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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagtcctctgtttctgtttttcttttgtttcttctttgggtaatttttatttttcatttatctgtggtttgtttttttttttttttttttggctgatattgtggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTGTTTGGTGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAAAG

Basic information

species Glycine max
transcript GLYMA04G11160.4
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G11160.4 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g43070.1 (Oryza sativa), 3'ss of exon 1
gtacagtcctctgtttctgtttttcttttgtttcttctttgggtaatttttatttttcatttatctgtggtttgtttttttttttttttttttggctgatattgtggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTGTTTGGTGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAAAG
     |||| | |       || ||    ||   | |  | | | |         | |     |   | |  || ||||||||||||||||  |  || |            ||||||||||| | |||||| ||||||||||| || || ||||| ||||| || ||| |||||||| | || || ||
-----gtcccccgccgtc--ttctcccgagtccttgccattgctcagcgaaggcgtgctcgcttgctttgcctgattttttttttttttttgggtttggtg-----------cagCCGTCGGAGGCGATCAGTAAGGTGGTGTTCGGCGGGCAGGTGACCGAGGAGGAGTTCGAGAGCCTCAACAAGAG

upper sequence: GLYMA04G11160.4 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G107473_T01 (Zea mays), 3'ss of exon 1
----gtacagt-cctctgtttctgtttttcttttgtttcttctttgggtaatt---tttatttttcatttatctgtggtttgtttttttttttttttttttgg-ctgatattgtggaatttc----agCCGTCGGATGGGATCAGGAAGGTGGTGTTTGGTGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAAAG
       |||  || |  | |  | | | ||  |  | | ||  || |||  |   | |   |  |  |   | |  |  ||    ||||  ||     |    ||   || |     || |    |||||||||| |  ||||||||||||||||| || |||||||||||||| || |||| ||| ||| | |  || ||
gtaacagcagcacccccatcttcgctctcctcctcctccctccatgcgtatctgcatcttcctccccctcccccgatgcgtgccgcttttgattgaccatcaaactcgcatcgctccgttgcgcgcagCCGTCGGAGGCTATCAGGAAGGTGGTGTTCGGGGGTCAGGTCACCGAGGAGGAGGCCGACAGCCTCACCAAGAG

upper sequence: GLYMA04G11160.4 (Glycine max), 3'ss of exon 2
lower sequence: AT1G78150.2 (Arabidopsis thaliana), 3'ss of exon 2
gtacagtcctctgtttctgtttttcttttgtttcttctttgggtaatttttatttttcatttatctgtggtttgtttttttttttttttttttggctgatattgtggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTGTTTGGTGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAAAG
                  ||  ||     |||||    ||    || ||| | |||   |||        | || |  |  | ||| |||      || | |  ||   ||  |||| ||||||||||| || || ||||||||||||||||| |||||||||||||| || |||||||| ||    ||
------------------gtacttgcaccgtttcgaaattcatgaaatttcactttgattttgatca--atctggtaatagtatttgtttcaattttggtttaatgtgtttgtagCCATCGGATGGGATTAGCAAAGTGGTGTTTGGTGGTCAAGTCACCGATGAAGAAGTTGAGAGCTTGAACCGCAG

upper sequence: GLYMA04G11160.4 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g05480.t01 (Vitis vinifera), 3'ss of exon 1
gtacagtcctctgtttctgtttttcttttgtttcttctttgggtaatttttatttttcatttatctgtggtttgtttttttttttttttttttggctgatattgtggaatttca-gCCGTCGGATGGGATCAGGAAGGTGGTGTTTGGTGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAAAG
                       |   |  ||| | |   |  |  |  |    ||  |  | | | |  ||| ||||  |  | |  |||  || | | |||      ||  | ||| || ||||||||||| |||||||||||||| || ||||| || ||||||||||  |||   ||    |||||
----------------------gtacctcatttttccccggactggtaatggagttgtacgtttttttttttttttttgatcgtgtaatttagggtttaaatttcatttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAAGAGGCGGAGGCTTTGTCGAAAAG

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|193527753|gb|FK485943.1|FK485943
EST:     CCGTTCGTTCTCACCAG                         CCGTCGGATGGGATCAGGAAGGTGGTGTTTGGTGGTCAGGTCACCGATGAA
genomic: CCGTTCGTTCTCACCAGgtacagtcct ... ggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTGTTTGGTGGTCAGGTCACCGATGAA
EST: gi|18848808|gb|BM567920.1|BM567920
EST:     CCATTTCTGATTCCCCAGCTCCTCCTTCCTCCGCCGTTCGTTCTCACCAG                         CCGTCGGATGGGATCAGGAAGGTGGTGTTTGGTGGTCAGGTCACCGATGAA
genomic: CCATTTCTGATTCCCCAGCTCCTCCTTCCTCCGCCGTTCGTTCTCACCAGgtacagtcct ... ggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTGTTTGGTGGTCAGGTCACCGATGAA
EST: gi|209713150|gb|BW681684.1|BW681684
EST:     CCATTTCTGATTCCCCAGCTCCTCCTTCCTCCGCCGTTCGTTCTCACCAG                         CCGTCGGATGGGATCAGGAAGGTGGTGTTTGGTGGTCAGGTCACCGATGAA
genomic: CCATTTCTGATTCCCCAGCTCCTCCTTCCTCCGCCGTTCGTTCTCACCAGgtacagtcct ... ggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTGTTTGGTGGTCAGGTCACCGATGAA
EST: gi|193677699|gb|FK614925.1|FK614925
EST:     CCATTTCTGATTCCCCAGCTCCTCCTTCCTCCGCCGTTCGTTCTCACCAG                         CCGTCGGATGGGATCAGGAAGGTGGTGTTTGGTGGTCAGGTCACCGATGAA
genomic: CCATTTCTGATTCCCCAGCTCCTCCTTCCTCCGCCGTTCGTTCTCACCAGgtacagtcct ... ggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTGTTTGGTGGTCAGGTCACCGATGAA
EST: gi|151400095|gb|EV269909.1|EV269909
EST:     CCATTTCTGATTCCCCAGCTCCTCCTTCCTCCGCCGTTCGTTCTCACCAG                         CCGTCGGATGGGATCAGGAAGGTGGCGTTTGGTGGTCAGGTCACCGATGAA
genomic: CCATTTCTGATTCCCCAGCTCCTCCTTCCTCCGCCGTTCGTTCTCACCAGgtacagtcct ... ggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTGTTTGGTGGTCAGGTCACCGATGAA
EST: gi|192324392|gb|FK015743.1|FK015743
EST:     CCATTTCTGATTCCCCAGCTCCTCCTTCCTCCGCCGTTCGTTCTCACCAG                         CCGTCGGATGGGATCAGGAAGGTGGTGTTTGGTGGTCAGGTCACCGATGAA
genomic: CCATTTCTGATTCCCCAGCTCCTCCTTCCTCCGCCGTTCGTTCTCACCAGgtacagtcct ... ggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTGTTTGGTGGTCAGGTCACCGATGAA
EST: gi|17022986|gb|BM094020.1|BM094020
EST:     CCATTTCTGATTCCCCAGCTCCTCCTTCCTCCGCCGTTCGTTCTCACCAG                         CCGTCGGATGGGATCAGGAAGGTGGTGTTTGGTGGTCAGGTCACCGATGAA
genomic: CCATTTCTGATTCCCCAGCTCCTCCTTCCTCCGCCGTTCGTTCTCACCAGgtacagtcct ... ggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTGTTTGGTGGTCAGGTCACCGATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatctgtggtttgtttttttttttttttttttggctgatattgtggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTGTTTGGTGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAAAG
                                 ggctgat  putative branch site (score: 4)
              tttttttttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacagtcctctgtttctgtttttcttttgtttcttctttgggtaatttttatttttcatttatctgtggtttgtttttttttttttttttttggctgatattgtggaatttcagCCGTCGGATGGGATCAGGAAGGTGGTGTTTGGTGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT