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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAGGATTGTTGGTCTGCATCAAAACACCCAAATTGGATCAACTGATATAACTGACACATGGGAACCACTAGAAGAAGGCCTTCTTCCgtatggatttttgtttcttctatgctaccttatcaaatactaaatttctgtgtttgggagtgattcctttggttttgtgttgtacttgcccag

Basic information

species Glycine max
transcript GLYMA06G15380.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G15380.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os04g34940.1 (Oryza sativa), 5'ss of exon 3
AGAAGGATTGTTGGTCTGCATCAAAACACCCAAATTGGATCAACTGATATAACTGACACATGGGAACCACTAGAAGAAGGCCTTCTTCCgtatggatttt----tgtttcttctatgctaccttatcaaatactaaa----tttctgtgtttgggagtgattcctttggttttgtgttgtacttgcccag
||||||||||||||||| ||||| || |||   |||| |||||  || ||||||||||| ||||||||| | |||||||| |||    |||  ||||       | ||| ||| |||   |  |||| | |    ||     || ||||||||  | |||||  ||||  ||| || |            
AGAAGGATTGTTGGTCTCCATCAGAATACCTCTATTGAATCAATCGACATAACTGACACTTGGGAACCATTGGAAGAAGGGCTTAACACgtgaggatcacacaatcttttttccatgtacctgtatctattttggaaagggcttatgtgtttgata-tgattg-tttgtctttatgatag----------

upper sequence: GLYMA06G15380.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G050982_T01 (Zea mays), 5'ss of exon 4
AGAAGGATTGTTGGTCTGCATCAAAACACCCAAATTGGATCAACTGATATAACTGACACATGGGAACCACTAGAAGAAGGCCTTCTTCCgtatggatttttgtttcttctatgctaccttatcaaatactaaatttctgtgtttgggagtgattcctttggttttgtgttgtacttgcccag
|||||| |||  ||||| ||||| ||||     | || |||   |||||| || ||||||||||||||  | |||||||||||||| ||||| |||| ||         |||  | | | |   |  |  | |||     | |         ||||||                        
AGAAGGGTTGGAGGTCTTCATCAGAACAGTGCCACTGAATCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaaggatattc-------ttatattccttcaaacagaaggagattgaaacgct--aacacacttccttacacag------------------

upper sequence: GLYMA06G15380.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv07s0031g02040.t01 (Vitis vinifera), 5'ss of exon 5
AGAAGGATTGTTGGTCTGCATCAAAACACCCAAATTGGATCAACTGATATAACTGACACATGGGAACCACTAGAAGAAGGCCTTCTTCCgtatggattttt-gtttcttctatgctaccttatcaaatactaaatttctgtgtttgggagtgattcctttggttttgtgttgtacttgcccag
|||||||||||||| || ||||| |||||   |||||||||||| |||||||| || |  ||||| ||| ||||||| |||||||||||||||| |    | |  | ||   || | |   || |      ||| | || ||  |    |  | ||| ||  |||| | ||| |         
AGAAGGATTGTTGGACTTCATCAGAACACATCAATTGGATCAACCGATATAACGGATATGTGGGAGCCATTAGAAGATGGCCTTCTTCCgtatgaaacagtagactgtttgttgttgctaaattatgc---aaaatactatgaattcatgataatccattacttttcttttgcag--------

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|298190263|gb|HO032384.1|HO032384
EST:     TCAACTGATATAACTGACACATGGGAACCACTAGAAGAAGGCCTTCTTCC                         TTTGGAGACTACTCGCCATGTTTCAATGATCACAATTACCTTGTCAAAGAA
genomic: TCAACTGATATAACTGACACATGGGAACCACTAGAAGAAGGCCTTCTTCCgtatggattt ... acttgcccagTTTGGAGACTACTCGCCATGTTTCAATGATCACAATTACCTTGTCAAAGAA
EST: gi|254343935|gb|GR857691.1|GR857691
EST:     TCAACTGATATAACTGACACATGGGAACCACTAGAAGAAGGCCTTCTTCC                         TTTGGAGACTACTCGCCATGTTTCAATGATCACAATTACCTTGTCAAAGAA
genomic: TCAACTGATATAACTGACACATGGGAACCACTAGAAGAAGGCCTTCTTCCgtatggattt ... acttgcccagTTTGGAGACTACTCGCCATGTTTCAATGATCACAATTACCTTGTCAAAGAA
EST: gi|120534511|gb|EH262644.1|EH262644
EST:     TCAACTGATATAACTGACACATGGGAACCACTAGAAGAAGGCCTTCTTCC                         TTTGGAGACTACTCGCCATGTTTCAATGATCACAATTACCTTGTCAAAGAA
genomic: TCAACTGATATAACTGACACATGGGAACCACTAGAAGAAGGCCTTCTTCCgtatggattt ... acttgcccagTTTGGAGACTACTCGCCATGTTTCAATGATCACAATTACCTTGTCAAAGAA
EST: gi|298186819|gb|HO037452.1|HO037452
EST:     TCAACTGATATAACTGACACATGGGAACCACTAGAAGAAGGCCTTCTTCC                         TTTGGAGACTACTCGCCATGTTTCAATGATCACAATTACCTTGTCAAAGAA
genomic: TCAACTGATATAACTGACACATGGGAACCACTAGAAGAAGGCCTTCTTCCgtatggattt ... acttgcccagTTTGGAGACTACTCGCCATGTTTCAATGATCACAATTACCTTGTCAAAGAA
EST: gi|120534428|gb|EH262561.1|EH262561
EST:     TCAACTGATATAACTGACACATGGGAACCACTAGAAGAAGGCCTTCTTCC                         TTTGGAGACTACTCGCCATGTTTCAATGATCACAATTACCTTGTCAAAGAA
genomic: TCAACTGATATAACTGACACATGGGAACCACTAGAAGAAGGCCTTCTTCCgtatggattt ... acttgcccagTTTGGAGACTACTCGCCATGTTTCAATGATCACAATTACCTTGTCAAAGAA
EST: gi|120530869|gb|EH259002.1|EH259002
EST:     TCAACTGATATAACTGACACATGGGAACCACTAGAAGAAGGCCTTCTTCC                         TTTGGAGACTACTCGCCATGTTTCAATGATCACAATTACCTTGTCAAAGAA
genomic: TCAACTGATATAACTGACACATGGGAACCACTAGAAGAAGGCCTTCTTCCgtatggattt ... acttgcccagTTTGGAGACTACTCGCCATGTTTCAATGATCACAATTACCTTGTCAAAGAA
EST: gi|298175747|gb|HO018344.1|HO018344
EST:     TCAACTGATATAACTGACACATGGGAACCACTAGAAGAAGGCCTTCTTCC                         TTTGAAGACTACTCGCCATGTTTCAATGATCACAATTACCTTGTCAAAGAA
genomic: TCAACTGATATAACTGACACATGGGAACCACTAGAAGAAGGCCTTCTTCCgtatggattt ... acttgcccagTTTGGAGACTACTCGCCATGTTTCAATGATCACAATTACCTTGTCAAAGAA
EST: gi|298191598|gb|HO039077.1|HO039077
EST:     TCAACTGATATAACTGACACATGGGAACCACTAGAAGAAGGCCTTCTTCC                         TTTGGAGACTACTCGCCA
genomic: TCAACTGATATAACTGACACATGGGAACCACTAGAAGAAGGCCTTCTTCCgtatggattt ... acttgcccagTTTGGAGACTACTCGCCA
EST: gi|15337539|gb|BI498195.1|BI498195
EST:     TCAACTGATATAACTGACACATGGGAACCACTAGAAGAAGGCCTTCTTCC                         TTTGGAGACTACTCGCCATGTTTCAATGATCACAATTACCTTGTCAAAGAA
genomic: TCAACTGATATAACTGACACATGGGAACCACTAGAAGAAGGCCTTCTTCCgtatggattt ... acttgcccagTTTGGAGACTACTCGCCATGTTTCAATGATCACAATTACCTTGTCAAAGAA
EST: gi|298172713|gb|HO019753.1|HO019753
EST:     TCAACTGATATAACTGACACATGGGAACCACTAGAAGAAGGCCTTCTTCC                         TTTGGAGACTACTCGCCATGTTTCAATGATCACAATTACCTTGTCAAAGAA
genomic: TCAACTGATATAACTGACACATGGGAACCACTAGAAGAAGGCCTTCTTCCgtatggattt ... acttgcccagTTTGGAGACTACTCGCCATGTTTCAATGATCACAATTACCTTGTCAAAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAGGATTGTTGGTCTGCATCAAAACACCCAAATTGGATCAACTGATATAACTGACACATGGGAACCACTAGAAGAAGGCCTTCTTCCgtatggatttttgtttcttctatgctaccttatcaaatactaaatttctgtgtttgggagtgattcctttggttttgtgttgtacttgcccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG