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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAGgtatttagcttctcactccccctccctcccccatcctaatgatggtttttaactgagaaaagagcaaaaatagattttcatcagggaaaaaaaaaattag...

Basic information

species Glycine max
transcript GLYMA09G34610.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G34610.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G178822_T01 (Zea mays), 5'ss of exon 12
ATATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAGgtatt-----tagcttctcactc------cccctccctcccccatcctaatgatggtttttaactgagaaaagagcaaaaatagattttcatcagggaaaaaaaaaattag
||||||||||||||||||| |||||||||||||| ||  | || | |||||| || || ||  ||||||| |     |  ||  |  ||       |   || ||| |  ||| |  || || ||| |   ||   |      |||  | || ||   |||     ||          
ATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAGgtaatatggttgactgtttgctggtaaagcttgtcactcacaaatcttt-tgctgctttcttgttggtcacct--taaagtttgacttatctcaaatttaatg--------

upper sequence: GLYMA09G34610.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G108829_T01 (Zea mays), 5'ss of exon 11
ATATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAGgtatttagcttctcactccccctccctcccccatcctaatgatggtttttaactgagaaaagagcaaaaatagattttcatcagggaaaaaaaaaattag---
||||||||||||||||||| |||||||||||| | ||  | || | |||||| || || ||  | ||||| |  | ||  |  | |      ||    | |   | | |    | |    ||   ||   |      |   || |  |     ||   || | ||     
ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAGgtaatatggttgactgtgcatgctgctaaagcttggcactcacaaatct--gttgctcaatttgtttgc-tgctttcttgttgttcaacttaatatttgacct

upper sequence: GLYMA09G34610.1 (Glycine max), 5'ss of exon 8
lower sequence: Vv02s0033g01110.t01 (Vitis vinifera), 5'ss of exon 8
ATATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAGgtatttagcttctcactccccctccctcccccatcctaatgatggtttttaactgagaaaagagcaaaaatagattttcatcagggaaaa----aaaaaattag-
|||||||||||||||||||||| ||||||||  | ||  |||| |||||||| || |||||  | |||||  |   || |   ||||| | ||| |    |  |  |  |    |||  ||   |  |  |  |   |  || ||   |  ||  ||    | | ||||   
ATATGTGGGCAATGGGTGCTATCATGGCTGAATTGTTTACTCTCCGTCCTCTCTTTCCAGGATCGAGgtaaatgtttttt---tcccctttccttctaggtattggtttttcccttttgcttttacta--gttatggtgtatgttgcacgtggttaattttacataattgaa

upper sequence: GLYMA09G34610.1 (Glycine max), 5'ss of exon 8
lower sequence: PP1S28_184V6.1 (Physcomitrella patens), 5'ss of exon 7
---------------------------------ATATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAGgtatttagcttctcactccccctccctcccccatcctaatgatggtttttaactgagaaaagagcaaaa-atagattttcatcagggaaaaaaaaaattag
                                 ||||||||||| |||| |||||||||||||| |||||| || |||| || ||||| || || || |||||         ||||| |   |   |   |  | || |   || | |  || |||| |  |||       |  | ||       ||| ||   | |  | 
TTCTTCAGTCACCAACTTATTCTCCTGCTATAGATATGTGGGCAGTGGGGGCTATAATGGCTGAACTTTTCACTTTTCGCCCACTTTTTCCTGGAGCAAGgtacagtatccgtcacttcagtttgattgact-tgcttacattgatatgaaattgagcattgagtttctcgttcacttctggtttggataatttagaagac

upper sequence: GLYMA09G34610.1 (Glycine max), 5'ss of exon 8
lower sequence: PP1S173_136V6.1 (Physcomitrella patens), 5'ss of exon 8
ATATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAGgtatttagcttctcactccccctccctccc-ccatcctaatgatggtttttaactgagaaaagagcaaaaatagattttcatcagggaaaaaaaaaattag
|| |||||||| |||| || ||||||||||| |||||| | |||||||| |||||||| ||||| |||||   |  |    |     | ||  |      |||    |     | | |  ||          |          | ||              | |||  
ATGTGTGGGCAGTGGGAGCAATAATGGCTGAACTTTTCACCCTTCGTCCACTTTTCCCTGGTGCAAGgtaggaatgtcaatatgtaacttcgtttaaattatctctctctctctctctctctctctctctctctctctctctctctctctctctctctctcacattg-

upper sequence: GLYMA09G34610.1 (Glycine max), 5'ss of exon 8
lower sequence: EFJ11811 (Selaginella moellendorffii), 5'ss of exon 6
---------------------------------ATATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAGgtatttagcttctcactccccctccctcccccatcctaatgatggtttttaactgagaaaagagcaaaaatagattttcatcagggaaaaaaaaaattag
                                 | |||||||||||||||||||| |||||||||||||||  |||  | ||| | || || || || ||||| ||      ||  |    | || || |  | | |     |  ||   | ||| | |                                         
TACTGCAGTCGTCTCTGTACAACTCTGCGGTCGACATGTGGGCAATGGGTGCTATCATGGCTGAGCTTTTCAATCTCAGGCCTATCTTTCCTGGCGCTAGgtaatttcgcagtctattggacgccatcgcttaccatt----tttttaccatctgtgcag----------------------------------------

upper sequence: GLYMA09G34610.1 (Glycine max), 5'ss of exon 8
lower sequence: EFJ22662 (Selaginella moellendorffii), 5'ss of exon 6
---------------------------------ATATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAGgtatttagcttctcactccccctccctcccccatcctaatgatggtttttaactgagaaaagagcaaaaatagattttcatcagggaaaaaaaaaattag
                                 | |||||||||||||||||||| |||||||||||||||  |||  | ||| | || || || || ||||| ||      ||  |    | |  || |  | | |     |  ||   | ||| | |                                         
TACTGCAGTCGTCTCTGTACAACTCTGCGGTCGACATGTGGGCAATGGGTGCTATCATGGCTGAGCTTTTCAATCTCAGGCCTATCTTTCCTGGCGCTAGgtaatttcgcagtctattggacgctatcgcttaccatt----tttttaccatctgtgcag----------------------------------------

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|207819657|gb|GD791705.1|GD791705
EST:     CTCTTCGTCCTCTTTTCCCAGGTGCCAG                         TGAAGCGGATGAGATTTACAAAATATGTGGTGTGATAGGCAATCCAACCTT
genomic: CTCTTCGTCCTCTTTTCCCAGGTGCCAGgtatttagct ... acacatgcagTGAAGCGGATGAGATTTACAAAATATGTGGTGTGATAGGCAATCCAACCTT
EST: gi|22521888|gb|BU080699.1|BU080699
EST:     GCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAG                         TGAAGCGGATGAGATTTACAAAATATGTGGTGTGATAGGCAATCCAACCTT
genomic: GCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAGgtatttagct ... acacatgcagTGAAGCGGATGAGATTTACAAAATATGTGGTGTGATAGGCAATCCAACCTT
EST: gi|4292143|gb|AI437720.1|AI437720
EST:     GCTATAATGGCTGAGCTTTTCTCTCTTCGTNCTCTTTTNCCAGGTGCCAG                         TGAAGCGGATGAGATTTACANAATATGT
genomic: GCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAGgtatttagct ... acacatgcagTGAAGCGGATGAGATTTACAAAATATGT
EST: gi|120533910|gb|EH262043.1|EH262043
EST:     CCCAGGTGCCAG                         TGAAGCGGATGAGATTTACAAAATATGTGGTGTGATAGGCAATCCAACCTT
genomic: CCCAGGTGCCAGgtatttagct ... acacatgcagTGAAGCGGATGAGATTTACAAAATATGTGGTGTGATAGGCAATCCAACCTT
EST: gi|308098976|gb|HO760817.1|HO760817
EST:     GCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAG                         TGAAGCGGATGAGATTTACAAAATATGTGGTGTGATAGGCAATCCAACCTT
genomic: GCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAGgtatttagct ... acacatgcagTGAAGCGGATGAGATTTACAAAATATGTGGTGTGATAGGCAATCCAACCTT
EST: gi|27426213|gb|CA937733.1|CA937733
EST:     GCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAG                         TGAAGCGGATGAGATTTACAAAATATGTGGTGTGATAGGCAATCCAACCTT
genomic: GCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAGgtatttagct ... acacatgcagTGAAGCGGATGAGATTTACAAAATATGTGGTGTGATAGGCAATCCAACCTT
EST: gi|26048713|gb|CA785166.1|CA785166
EST:     GCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAG                         TGAAGCGGATGAGATTTACAAAATATGTGGTGTGATAGGCAATCCAACCTT
genomic: GCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAGgtatttagct ... acacatgcagTGAAGCGGATGAGATTTACAAAATATGTGGTGTGATAGGCAATCCAACCTT
EST: gi|15662868|gb|BI700239.1|BI700239
EST:     TAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAG                         TGAAGCGGATGAGATTTACAAAATATGTGGTGTGATAGGCAATCCAACCTT
genomic: TAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAGgtatttagct ... acacatgcagTGAAGCGGATGAGATTTACAAAATATGTGGTGTGATAGGCAATCCAACCTT
EST: gi|151399948|gb|EV269819.1|EV269819
EST:     GCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAG                         TGAAGCGGATGAGATTTACAAAATATGTGGTGTGATAGGCAATCCAACCTT
genomic: GCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAGgtatttagct ... acacatgcagTGAAGCGGATGAGATTTACAAAATATGTGGTGTGATAGGCAATCCAACCTT
EST: gi|120533985|gb|EH262118.1|EH262118
EST:     CCCAGGTGCCAG                         TGAAGCGGATGAGATTTACAAAATATGTGGTGTGATAGGCAATCCAACCTT
genomic: CCCAGGTGCCAGgtatttagct ... acacatgcagTGAAGCGGATGAGATTTACAAAATATGTGGTGTGATAGGCAATCCAACCTT
EST: gi|192325797|gb|FK018019.1|FK018019
EST:     GCTATAATGGCTGAGCCTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAG                         TGAAGCGGATGAGATTTACAAAATATGTGGTGTGATAGGCAATCCAACCTT
genomic: GCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAGgtatttagct ... acacatgcagTGAAGCGGATGAGATTTACAAAATATGTGGTGTGATAGGCAATCCAACCTT
EST: gi|9565983|gb|BE475492.1|BE475492
EST:     GCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAG                         TGAAGCGGATGAGATTTACAAAATATGTGGTGTGATAGGCAATCCAACCTT
genomic: GCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAGgtatttagct ... acacatgcagTGAAGCGGATGAGATTTACAAAATATGTGGTGTGATAGGCAATCCAACCTT
EST: gi|6951635|gb|AW423703.1|AW423703
EST:     GCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAG                         TGAAGCGGATGAGATTTACAAAATATGTGGTGTGATAGGCAATCCAACCTT
genomic: GCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAGgtatttagct ... acacatgcagTGAAGCGGATGAGATTTACAAAATATGTGGTGTGATAGGCAATCCAACCTT
EST: gi|208124722|gb|GD924168.1|GD924168
EST:     CTCTTCGTCCTCTTTTCCCAGGTGCCAG                         TGAAGCGGATGAGATTTAACAAAAATATGTGGTGTGATAGGCAATCCAACC
genomic: CTCTTCGTCCTCTTTTCCCAGGTGCCAGgtatttagct ... acacatgcagTGAAGCGGATGAGATTT-AC-AAAATATGTGGTGTGATAGGCAATCCAACC
EST: gi|193536878|gb|FK490090.1|FK490090
EST:     GCTATAATGGCTGAACTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAG                         TGAAGCGGATGAGATTTAACAAAATATGTGGTGTGATAGGCAAT
genomic: GCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAGgtatttagct ... acacatgcagTGAAGCGGATGAGATTTA-CAAAATATGTGGTGTGATAGGCAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAGgtatttagcttctcactccccctccctcccccatcctaatgatggtttttaactgagaaaagagcaaaaatagattttcatcagggaaaaaaaaaattag

- - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaaaaaa