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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttattattgcttaggtttagctgtaactttagcttcgactgggatcattgtgcatagttggtcagcggcagaaatattaacttgagtttttaattctgttgttgaagCATTTATGGCCCAGTGCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGCTTTGTTACCTTTGTTTATCCAGAGACTGTGAAGCTTATTCTA

Basic information

species Glycine max
transcript GLYMA09G35980.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G35980.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g48410.2 (Oryza sativa), 3'ss of exon 2
gttattattgcttaggtttagctgtaactttagcttcgactgggatcattgtgcatagttggtcagcggcagaaatattaacttgagtttttaattctgttgttgaagCATTTATGGCCCAGTGCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGCTTTGTTACCTTTGTTTATCCAGAGACTGTGAAGCTTATTCTA
                              |||  |    |     ||  |  ||  ||         ||   |   ||||  |||  |  |          ||||||||| || ||||| || || |||||  | ||||| |||||||||||||| ||||| ||||| || ||||| || || || ||||| |||||||| ||||| 
-----------------------------gtagtatactataatcccaccgcccaccgtcaccgccatgccatagctttaatctga--tgatgccctctcaattgaagCATCTACGGCCCCGTCCACGACGTTCGCATCCCGTACCAGCAGAAGCGCATGTTCGGCTTCGTCACCTTCGTCTACCCGGAGACGGTGAAGCTGATTCTC

upper sequence: GLYMA09G35980.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g21160.1 (Oryza sativa), 3'ss of exon 2
gttattattgcttaggtttagctgtaactttagcttcgactgggatcattgtgcatagttggtcagcggcagaaatattaacttga--gtttttaattctgt----tgttgaagCATTTATGGCCCAGTGCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGCTTTGTTACCTTTGTTTATCCAGAGACTGTGAAGCTTATTCTA
||   || |||   | |  |    |   | |  ||||      |        |    |  |      |   |  || ||  | |    ||| ||      |      | || ||||| || || || ||||| |||||| | ||||| |||||||||||||| ||||| || || || ||||| ||||| || ||||| |||||||| ||  | 
gtatataatgcgatgttgcaatgatgcttcttccttctttcatggcgggctcggtaggacgcgatctgattggcatttttgcattgctgttcttggcaacgcgccgcgctgcagCATCTACGGGCCGGTGCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTTTACCCGGAGACGGTGAAGCTGATCTTG

upper sequence: GLYMA09G35980.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os11g03220.1 (Oryza sativa), 3'ss of exon 2
-----------gttattattgcttaggtttagctgtaactttagcttcgac-tgggatcattgtgcatagttggtcagcggcagaaatattaacttgagtttttaattctgttgttga-agCATTTATGGCCCAGTGCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGCTTTGTTACCTTTGTTTATCCAGAGACTGTGAAGCTTATTCTA
              |  || |      | | | |||  |||  | ||| |  | ||| ||||    | | ||  | |  |  |    | ||  ||||  | | |  |   |        ||||| |||||    |||||||| ||| | |||||||||||| ||||||| |||||||| ||||| ||||| |  || | | |||| |||||||| ||||| 
gtatcacatgttccaccatagtgcccctattgatgtgtctt--gtttcaatattggagcatttcata-atttaatgaatgcaatctgttttggcttgtttgtgttgtgtggggacaaccagCATGTATGGGATGGTGCAAGATGTGCGTATCCCATACCAGGAGAAGCGCATGTTTGGTTTTGTCACCTTCGCCTACCAAAAGACAGTGAAGCTAATTCTT

upper sequence: GLYMA09G35980.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G819035_T01 (Zea mays), 3'ss of exon 3
gttattattgcttaggtttagctgtaactttagcttcgactgggatcattgtgcatagttggtcagcggcagaaatattaacttgagtttttaattctgttgttgaagCATTTATGGCCCAGTGCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGCTTTGTTACCTTTGTTTATCCAGAGACTGTGAAGCTTATTCTA
  |||   |||  |        ||| |     ||| | |           ||  | |   | |  |  ||   | |     || | | || | |       | || ||||| || || ||||| || |||||| | ||||| |||||||||||||| ||||| || || || ||||| || ||||||||||| |||||||| || || 
-gtatgcatgcacacacggtaatgtgat----gctccaatctttgcgtccgtagaaacccgtttggttgcgtgacttgaccctcgcgcttcttagcaatgcggtgtagCATCTACGGTCCAGTTCACGACGTGCGCATCCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTCTATCCAGAGACCGTGAAGCTCATCCTG

upper sequence: GLYMA09G35980.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G353762_T01 (Zea mays), 3'ss of exon 7
gttattattgcttaggtttagctgtaactttagcttcgactgggatcattgtgcatagttggtcagcggcagaaatattaacttgagtttttaattctgttgttga-agCATTTATGGCCCAGTGCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGCTTTGTTACCTTTGTTTATCCAGAGACTGTGAAGCTTATTCTA
||    |  ||  | |    ||  | | |    |  |  ||  | |||||  |  | |||   ||   || |    || |  |||       |    ||        ||||| | ||| || ||||| |||||| | |||||||||||||||||||| ||||| ||||| |  ||||| || ||| | ||||| ||||||   || || 
gtacccagagcacacgcc--gccattattggcacccctgctccgctcattccgtttcgttt-ccactagccgtccaataatgttgccccgccatcgatggaccgagcagCATGTTTGGGCCGGTGCAGGACGTGCGCATCCCATACCAGCAGAAGCGCATGTTCGGCTTCGCCACCTTCGTGTATGCCGAGACGGTGAAGGCCATACTG

upper sequence: GLYMA09G35980.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G003424_T01 (Zea mays), 3'ss of exon 2
gttattat-tgcttaggtttagctgtaactttagcttcgactgggatcattgtgcatagttggtcagcggcagaaatattaacttgagtttttaattctgttgttgaagCATTTATGGCCCAGTGCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGCTTTGTTACCTTTGTTTATCCAGAGACTGTGAAGCTTATTCTA
||    ||   |  | | | |  ||   ||  |   |   ||    |       | |  |||||  || |     |   |  |     || ||     ||  || | ||||| || || ||||| || |||||| | ||||| |||||||||||||| ||||| || || || ||||| || || |||||||| |||||||| || || 
gtatgcatgcacacacggtaatgtgatgctccaatctttgcttccgtagaaccccgt--ttggttggctgacttgaccatcgcgcttcttgttggcaatgcggt-gcagCATCTACGGTCCAGTTCACGACGTGCGCATCCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTCTACCCAGAGACGGTGAAGCTCATCCTG

upper sequence: GLYMA09G35980.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G166062_T01 (Zea mays), 3'ss of exon 7
gttattattgcttaggtttagctgtaactttagcttcgactgggatcattgtgcatagttggtcagcggcagaaatattaacttgagtttttaattctgt-tgttgaagCATTTATGGCCCAGTGCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGCTTTGTTACCTTTGTTTATCCAGAGACTGTGAAGCTTATTCTA
       |||| |   ||  || |  |     ||     ||  | || ||  |  | |||   ||   ||      || |  |||       |    |||     | ||||| |  || || ||||| ||| || | |||||||||||||||||||| ||||| ||||| || |||||  | ||| | ||||| ||||||   || || 
-------ttgccttttttccgccgccaaacccgccctt-ctccgctcgttccgtttcgttt-ccactagccatccaataatgttgccccaccatcgatgtaccgagcagCATATTCGGGCCGGTGCAGGACATGCGCATCCCATACCAGCAGAAGCGCATGTTCGGCTTCGTCACCTTCATGTATGCCGAGACGGTGAAGGCCATCCTG

upper sequence: GLYMA09G35980.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0158g00370.t01 (Vitis vinifera), 3'ss of exon 3
gttattattgc--ttaggtttagctgtaactttagcttcgactgggatcattgtgcatagttg---gtcagcggcagaaatattaacttgagtttttaattctgttgttgaagCATTTATGGCCCAGTGCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGCTTTGTTACCTTTGTTTATCCAGAGACTGTGAAGCTTATTCTA
||| | |   |  ||    | |  |||  |||  | || |         ||||||   |||||   |    |||  |   | | ||     |||||   || ||||||||||||||||  || ||||| ||||| |||||||||||||| ||||||||| | ||||| || ||||| ||||| |||||||||||||| |||||||| ||| | 
gttttgaccacaattttcatgaattgtttctt-ggttttgtgcaattgaattgtgggaagttgagagctttcggttggtttctaaatcgctgtttt--gttttgttgttgaagCATTTTCGGTCCAGTTCAAGATGTGAGGATCCCATATCAGCAGAAGAGGATGTTCGGGTTTGTAACCTTCGTTTATCCAGAGACAGTGAAGCTCATTTTG

upper sequence: GLYMA09G35980.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S31_251V6.1 (Physcomitrella patens), 3'ss of exon 2
gttattattgcttaggtttagctgtaactttagcttcgactgggatcattgtgcatagttggtcagcggcagaaatattaacttgagtttttaattctgttgttgaagCATTTATGGCCCAGTGCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGCTTTGTTACCTTTGTTTATCCAGAGACTGTGAAGCTTATTCTA
|| |    ||     |  |  |||||  ||| || |  | ||  ||  |||   ||  |        | |  |   |||  ||     |||        |   || ||   ||| || ||||| ||||| ||  ||||||| || ||||||||||| |||||||| ||||| || ||||| ||| |||| ||||| ||    ||| | 
gtcaacggtgac--agccttactgtactttttgcat--attgaaatacttggagatcctc---ttatgaccaatcaattttctca---tttgtgcgggatgaatgcagGGCTTACGGTCCAGTCCAAGATGTTCGGATCCCCTATCAGCAGAAGCGGATGTTTGGTTTTGTGACTTTTGTATATTCAGAAACTGTTAAAGCAATTTTG

