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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGCTCTCGCTCTCCAGTGCGAACTCTCAGATCTCCGTGTTCAGACCCAAGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCGgttcgttctctgttactatgtttcggttctgaattttgattttggataataatatggtttgtgttgttggtgatcgaagtaacctaaagcaattatacaa...

Basic information

species Glycine max
transcript GLYMA10G10270.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G10270.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os03g44560.1 (Oryza sativa), 5'ss of exon 1
GAGGCTCTCGCTCTCCAGTGCGAACTCTCAGATCTCCGTGTTCAGACCCAAGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTC---CTTCGTCGCGgttcgttctctgttactatgtttcggttctgaattttg-attttggataataatatggtttgtgttgttggtgatcgaagtaacctaaagcaattatacaa-
  | |||   ||| ||    |   |   ||| || |||| ||| | |||||||||||||||||||| ||||||||| | ||  |  || |   ||||  | | ||  |  |       | |  || |  ||||    |       |   ||     | ||||||   ||| | | | | |  | | ||    |   ||   |   
CCGCCTCAGCCTCGCCTCCTCCGGC---CAGCTCGCCGTCTTCCGCCCCAAGGTCGACGAGATCTCCCTCCTCACCATCAACACCACCACCGGCTTCAACCCCgtaagcccatcccccccaccttccccttcttccctgcacgcgtctcatgggggt-tggtttactttggttg-ggtgggtggatccggtggagcttgcgccgt

upper sequence: GLYMA10G10270.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os03g57320.1 (Oryza sativa), 5'ss of exon 1
GAGGCTCTCGCTCTCCAGTGCGAACTCTCAGATCTCCGTGTTCAGACCCAAGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCGgttcgttctctgttactatgtttcggttctgaattttgattttggataataatatggttt-gtg-ttgttggtgatcgaagtaacctaaagcaattatacaa----------
      || ||   | || |||    |  || || | |||||| | ||| ||||||||||||| |||||||||||||| ||  | ||| ||  ||  | || |    | | || |||| |   | | || || |||| |  |     |      || |||  || ||  ||  |||     |  |  |  |    || |||           
-----GCTGGCGTCCAAGGGCG----CCAAGCTCGCGGTGTTCCGCCCCGAGGTCGACGAGATTTCGCTCCTCACCGTCAACACCTCCGCCGCCG--GTGGCTTCGACCCGgtaactaaggccctggtc-gacttttcacctctagaagcttcgtgttttcatgcttaatgtcgatttttatgtcagatggtgtatacacacgaggaaccct

upper sequence: GLYMA10G10270.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os03g57320.2 (Oryza sativa), 5'ss of exon 1
GAGGCTCTCGCTCTCCAGTGCGAACTCTCAGATCTCCGTGTTCAGACCCAAGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCGgttcgttctctgttactatgtttcggttctgaattttgattttggataataatatggtttgtgttgttggtgatcgaagtaacctaaagcaattatacaa
      || ||   | || |||    |  || || | |||||| | ||| ||||||||||||| |||||||||||||| ||  | ||| ||  ||  | || |    | | || |||| |   | | || || |||| |  |     |      || |||   |  ||  ||       | |  | |             
-----GCTGGCGTCCAAGGGCG----CCAAGCTCGCGGTGTTCCGCCCCGAGGTCGACGAGATTTCGCTCCTCACCGTCAACACCTCCGCCGCCG--GTGGCTTCGACCCGgtaactaaggccctggtc-gacttttcacctctagaagcttcgtgtttt-catgcttaatgtcgatttttatgtcag------------

upper sequence: GLYMA10G10270.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G029101_T02 (Zea mays), 5'ss of exon 1
---GAGGCTCTCGCTCTCCAGTGCGAACTCTCAGATCTCCGTGTTCAGACCCAAGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCGgttcg-ttctctgttactatgtttcgg-ttctgaattttgattttggataataatatggtt-tgtgttgttggtgatcgaagtaacctaaagcaattatacaa
     | |||  |||| |||       | | ||| || |  ||||| | ||| ||||||||||||| |||||||||||||| || || |||||||||| | ||||  | | |||  |  | |||||     ||   || |  | || |||||  |  ||| |||       ||| | |   |  || |    ||    | |  || 
CAGCCGCCTCGGGCTCGCCAACC---GCGCGCAGGTCGCGCTGTTCCGCCCCCAGGTCGACGAGATTTCGCTCCTCACCGTCAACTCCTCCTCCTTCGACCCGgtgagctcctccatcgccatgttaaaccttactaactgcgcttgtggatt-tcgtatagttgccaaaagtttgcgcgaggtgtgataggaattg-tgacgca-

upper sequence: GLYMA10G10270.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G023392_T02 (Zea mays), 5'ss of exon 1
GAGGCTCTCGCTCTCCAGTGCGAACTCTCAGATCTCCGTGTTCAGACCCAAGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCC---TTCGTCGCGgttcgttctctgttactatgtttcggttctgaattttgattttggataataatatggtttgtgttgttggtgatcgaagtaacctaaagcaattatacaa-
    | |     |  |  |||   |   ||| || |||| ||| | |||||||||||||||||||| ||||||||| | ||  |  |  ||   |||  | | ||  |   ||        ||    | ||     || | ||||    |   ||||   |  || | |   |    |||| |       ||     || |   
---CCGCCTCAACCTCGCTGCCTCCGGGCAGCTCGCCGTCTTCCGCCCCAAGGTCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatcctgagtcctgacctgctttgagtttctaatttcttgtttgaata-aataagtttggggcggatccgaattccatctgagtttgcattcttc

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|5770452|gb|AI973626.1|AI973626
EST:     AGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCG                         GACTCATATGGCTATATGGTTGCATTTGCTGGCCACAGATATGCAGCAAGA
genomic: AGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCGgttcgttctc ... ccttgtgcagGACTCATATGGCTATATGGTTGCATTTGCTGGCCACAGATATGCAGCAAGA
EST: gi|298174172|gb|HO017508.1|HO017508
EST:     AGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCG                         GACTCATATGGCTATATGGTTGCATTTGCTGGCCACAGATATGCAGCAAGA
genomic: AGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCGgttcgttctc ... ccttgtgcagGACTCATATGGCTATATGGTTGCATTTGCTGGCCACAGATATGCAGCAAGA
EST: gi|298184144|gb|HO029357.1|HO029357
EST:     GGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCG                         GACTCATATGGCTATATGGTTGCATTTGCTGGCCACAGATATGCAGCAAGA
genomic: AGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCGgttcgttctc ... ccttgtgcagGACTCATATGGCTATATGGTTGCATTTGCTGGCCACAGATATGCAGCAAGA
EST: gi|192294605|gb|FG986454.1|FG986454
EST:     ATCCTCCTTCGTCGCG                         GACTCATATGGCTATATGGTTGCATTTGCTGGCCACAGATATGCAGCAAGG
genomic: ATCCTCCTTCGTCGCGgttcgttctc ... ccttgtgcagGACTCATATGGCTATATGGTTGCATTTGCTGGCCACAGATATGCAGCAAGA
EST: gi|298180808|gb|HO022247.1|HO022247
EST:     AGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCG                         GACTCATATGGCTATATGGTTGCATTTGCTGGCCACAGATATGCAGCAAGA
genomic: AGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCGgttcgttctc ... ccttgtgcagGACTCATATGGCTATATGGTTGCATTTGCTGGCCACAGATATGCAGCAAGA
EST: gi|7796558|gb|AW781955.1|AW781955
EST:     AGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCG                         GACTCATATGGCTATATGGATGCATTTGCTGGCCACAGATATGCAGCAAGA
genomic: AGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCGgttcgttctc ... ccttgtgcagGACTCATATGGCTATATGGTTGCATTTGCTGGCCACAGATATGCAGCAAGA
EST: gi|20448531|gb|BQ252655.1|BQ252655
EST:     AGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCG                         GACTCATATGGCTATATGGTTGCATTTGCTGGCCACAGATATGCAGAAAGA
genomic: AGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCGgttcgttctc ... ccttgtgcagGACTCATATGGCTATATGGTTGCATTTGCTGGCCACAGATATGCAGCAAGA
EST: gi|57575725|gb|CX548700.1|CX548700
EST:     AGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCG                         GACTCATATGGCTATATGGTTGCATTTGCTGGCCACAGATATGCAGCAAGA
genomic: AGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCGgttcgttctc ... ccttgtgcagGACTCATATGGCTATATGGTTGCATTTGCTGGCCACAGATATGCAGCAAGA
EST: gi|26268621|gb|CA819684.1|CA819684
EST:     AGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCG                         GACTCATATGGCTATATGGTTGCATTTGCTGGCCACAGATATGCAGCAAGA
genomic: AGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCGgttcgttctc ... ccttgtgcagGACTCATATGGCTATATGGTTGCATTTGCTGGCCACAGATATGCAGCAAGA
EST: gi|7284325|gb|AW596919.1|AW596919
EST:     AGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCG                         GACTCATATGGCTATATGGTTGCATTTGCTGGCCACAGATATGCAGCAAGA
genomic: AGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCGgttcgttctc ... ccttgtgcagGACTCATATGGCTATATGGTTGCATTTGCTGGCCACAGATATGCAGCAAGA
EST: gi|57575565|gb|CX548540.1|CX548540
EST:     AGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCG                         GACTCATATGGCTATATGGTTGCATTTGCTGGCCACAGATATGCAGCAAGA
genomic: AGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCGgttcgttctc ... ccttgtgcagGACTCATATGGCTATATGGTTGCATTTGCTGGCCACAGATATGCAGCAAGA
EST: gi|6724741|gb|AW309140.1|AW309140
EST:     AGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCG                         GACTCATATGGCTATATGGTTGCATTTGCTGGCCACAGATATGCAGCAAGA
genomic: AGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCGgttcgttctc ... ccttgtgcagGACTCATATGGCTATATGGTTGCATTTGCTGGCCACAGATATGCAGCAAGA
EST: gi|192326820|gb|FK018917.1|FK018917
EST:     AGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCG                         GACTCATATGGCTATATGGTTGCATTTGCTGGTCACAGATATGCAGCAAGA
genomic: AGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCGgttcgttctc ... ccttgtgcagGACTCATATGGCTATATGGTTGCATTTGCTGGCCACAGATATGCAGCAAGA
EST: gi|14991159|gb|BI316832.1|BI316832
EST:     AGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCG                         GACTCATATGGCTATATGGTTGCATTTGCTGGCCACAGATATGCAGCAAGA
genomic: AGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCGgttcgttctc ... ccttgtgcagGACTCATATGGCTATATGGTTGCATTTGCTGGCCACAGATATGCAGCAAGA
EST: gi|298179682|gb|HO024897.1|HO024897
EST:     AGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCG                         GACTCATATGGCTATATGGTTGCATTTGCTGGCCACAGATATGCAGCAAGA
genomic: AGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCGgttcgttctc ... ccttgtgcagGACTCATATGGCTATATGGTTGCATTTGCTGGCCACAGATATGCAGCAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGCTCTCGCTCTCCAGTGCGAACTCTCAGATCTCCGTGTTCAGACCCAAGGTCGACGAGATCTCGCTCCTCACCGTTAATTCATCCTCCTTCGTCGCGgttcgttctctgttactatgtttcggttctgaattttgattttggataataatatggtttgtgttgttggtgatcgaagtaacctaaagcaattatacaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC