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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgactacacttcttgaactttccaatcatcttaagcacatgcaccagcattttgaatgccatgatttccttatgaattaccacataccaactcactatttctttggtttgctatacagCAAGTATACATGTACTTCCGCGGCAGTGGGAAGGCCGCTGAGATGAAACGGGAGGCCGCAAGGGGAGCACTGAGGGCTGCAATATGATTCATCAGTCTTG

Basic information

species Glycine max
transcript GLYMA13G25460.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G25460.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 11
gtttgactacacttcttgaactttccaatcatcttaagcacat-gcaccagcattttgaatgccatgatttccttatgaattaccacataccaactcact-atttctttggtttgctatacagCAAGTATACATGTACTTCCGCGGCAGTGGGAAGGCCGCTGAGATGAAACGGGAGGCCGCAAGGGGAGCACTGAGGGCTGCAATATGATTCATCAGTCTTG
                        || |  || ||   |   | |||  |  ||||    ||| ||| | || | ||    | |          |   || |  |     |||||  || ||||||||||||||||| ||||| || ||||||||||| |||||||||||||| ||||| ||  | || ||  ||||  | ||  | ||||  | | |  | |
-----------------------ccctaagattttgttcttgttgcaataaaatttccgctgcaatgctgtcttcattttctcctgggagatgtcattctgaacttggccgtttgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGTGAGGCAGCTCGTGGTGCTATGAGATCGGCCTTTTGATAGAGCTGCTTCG

upper sequence: GLYMA13G25460.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os05g42330.1 (Oryza sativa), 3'ss of exon 11
gtttgactacacttcttgaactttccaatcatcttaagcacatgcaccagcattttgaatgccatgatttccttatgaattaccacataccaactcactatttctttggtttgctatacagCAAGTATACATGTACTTCCGCGGCAGTGGGAAGGCCGCTGAGATGAAACGGGAGGCCGCAAGGGGAGCACTGAGGGCTGCAATATGATTCATCA-GTCTTG
          |  |     |         |||  | | || |     ||    |||    | ||   |||| || |  || |  ||         || |  ||  |   |   | || ||||||||||||||||||||||| || ||||| || ||||| ||||||||||| ||||| ||| | || || |||||  | ||| | ||||  | || | ||| 
----------aggttcaacatagcatggacattctta-catacatttcaatcgtttcttagtcaaattttcattttagatcatgac---------cattgattgctcactcaac-atgcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCCGCAGAGATGAAACGTGAGGCGGCACGTGGTGCTCTGAGCTCCGCATTCTGATGAAACATGCCTT-

upper sequence: GLYMA13G25460.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 12
-------------------------------------------------------gtttgactacacttcttgaactttccaatcatcttaagcacatgcacc-----agcattttga-atgccatg--------atttccttatgaatta-----ccacata--ccaactcactatttctttggtttgcta-tacagCAAGTATACATGTACTTCCGCGGCAGTGGGAAGGCCGCTGAGATGAAACGGGAGGCCGCAAGGGGAGCACTGAGGGCTGCAATATGATTCATCAGTCTTG-
                                                         ||| | | | ||| |  |  |   ||| |   ||  || |||   |     ||  || | | ||   | |        || |  ||||||| ||      ||  ||  | | || |    || |    ||||  | | |||||||| |||||||||||||| || ||||| || || ||||||||||| || || ||  | ||||| ||  || |||| ||  | | ||| |||||    | 
gtcagtcctgcgaataacaaatactccctccgtttcatattataagactttctagcattgcccata-ttcatatagatgttaataaatctagacatatgtgtctagaaagtcttataatataaaacggagaaagtatgtttttatgaaataaattctcaagtagtctatctgagccgttttgacatttgtgaatgcagCAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGTGATGCAACTAGGGGTGCTATGCGGGCAGCTTTTTAATT-ATCAGAAAAGA

upper sequence: GLYMA13G25460.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G169773_T01 (Zea mays), 3'ss of exon 10
-------------------------gtttgactacacttcttgaactttccaatcatcttaagca-catg-caccagcattttgaatgccatgatttccttatgaattaccac-ataccaactcactatttctttggtttgctata---------------cagCAAGTATACATGTACTTCCGCGGCAGTGGGAAGGCCGCTGAGATGAAACGGGAGGCCGCAAGGGGAGCACTGAGGGCTGCAATATGATTCATCAGTCTTG
                          | |  ||| | ||||      |    ||  || | |||| ||||         | |       ||| || ||  | | | || | |  || | |    |    |  ||||   |  |||                ||||||||||||||||||||||| || ||||| || || || |||||||| || ||||| ||  | || ||  |||||  |||  | ||||  | |   || |
gtgggtatcatgtttttaccttttgctgtccctagaattctgatgtgtagggatattcattagcaacatggtgtttctgtctcatgcatcataatctctctttaagtttcaattattctagaagagagctgttttgagatattattgttctgaacttgtttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGAGAGGCGGCCCGTGGTGCTATGAGGAATGCCTTTTGATAGAGCGACCTAG

upper sequence: GLYMA13G25460.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 12
gtttgactacacttcttgaactttccaatcatcttaagcacatgcaccagcattttgaatgccatgatttccttatgaattaccacatacca-actcactatttctttggtttgctatacagCAAGTATACATGTACTTCCGCGGCAGTGGGAAGGCCGCTGAGATGAAACGGGAGGCCGCAAGGGGAGCACTGAGGGCTGCAATATGATTCATCAGTCTTG
                                     |    |   | |  ||      | | |   || |   |  || | |    |  || |||       | |||||   ||  | |||||||| |||||||||||||| || ||||| ||||| || |||||||| || || ||  | ||||| ||| |||| || ||| | | | |     ||  | 
-------------------------------------gtcagttttctattatcaaccgttctaattttcctgaaccaacttcagtgtgacatacttgagccctttttggaccgc-gtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGTGATGCGACGAGGGGTGCAATGAGAGCCGCATTTTAAGTGTGGTGTGGTA

upper sequence: GLYMA13G25460.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 12
gtttgactacacttcttgaactttccaatcatcttaagcacatgcaccagcattttgaatgccatgatttccttatgaattaccacataccaactcactat-ttctttggtttgctatacagCAAGTATACATGTACTTCCGCGGCAGTGGGAAGGCCGCTGAGATGAAACGGGAGGCCGCAAGGGGAGCACTGAGGGCTGCAATATGATTCATCAGTCTTG
||   ||| | |||    |  || | ||| |||      |      | | |  |   |||   ||||       || |   | | | |    |||   | | || |||    || | | ||||||||||| ||||||||||| |||||||| || || ||||||||||| || || |||||||| |||||  ||||||||||| | | |  |  || |    
gtccaacttctctttccca--ttcctaataatcacggaaagcatagctacctctgctaataggatga-------atcatgcagctcttgttcactgtttctgttgtttcacctggtttgcagCAAGTATATATGTACTTCCGAGGCAGTGGCAAAGCAGCTGAGATGAAGCGTGAAGCCGCAAGAGGAGCCATGAGGGCTGCATTGTAAGGCTGCAATTCCC

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|7638999|gb|AW733331.1|AW733331
EST:     CTGCGTTGAAACTTTGATCAGCATTTGGGTTATTCAG                         CAAGTATACATGTACTTCCGCGGCAGTGGGAAGGCCGCTGAGATGAAACGG
genomic: CTGCGTTGAAACTTTGATCAGCATTTGGGTTATTCAGgtttgactac ... tgctatacagCAAGTATACATGTACTTCCGCGGCAGTGGGAAGGCCGCTGAGATGAAACGG
EST: gi|7589230|gb|AW705008.1|AW705008
EST:     GATTTGGATTGTTCTGCGTTGAAACTTTGATCAGCATTTGGGTTATTCAG                         CAAGTATACATGTACTTCCGCGGCAGTGGGAAGGCCGCTGAGATGAAACGG
genomic: GATTTGGATTGTTCTGCGTTGAAACTTTGATCAGCATTTGGGTTATTCAGgtttgactac ... tgctatacagCAAGTATACATGTACTTCCGCGGCAGTGGGAAGGCCGCTGAGATGAAACGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttccttatgaattaccacataccaactcactatttctttggtttgctatacagCAAGTATACATGTACTTCCGCGGCAGTGGGAAGGCCGCTGAGATGAAACGGGAGGCCGCAAGGGGAGCACTGAGGGCTGCAATATGATTCATCAGTCTTG
                         aactcac  putative branch site (score: 2)
      ttatgaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgactacacttcttgaactttccaatcatcttaagcacatgcaccagcattttgaatgccatgatttccttatgaattaccacataccaactcactatttctttggtttgctatacagCAAGTATACATGTACTTCCGCGGCAGTGGGAAGGCCGCTGAGATGAAACGGGAGGCCGCAAGGGGAGCACTGAGGGCTGCAATATGATTCATCAGTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA