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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttcttttaatatctggaccagtatctattatacattttcatgcacatttgtagggttgtggtccagcgtatgataatacaagtgtattgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTATG

Basic information

species Glycine max
transcript GLYMA08G19970.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G19970.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os03g45770.2 (Oryza sativa), 3'ss of exon 10
gttcttttaatatctggaccagtatctattatacattttcatgcacatttgtagggttgt--ggtccagcgtatgataataca---agtgtattgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTATG
   | ||||| || || | |  | || |  || |||| |||      ||   | |  |      | | |  | |   |||  |   | | |  |||   |||||||||  | ||| | ||||||||| ||||||| || ||||| || |||||||||||| |||| |||||||| || |||||||| ||  | ||||
---catttaacatttgcaac--tttcaagcatgcattatcagaattgttgtcatgcatagcaaattcggtctgtctgaatttactgaattttgtgtcctttgcagTGTGAGGACATCTATATCAATGCAGTTCTTCCCGCGCTTTTTCTTGCTGTATTTCTTGGTTTTCCACATTTACTTCTTCTCGTACACATATG

upper sequence: GLYMA08G19970.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM5G814310_T02 (Zea mays), 3'ss of exon 2
----gttcttttaatatctggaccagtatctattatacattttcatgcacatttgtagggttgtggtccagcgtatgataatacaagtgtattgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTATG--------
    ||    | |||   |  | ||| |   ||  |   |    | | | ||||  | | |  |  | |     ||  | || |     | || |   || |||||| || ||| | ||||| ||| |||||||||| |||||||| |||||||||||  |||| ||||| || || |||||||| ||| | ||||        
gcgggtagcatgaatgcatctatcagaaatgatcttgtgtagg-acgaa-attttcaagctaatcattct-taaatacttatccttaaatctt-tgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATGGTATGTGT

upper sequence: GLYMA08G19970.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM5G814310_T01 (Zea mays), 3'ss of exon 2
----gttcttttaatatctggaccagtatctattatacattttcatgcacatttgtagggttgtggtccagcgtatgataatacaagtgtattgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTATG
    ||    | |||   |  | ||| |   ||  |   |    | | | ||||  | | |  |  | |     ||  | || |     | || |   || |||||| || ||| | ||||| ||| |||||||||| |||||||| |||||||||||  |||| ||||| || || |||||||| ||| | ||||
gcgggtagcatgaatgcatctatcagaaatgatcttgtgtagg-acgaa-attttcaagctaatcattct-taaatacttatccttaaatctt-tgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATG

upper sequence: GLYMA08G19970.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G60995.1 (Arabidopsis thaliana), 3'ss of exon 12
-------------------------------gttcttttaatatctggaccagtatct-attata----cattttcatgc--acatttgtagggttgtggtccagcgta-tgataatacaagtgtatt----gtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTATG
                               ||  ||  | |||   |  |  |  ||  | |||    || |  || |   |  ||| |   || |  || ||  | | | |||| | |    |||      ||  |||||||||| | ||||||||||| ||||||||||| || || ||||| |||||||| ||| |||| ||||| || ||||||||||| ||||| ||||
gttttggtctcctcttttgcctcagtcacctgtatttccactatgaagctcttttgctcgtgataatctcactgccaagttaaagttttttttgtagctgttcaatggaataataacaaactcttatcctccatatattgcagTGTCAGGACACCAATATCGATGAAGTTCTTCCCGCGTTTCTTCTTGCTGTACTTCTTGGTGTTCCATATTTATTTCTTCTCATATGCATATG

upper sequence: GLYMA08G19970.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S96_202V6.1 (Physcomitrella patens), 3'ss of exon 12
---gttcttttaatatctggaccagtatctattatacattttcatgcacatttgtagggttgtggtccagcgtatgataatacaagtgtattgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTATG
    || |||   ||   ||     ||| |  | |  | ||  | ||    ||  | || | | |||  |||      |      ||   |   |  |||||| ||  | || ||  |||| ||| |||||||||||||||||||||| || |||||| |||  |||||||| || |||||||||||| | || |
gaatttttttctgtaagcggttgtttatttcatttggaattataagcttcctttgacggatattgtcacgcg---agcaccctttgtacttgccattttgcagCGTGAGGACGCCCCTATCGATGCAGTTCTTTCCTCGCTTCTTTTTTCTCTATTTCATGGCTTTCCACATTTACTTCTTCTCTTATACCTACG

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|57575248|gb|CX548223.1|CX548223
EST:     TTCATGGTCTTGATTCTTGTCTGGTTGTGTGAACTTTTTACTCTCATTAG                         TGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTA
genomic: TTCATGGTCTTGATTCTTGTCTGGTTGTGTGAACTTTTTACTCTCATTAGgtctgtttct ... taacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTA
EST: gi|7589379|gb|AW705154.1|AW705154
EST:     TTCATGGTCTTGATTCTTGTCTGGTTGTGTGAACTTTTTACTCTCATTAG                         TGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTA
genomic: TTCATGGTCTTGATTCTTGTCTGGTTGTGTGAACTTTTTACTCTCATTAGgtctgtttct ... taacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTA
EST: gi|5606329|gb|AI900427.1|AI900427
EST:     TTCATGGTCTTGATTCTTGTCTGGTTGTGTGAACTTTTTACTCTCATTAG                         TGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTNTGCTGTA
genomic: TTCATGGTCTTGATTCTTGTCTGGTTGTGTGAACTTTTTACTCTCATTAGgtctgtttct ... taacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTA
EST: gi|58023297|gb|CX710038.1|CX710038
EST:     TTCATGGTCTTGATTCTTGTCTGGTTGTGTGAACTTTTTACTCTCATTAG                         TGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTA
genomic: TTCATGGTCTTGATTCTTGTCTGGTTGTGTGAACTTTTTACTCTCATTAGgtctgtttct ... taacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttgtagggttgtggtccagcgtatgataatacaagtgtattgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTATG
                                          ttgtaac  putative branch site (score: 2)
                        tatgataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcttttaatatctggaccagtatctattatacattttcatgcacatttgtagggttgtggtccagcgtatgataatacaagtgtattgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTATG

- - - - - - - - - - - - - - - - - - - -catgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - ggttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caagtgt