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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGAAGCTGCAGGATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttctttggcaaatgcctggttaaggaaggacaagtagaaagttttttattgggatgtgtaacaatgcgctcccccatgattttaaatgcttctc...

Basic information

species Glycine max
transcript GLYMA04G33180.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G33180.2 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os09g24540.1 (Oryza sativa), 5'ss of exon 2
CTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGAAGCTGCAGGATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttctttggcaaatgcctggttaaggaaggacaagtagaaagttttttattgggatgtgtaacaatgcgctcccccatgattttaaatgcttctc
  | || ||||| ||||| |||||||||||||| ||||||||| |||||||||| ||| |   |||||| || |||||||| || || |||||||||||||||     |    | | ||||           |  || | |            |   |   ||     | | |  |   |     |||   |   |  | 
ACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGAAGTTGCAGGATGGCTGGTTGGACAACGGGGACAAGGTCCCTCCTGCCGAGTTTGCAAAGgtaagcggcagatgtacatgcagctcagcttgaaaactaatgtggttggcccaaagagagagtaaggaattacagttttcaggagtttggtacattcgta

upper sequence: GLYMA04G33180.2 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G048277_T03 (Zea mays), 5'ss of exon 2
CTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGAAGCTGCAGGATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct------ttggcaaatgcctggttaaggaaggacaagtagaaagttttttattgggatgtgtaacaatgcgctcccccatgattttaaatgcttctc
 || |||||||| || || |||||||||||||| || |||||| |||||||||| |||||    || || || || || || || ||||||||||| ||||||     |         ||||     |   |     | |  |||| | |      |||  |  || |   |     | | | | | |||    |  ||       
ATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGAAGTTGCAGGATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGAGTTTGCTAAGgtaaggacccgaatgacgggcagtcctccactcttctaggctcaaggatagttaggtttgcttagacgaaaagggtagtgatgcactatgcgcattgata------

upper sequence: GLYMA04G33180.2 (Glycine max), 5'ss of exon 3
lower sequence: AT1G26550.1 (Arabidopsis thaliana), 5'ss of exon 3
CTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGAAGCTGCAGGATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttctttggcaaatgcctggttaaggaaggacaagtagaaagtttt--ttattgggatgtgtaacaatgcgctcccccatgattttaa-atgcttctc
 || || ||||| ||||| |||||||| || |||||||| ||| |||||||||||||| |  |||||||||| ||||| || || |||||||||||||||||   | || ||  |   |   | ||  | ||     ||  |  ||  |    |  ||  |||  |||    |     |  |  | | | | | |||    | 
TTTGTGCGAGAAGCAAGGAAAGATCAACGAGGCCTACAAAAAGTTGCAGGATGGTTGGTTGAGCAACGGAGACAAGGTTCCTCCTGCTGAGTTTGCAAAGgtgaatatcctt--cttcttttttgtctatgagatcaaaacatcaatctaagatagttcagata-gtattgtttattccatctctaactgtgatatgtacgta

upper sequence: GLYMA04G33180.2 (Glycine max), 5'ss of exon 3
lower sequence: Vv17s0000g06430.t01 (Vitis vinifera), 5'ss of exon 3
CTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGAAGCTGCAGGATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttctttggcaaatgcctggttaaggaaggacaagtagaaagttttttattgggatgtgtaac-aatgcgctcccccatgattttaaatgcttctc---
|||||||||||| ||||| || || |||||||| ||||||||||| || ||||| |||||| | || ||||| ||||| ||||||||||||||||| ||||||  || ||     | || |     |          |  |       ||  ||   |||  || |        ||| |      || ||  |      ||   
CTTATGTGAGAAGCAAGGCAAAATTAATGAAGCATACAAGAAGCTACAAGATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAGgtaaattccta----acatcctatccttccattttttatatttttcccttcataaaaggaattgaagttggcaggctgctttgatatatttgacttggatccat

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|298180788|gb|HO022227.1|HO022227
EST:     ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAG                         ATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
EST: gi|192310836|gb|FK000322.1|FK000322
EST:     ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAG                         ATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
EST: gi|192310835|gb|FK000321.1|FK000321
EST:     ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAG                         ATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
EST: gi|209720765|gb|BW677555.1|BW677555
EST:     ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAG                         ATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
EST: gi|9564338|gb|BE473847.1|BE473847
EST:     ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAG                         ATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
EST: gi|10255640|gb|BE823406.1|BE823406
EST:     ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAG                         ATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
EST: gi|9986791|gb|BE660899.1|BE660899
EST:     ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAG                         ATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
EST: gi|192328239|gb|FK020458.1|FK020458
EST:     ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAG                         ATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
EST: gi|298165798|gb|HO008769.1|HO008769
EST:     ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAG                         ATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
EST: gi|298182306|gb|HO026481.1|HO026481
EST:     ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAG                         ATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
EST: gi|23731993|gb|BU764147.1|BU764147
EST:     ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAG                         ATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
EST: gi|298168618|gb|HO009548.1|HO009548
EST:     ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAG                         ATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
EST: gi|209720766|gb|BW677556.1|BW677556
EST:     ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAG                         ATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
EST: gi|9820183|gb|BE555693.1|BE555693
EST:     ATGGTTGGCTTTGTAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAG                         ATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
EST: gi|27423863|gb|CA935383.1|CA935383
EST:     ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAG                         ATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
EST: gi|41145676|gb|CK605887.1|CK605887
EST:     ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAG                         ATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT
genomic: ATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttct ... gacttcacagATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGAAGCTGCAGGATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGAGTTTGCAAAGgtatttttctttggcaaatgcctggttaaggaaggacaagtagaaagttttttattgggatgtgtaacaatgcgctcccccatgattttaaatgcttctc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG