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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctattatgtagaatttccatctctacattcagtcccaaagatttggtgcagactgcttatgctaattttcagtttcttttccttttactgataaatctagAGTACGATTCTGATGATAATCCACAAGAAGAGACAATCAAACCTATGGTGGATGGTGGGACTGAAGGTTTCAAGGGCCATGCTAGGGTTATCATGCCAGG

Basic information

species Glycine max
transcript GLYMA07G38770.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G38770.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g16540.1 (Oryza sativa), 3'ss of exon 3
ctattatgtagaatttccatctctacattcagtcccaaagatttggtgcagactgcttatgctaattttcagtttcttttcct----tttactgataaatctagAGTACGATTCTGATGATAATCCACAAGAAGAGACAATCAAACCTATGGTGGATGGTGGGACTGAAGGTTTCAAGGGCCATGCTAGGGTTATCATGCCAGG
   | |||   ||     |  | ||   | | || | | |   ||   || |||   |||  | | |       | |  | ||    | || |   || |  |||||| || || ||||| || |||      |||||  | ||||||||||| ||||||||||||||||||||||| || |||||||| || ||||| || ||
---tgatgcccaaacag-aggtatattgttattcactatgtactgtaccaaactcagtatattcagtgcagtgctatagtgctaatatgtaattgcaattgcagAGTATGACTCAGATGACAAGCCAATCCCTGAGACGCTTAAACCTATGGTCGATGGTGGGACTGAAGGTTTCAAAGGTCATGCTAGAGTCATCATACCTGG

upper sequence: GLYMA07G38770.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G19180.1 (Arabidopsis thaliana), 3'ss of exon 3
ctattatgtagaatttccatctctacattcagtcccaaagatttggtgcagactgcttatgctaattttcagtttcttttccttttactgataaatctagAGTACGATTCTGATGATAATCCACAAGAAGAGACAATCAAACCTATGGTGGATGGTGGGACTGAAGGTTTCAAGGGCCATGCTAGGGTTATCATGCCAGG
             | | ||  |     || |  |   || | ||  | |   | |||| |   | || || ||  ||  |  | |   ||  |||| |||||||  ||   ||||||| |||  ||  ||| || ||||| || ||||| ||||| || ||||||||||||||||| |||||||| |||||| |||| ||
------------gtatgcaaattc---tttaacctttaatactttatccct-cggctttttgaagttctctgt--ctgataatgtgcttgtgaaatgtagAGTATAATGAAGATGATACTCCGAAAAGAGAAACGATCAAGCCAATGGTAGATGGGGGAACTGAAGGTTTCAAGGGTCATGCTAGAGTTATCTTGCCTGG

upper sequence: GLYMA07G38770.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0020g02820.t01 (Vitis vinifera), 3'ss of exon 3
-ctattatgtagaatttccatctctacatt-cagtcccaaagatttggtgcagactgcttatgctaattttcagtttcttttccttttactgataaatctagAGTACGATTCTGATGATAATCCACAAGAAGAGACAATCAAACCTATGGTGGATGGTGGGACTGAAGGTTTCAAGGGCCATGCTAGGGTTATCATGCCAGG
 || ||  | |  |  |   | ||    |   |||    |   |||  | ||  |||| |   || || |  |||    |     | |  |   |||| ||||||| |||||||||||||| ||||  ||||| ||||| |||||||||||||||||||| |||||||| |||||||| ||||| ||||||||||| |||||
gcttttgagaatcaaatgtgtgtcattttcatagtgagtagatttttctacattctgcctcatcttatct--agtcgtctcattgtgtttttggaaatttagAGTATGATTCTGATGATAAACCACTGGAAGAAACAATTAAACCTATGGTGGATGGTGGAACTGAAGGCTTCAAGGGTCATGCCAGGGTTATCATTCCAGG

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|298187660|gb|HO034809.1|HO034809
EST:     TTCCATTGAGGCCCGCAGTTATATCAATACTGTTGCCTGCAGTTTTCTAG                         AGTACGATTCTGATGA
genomic: TTCCATTGAGGCCCGCAGTTATATCAATACTGTTGCCTGCAGTTTTCTAGgtctgttttc ... ataaatctagAGTACGATTCTGATGA
EST: gi|254322096|gb|GR837510.1|GR837510
EST:     TTCCATTGAGGCCCGCAGTTATATCAATACTGTTGCCTGCAGTTTTCTAG                         AGTACGATTCTGATGATAATCCACAAGAAGAGACAATCAAACCTATGGTGG
genomic: TTCCATTGAGGCCCGCAGTTATATCAATACTGTTGCCTGCAGTTTTCTAGgtctgttttc ... ataaatctagAGTACGATTCTGATGATAATCCACAAGAAGAGACAATCAAACCTATGGTGG
EST: gi|17024070|gb|BM095104.1|BM095104
EST:     TTCCATTGAGGCCCGCAGTTATATCAATACTGTTGCCTGCAGTTTTCTAG                         AGTACGATTCTGATGATAA
genomic: TTCCATTGAGGCCCGCAGTTATATCAATACTGTTGCCTGCAGTTTTCTAGgtctgttttc ... ataaatctagAGTACGATTCTGATGATAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcagactgcttatgctaattttcagtttcttttccttttactgataaatctagAGTACGATTCTGATGATAATCCACAAGAAGAGACAATCAAACCTATGGTGGATGGTGGGACTGAAGGTTTCAAGGGCCATGCTAGGGTTATCATGCCAGG
                                        tactgat  putative branch site (score: 2)
                                     ttttactgataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctattatgtagaatttccatctctacattcagtcccaaagatttggtgcagactgcttatgctaattttcagtttcttttccttttactgataaatctagAGTACGATTCTGATGATAATCCACAAGAAGAGACAATCAAACCTATGGTGGATGGTGGGACTGAAGGTTTCAAGGGCCATGCTAGGGTTATCATGCCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - tatgtag
- - - - - - - - ccatctc
- - - - - - - - - - - - - - -cagtccc
- - - - - - - - - - - - - - - - - - - - - - - tgcagac
- - - - - - - - - - - - - - - - - - - - - - - - - - - gcttatg