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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttccctcctcctatatactattagaggtcttggttgtggctgaccttgatcctctttcctaacatttactgatatttctggccatcttttgagattgcagAAAACAAACATTATTCGAGATTATCTGGAAGACATCAATGAGATCCCCAAGTCACGCATGTTTTGGCCACGACAGATTTGGAGTAAATATGTTAACAAAC

Basic information

species Glycine max
transcript GLYMA11G11960.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G11960.3 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g10130.1 (Oryza sativa), 3'ss of exon 6
----------------------------------ttccctcctcctatatactattagag-------gtcttggttgtgg-ctgaccttgatcctctttcctaacatttactgatatttctggccatcttttgagattgcagAAAACAAACATTATTCGAGATTATCTGGAAGACATCAATGAGATCCCCAAGTCACGCATGTTTTGGCCACGACAGATTTGGAGTAAATATGTTAACAAAC
                                  ||    | | ||  |||| || ||||         ||||  ||    || |||||| |      ||      | |    | |||| |  |  | |      ||||||||||   || |||| ||| ||||| ||||| ||||| |||||||| || || ||||||||||| ||||||||| | || ||||||||||||||| ||||||
gtatattgataattattctagtctggtgtttggcttttgacttgctgaatacaatcagagcatcctcaccttgtctggaaactcaccttgttggcaactcaccttgtctggaaacattttttacagtttaaatctattgcagAAAGTCAATATTACTCGGGATTACCTGGAGGACATAAATGAGATACCAAAATCACGCATGTTCTGGCCACGAGAAATATGGAGTAAATATGTTGACAAAC

upper sequence: GLYMA11G11960.3 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g59040.1 (Oryza sativa), 3'ss of exon 6
ttccctcctcctatatactattagaggtcttggttgtg-gctgaccttgatcctctttcctaacatttactgatatttctggccatcttttgagattgcagAAAACAAACATTATTCGAGATTATCTGGAAGACATCAATGAGATCCCCAAGTCACGCATGTTTTGGCCACGACAGATTTGGAGTAAATATGTTAACAAAC
     |  |  |  ||  | ||  |    |  ||| || ||       | | ||  ||  |   | | ||  ||||  |||| | |      | | |||||||||  || || ||| | |||||| |||| ||||| || ||||| || |||||||| ||||| ||||| ||| | || |||||||||||||| || ||||
---gttttttgttgattttgttgaa----tcagttatgtgcacttacagtttctaattgttgttagtaaccaatat--ctggactt------acactgcagAAAATCAATATAATTAGGGATTATTTGGAGGACATAAACGAGATACCAAAGTCACGTATGTTCTGGCCTCGAGAAATATGGAGTAAATATGTCAATAAAC

upper sequence: GLYMA11G11960.3 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G108225_T01 (Zea mays), 3'ss of exon 6
------ttccctcctcctatatactattagaggtcttggttg-----tggctgaccttgatcctctttcctaacatttactgatatttctggccatcttttg--agattgcagAAAACAAACATTATTCGAGATTATCTGGAAGACATCAATGAGATCCCCAAGTCACGCATGTTTTGGCCACGACAGATTTGGAGTAAATATGTTAACAAAC
      ||          ||  |  |   ||    ||  |||     ||  |||  | ||   ||| |  | | ||||     || |       |  | |    | |||||||||||| ||||| ||| | || ||| |||| ||||| |||||||| || ||||| |||||||| ||||| ||| |||| |||||||||||||   | ||||
gtatgtttattggtgtgaatgaatcaactgaaccattttttgcttcctgtgtgaaatggaatttctgttttgagattttgcattactaacaagtacttgtcatcaaattgcagAAAACTAACATAATTAGGGACTATTTGGAGGACATAAATGAGATACCAAAGTCCCGCATGTTCTGGCCTCGAGAGATATGGAGTAAATATGCAGATAAAC

upper sequence: GLYMA11G11960.3 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G029396_T02 (Zea mays), 3'ss of exon 2
-----ttccctcctccta-tatactattagaggtcttggttg-tggctgaccttgatcc--tctttcctaacatttactgatatttctggccatcttt--tgagattgcagAAAACAAACATTATTCGAGATTATCTGGAAGACATCAATGAGATCCCCAAGTCACGCATGTTTTGGCCACGACAGATTTGGAGTAAATATGTTAACAAAC
     ||   |  ||  | |  |  |    |    ||  ||| |  |||      || |   || |    | | ||  ||  |||       || | |  | | || ||||||||| || || ||| | |||||| |||| ||||| |||||||| || ||||| |||||||| ||||| ||| |||| |||||||||||||   | ||||
gtatgttaattggtctgaatgaatcaaccaaaccgtttcttgctccctgtgtgaaatgcaacctgtttcgagagtttgtgtcattaacaagtatttgtcatcaaatcgcagAAAACTAATATAATTAGGGATTATTTGGAGGACATAAATGAGATACCAAAGTCCCGCATGTTCTGGCCTCGAGAGATATGGAGTAAATATGCAGATAAAC

upper sequence: GLYMA11G11960.3 (Glycine max), 3'ss of exon 6
lower sequence: AT4G34650.1 (Arabidopsis thaliana), 3'ss of exon 6
---ttccctcctcctatatactattagaggtcttggttgtggctgaccttgatcctctttcctaacatttactgatatttctg-gccatcttttgagattgcagAAAACAAACATTATTCGAGATTATCTGGAAGACATCAATGAGATCCCCAAGTCACGCATGTTTTGGCCACGACAGATTTGGAGTAAATATGTTAACAAAC
   |||  | |     |||| |||| ||  | |     ||  ||  |||  |   | |||   ||  |||   |   ||| |  |  || | || |  |   ||||||||||||||||   ||||||||| |||||||| |||||||  || ||||| |||||||||||||| ||  |||||||| | ||||||||| ||||||
gtattcattacaatggtataatatt-gacatgtacaaggtttctt-cctcaaatgttttttgcaatctttgaagtcttttgtatgttatatctt-atttgctagAAAACAAACATTATCAAAGATTATCTTGAAGACATTAATGAGAGACCAAAGTCGCGCATGTTTTGGCCTCGTGAGATTTGGGGAAAATATGTTGACAAAC

upper sequence: GLYMA11G11960.3 (Glycine max), 3'ss of exon 6
lower sequence: AT4G34640.1 (Arabidopsis thaliana), 3'ss of exon 6
ttccctcctcctatatactattagaggtcttg-gttgtggctgaccttgatcctct----ttcctaacatttactgatatt-------tctggccatcttttgagattgcagAAAACAAACATTATTCGAGATTATCTGGAAGACATCAATGAGATCCCCAAGTCACGCATGTTTTGGCCACGACAGATTTGGAGTAAATATGTTAACAAAC
     | |  | || || | | ||  ||     |||    ||  |    ||| | |    || |  ||| || ||   |||       |     ||    |     ||||||||||||||||||||  |||||||||| || ||||| |||||||| || || || |||||||||||||| ||  |||||||| | ||||||| | |||| |
----gtacaacaatgtattttgaggtgtacaatgtttcttcttcctcaaatcttttgcaatttcggacaatttctatcattgaatgatttataacactggtcttatttgcagAAAACAAACATTATCAGAGATTATCTTGAGGACATTAATGAGATACCAAAATCCCGCATGTTTTGGCCTCGCGAGATTTGGGGCAAATATGCTGACAAGC

upper sequence: GLYMA11G11960.3 (Glycine max), 3'ss of exon 6
lower sequence: Vv03s0038g00450.t01 (Vitis vinifera), 3'ss of exon 6
ttccctcctcctatatactattagaggtcttggttgtggctgaccttgatcctctttcctaacatttactgatatttctggccatcttttgagattgcagAAAACAAACATTATTCGAGATTATCTGGAAGACATCAATGAGATCCCCAAGTCACGCATGTTTTGGCCACGACAGATTTGGAGTAAATATGTTAACAAAC
                  || |||  || ||  || ||    |   ||   ||  |      |||    |   |  | |     |||  | | ||  ||||||||||| || || |||||||||||||| || || ||||||||||| |||||||||||||||||||| ||  |||||||||||||||||||||||||||
-----------------gtaatagttgtattaatt-tgatatatgctgcaactggtatgcttcatcccgtctcaactttttgtgtctcat-aaatcccagAAAACAAATATAATCCGAGATTATCTGGAGGATATAAATGAGATCCCAAAGTCACGCATGTTTTGGCCCCGTGAGATTTGGAGTAAATATGTTAACAAAC

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|208157007|gb|GD956393.1|GD956393
EST:     AAGATCTGGCTCCAGATGACCTTTCCAATTCAATGGGCTTGTTTCTACAG                         AAAACAAACATTATTCGAGATTATCTGGAAGACATCAATGAGATCCCCAAG
genomic: AAGATCTGGCTCCAGATGACCTTTCCAATTCAATGGGCTTGTTTCTACAGgtatcatatc ... gagattgcagAAAACAAACATTATTCGAGATTATCTGGAAGACATCAATGAGATCCCCAAG
EST: gi|14010995|gb|BG725917.1|BG725917
EST:     AAGATCTGGCTCCAGATGACCTTTCCAATTCAATGGGCTTGTTTCTACAG                         AAAACAAACATTATTCGAGATTATCTGGAAGACATCAATGAGATCCCCAAG
genomic: AAGATCTGGCTCCAGATGACCTTTCCAATTCAATGGGCTTGTTTCTACAGgtatcatatc ... gagattgcagAAAACAAACATTATTCGAGATTATCTGGAAGACATCAATGAGATCCCCAAG
EST: gi|7478069|gb|AW666124.1|AW666124
EST:     TGACCTTTCCAATTCAATGGGCTTGTTTCTACAG                         AAAACAAACATTATTCGAGATTATCTGGAAGACATCAATGAGATCCCCAAG
genomic: TGACCTTTCCAATTCAATGGGCTTGTTTCTACAGgtatcatatc ... gagattgcagAAAACAAACATTATTCGAGATTATCTGGAAGACATCAATGAGATCCCCAAG
EST: gi|58014892|gb|CX701634.1|CX701634
EST:     AGATCTGGCTCCAGATGACC-TTCCAAATTCAATGGGC-TGTTTCTACAG                         AAAACAAACATTATTCGAGA-TATCTGGAAGACATCAATGAGATCCCCAAG
genomic: AGATCTGGCTCCAGATGACCTTTCC-AATTCAATGGGCTTGTTTCTACAGgtatcatatc ... gagattgcagAAAACAAACATTATTCGAGATTATCTGGAAGACATCAATGAGATCCCCAAG
EST: gi|193655424|gb|FK607480.1|FK607480
EST:     AAGATCTGGCTCCAGATGACCTTTCCAATTCAATGGGCTTGTTTCTACAG                         AAAACAAACATTATTCGAGATTATCTGGAA
genomic: AAGATCTGGCTCCAGATGACCTTTCCAATTCAATGGGCTTGTTTCTACAGgtatcatatc ... gagattgcagAAAACAAACATTATTCGAGATTATCTGGAA
EST: gi|207799180|gb|GD771735.1|GD771735
EST:     ATGACCTTTCCAATTCAATGGGCTTGTTTCTTACAG                         AAAACAAACATTATTCGAGATTATCTGGAAGACATCAATGAGATCCCCAA
genomic: ATGACCTTTCCAATTCAATGGGCTTGTTTC-TACAGgtatcatatc ... gagattgcagAAAACAAACATTATTCGAGATTATCTGGAAGACATCAATGAGATCCCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatcctctttcctaacatttactgatatttctggccatcttttgagattgcagAAAACAAACATTATTCGAGATTATCTGGAAGACATCAATGAGATCCCCAAGTCACGCATGTTTTGGCCACGACAGATTTGGAGTAAATATGTTAACAAAC
                                       tcttttg  CT-rich tract
                  atttactgatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttccctcctcctatatactattagaggtcttggttgtggctgaccttgatcctctttcctaacatttactgatatttctggccatcttttgagattgcagAAAACAAACATTATTCGAGATTATCTGGAAGACATCAATGAGATCCCCAAGTCACGCATGTTTTGGCCACGACAGATTTGGAGTAAATATGTTAACAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG