTTCCTGCCTGGCTAAGTTGCTTGCCTATAAAAGGTGATTTAATTGAAGCTAAGGTTGTGCATGACCAACTTTGTTCAATGGTTGAAAG

Basic information

species Glycine max
transcript GLYMA19G29010.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G29010.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os07g38760.1 (Oryza sativa), 3'ss of exon 17
------gacactga----ttttttaaatccttatggaaatgaaagtttagagaaaaatcctctgcctgtgtttttgatttctaacttcaatcattattgcttgatatcagGTTGTTCCTGCCTGGCTAAGTTGCTTGCCTATAAAAGGTGATTTAATTGAAGCTAAGGTTGTGCATGACCAACTTTGTTCAATGGTTGAAAG
       |  ||||    | |||| |   |   |   |    |  ||   | ||| || |        |||| |    | || |    |   |||  ||||     | ||||  |||||||||||||  |||||||||||||||||| |||    |||||||| || ||||| || || || || |  ||||||||||||||
tagatttagtctgaaccttgttttcagctcccgtaagaccatatattgctaaaaagatac-------atgttgtattatcctcatccaatgtattcatgctct---ttagGTCATTCCTGCCTGGCTTGGTTGCTTGCCTATAAAAGATGACAAGATTGAAGCAAAAGTTGTACACGATCAGCTCTCCTCAATGGTTGAAAG

upper sequence: GLYMA19G29010.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G011246_T01 (Zea mays), 3'ss of exon 1
gacactgattttttaaatcctta-tggaaatgaaagttt---agagaaaaatcctctgcctgtgtttttgatttctaacttcaatcattattgcttgatatcagGTTGTTCCTGCCTGGCTAAGTTGCTTGCCTATAAAAGGTGATTTAATTGAAGCTAAGGTTGTGCATGACCAACTTTGTTCAATGGTTGAAAG
 | |  |  |  ||||  |     ||  | | |  |      | |  ||  | ||||||   ||    |   ||||||  | |||||  |||  |   | |||||||||||| |||||||| |  |||||||| ||||||| |||    ||||||||||| | ||| ||||| |||||||| |||||||| || ||
tataaggtgtccttaacccaaaggtgagactcagcgcccgccacatgaatttactctgcgcatgaaacta--ttctaaactgaatca--attcatgcttctcagGTTGTTCCAGCCTGGCTTAACTGCTTGCCAATAAAAGATGACAAGATTGAAGCTAAAGCTGTACATGAACAACTTTGCTCAATGGTGGAGAG

upper sequence: GLYMA19G29010.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM5G887631_T01 (Zea mays), 3'ss of exon 16
----gacactg-attttttaaatccttatggaaatgaaagtttagagaaaaatcctctgcctgtgtttttgatttctaacttcaatcattattgcttgatatcagGTTGTTCCTGCCTGGCTAAGTTGCTTGCCTATAAAAGGTGATTTAATTGAAGCTAAGGTTGTGCATGACCAACTTTGTTCAATGGTTGAAAG
       | || ||  | |  ||  |  ||  |      | |  ||||||  | || ||    |     |  |  | ||||  |   |||  || ||    |||||||||||| |||||||| || ||||||||||||||||  ||     |||||||||| ||||| ||||  || ||||| || ||||| || ||
aaagtgtattgcatggtgtcgattttgctgttagcttt-gctaggagaaagttactttgtgcatagaactagtc-caaactgaaccaattcatgtttc---tcagGTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAAGCTAAAGTTGTACATGGACAGCTTTGCTCCATGGTGGAGAG

upper sequence: GLYMA19G29010.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv08s0007g07240.t01 (Vitis vinifera), 3'ss of exon 17
gacactgattttttaaatccttatggaaatgaaagtttagagaa---aaatcctctgcctgtgtttttgatttctaacttcaatcattattgcttgatatcagGTTGTTCCTGCCTGGCTAAGTTGCTTGCCTATAAAAGGTGATTTAATTGAAGCTAAGGTTGTGCATGACCAACTTTGTTCAATGGTTGAAAG
     | | |    || ||    |  |    |    ||  | |    || |   |  |     ||| | | || |   ||   |  ||| |  ||     ||| |||||||||| ||| |||||||||||||| ||||||||||||| ||||| || || ||||||||||||||||| ||||||||||| |||||
---gttcaatggcgaattctaggttaagccaatctattgcaaatcccaacttacccacacagctttctaaatttttttttttttttttaatttttttgggcagATTGTTCCTGCTTGGTTAAGTTGCTTGCCTTTAAAAGGTGATTTGATTGAGGCCAAAGTTGTGCATGACCAACTATGTTCAATGGTGGAAAG

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|17023096|gb|BM094130.1|BM094130
EST:     CTCTTGGAAAAATATGCCAATTCCATCGTGATAGCATAAATGCAGCACAG                         GTTGTTCCTGCCTGGCTAAGTTGCTTGCCTATA
genomic: CTCTTGGAAAAATATGCCAATTCCATCGTGATAGCATAAATGCAGCACAGgtattttaca ... ttgatatcagGTTGTTCCTGCCTGGCTAAGTTGCTTGCCTATA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcctctgcctgtgtttttgatttctaacttcaatcattattgcttgatatcagGTTGTTCCTGCCTGGCTAAGTTGCTTGCCTATAAAAGGTGATTTAATTGAAGCTAAGGTTGTGCATGACCAACTTTGTTCAATGGTTGAAAG
               tttttgatttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacactgattttttaaatccttatggaaatgaaagtttagagaaaaatcctctgcctgtgtttttgatttctaacttcaatcattattgcttgatatcagGTTGTTCCTGCCTGGCTAAGTTGCTTGCCTATAAAAGGTGATTTAATTGAAGCTAAGGTTGTGCATGACCAACTTTGTTCAATGGTTGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
gacactg
- - - - - - - - - ccttatg
- - - - - - - - - - - - - aaatgaaa
- - - - - - - - - - - - - - - - - - - - agaaaaa