upper sequence: GLYMA09G35980.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ13340 (Selaginella moellendorffii), 3'ss of exon 3
gttattattgcttaggtttagctgtaactttagcttcgactgggatcattgtgcatagttggtcagcggcagaaatattaacttgagtttttaattctgttgttgaagCATTTATGGCCCAGTGCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGCTTTGTTACCTTTGTTTATCCAGAGACTGTGAAGCTTATTCTA
                                     |  || |||      | | |     |||  |    |   || |   |     |||  ||   ||| | |    |||  ||||| || |||||||||||||| || |||||||| ||| ||||||||||||| || ||||||   ||  | ||||| ||   |   || || 
-------------------------------------gtatgtgattgagaagaaaatcgcatcattgttttattcatgattct-----tttcttttcattgctcagTTCTTTCGGGCCC-GTACAAGACGTGAGGATTCCTTACCAGCAAAAGAGAATGTTTGGCTTCGTCACCTTTACGTACTCGGAGACCGTACGGACAATCCTG

upper sequence: GLYMA09G35980.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ24679 (Selaginella moellendorffii), 3'ss of exon 3
gttattattgcttaggtttagctgtaactttagcttcgactgggatcattgtgcatagttggtcagcggcagaaatattaac-ttgagtttttaattctgtt-gttga--agCATTTATGGCCCAGTGCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGCTTTGTTACCTTTGTTTATCCAGAGACTGTGAAGCTTATTCTA
                                                  ||   |  |||   ||        ||   |   ||  |||| |  |||| || ||||   ||   ||  || || || |||||||||||||| || |||||||| ||| ||||||||||||| || ||||||   ||  | ||||| ||   |   || || 
--------------------------------------------------gtatgtgattgagaagaaaatcgcatggcattgttttgtttatggttcttttcgttgctcagTTCTTTCGGGCCCGTACAAGACGTGAGGATTCCTTACCAGCAAAAGAGAATGTTTGGCTTCGTCACCTTTACGTACTCGGAGACCGTACGGACGATCCTG

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|193716366|gb|FK652454.1|FK652454
EST:     TTCCCAGCAGATAGCACTTTCAGAGAGGAAGATGTTTCAAACTACTTCAG                         CATTTATGGCCCAGTGCAAGACGTGAGGATACCCATACCAGCA
genomic: TTCCCAGCAGATAGCACTTTCAGAGAGGAAGATGTTTCAAACTACTTCAGgttattattg ... gttgttgaagCATTTATGGCCCAGTGCAAGACGTGAGGAT-CCCATACCAGCA
EST: gi|193576783|gb|FK537980.1|FK537980
EST:     GAGGAAGATGTTTCAAACTACTTCAG                         CATTTATGGCCCAGTACAAGACGTGAGGATCCCATACCAGCAGAAGCGAAT
genomic: GAGGAAGATGTTTCAAACTACTTCAGgttattattg ... gttgttgaagCATTTATGGCCCAGTGCAAGACGTGAGGATCCCATACCAGCAGAAGCGAAT
EST: gi|208102524|gb|GD900233.1|GD900233
EST:     TTCCCAGCAGATAGCACTTTCAGAGAGGAAGATGTTTCAAACTACTTCAG                         CATTTATGGCCCAGTGCAAGACGTGAGGATCCCATACCAGCAGAAGCGAAT
genomic: TTCCCAGCAGATAGCACTTTCAGAGAGGAAGATGTTTCAAACTACTTCAGgttattattg ... gttgttgaagCATTTATGGCCCAGTGCAAGACGTGAGGATCCCATACCAGCAGAAGCGAAT
EST: gi|17152898|gb|BM142831.1|BM142831
EST:     TTCCCAGCAGATAGCACTTTCAGAGAGGAAGATGTTTCAAACTACTTCAG                         CATTTATGGCCCAGTGCAAGACGTGAGGATCCCATACCAGCAGAAGCGAAT
genomic: TTCCCAGCAGATAGCACTTTCAGAGAGGAAGATGTTTCAAACTACTTCAGgttattattg ... gttgttgaagCATTTATGGCCCAGTGCAAGACGTGAGGATCCCATACCAGCAGAAGCGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catagttggtcagcggcagaaatattaacttgagtttttaattctgttgttgaagCATTTATGGCCCAGTGCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGCTTTGTTACCTTTGTTTATCCAGAGACTGTGAAGCTTATTCTA
                                         ttctgtt  CT-rich tract
                   aaatattaacttgagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttattattgcttaggtttagctgtaactttagcttcgactgggatcattgtgcatagttggtcagcggcagaaatattaacttgagtttttaattctgttgttgaagCATTTATGGCCCAGTGCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGCTTTGTTACCTTTGTTTATCCAGAGACTGTGAAGCTTATTCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC