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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGACCTTGGATGGTTTCCCCGAGGAAAGATGGCTGGGCCATTTCAGGAAGTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctcttgtactcttaacttttattttcctgattagcacctgtgccccttctcttcttcatttaggcagacctgctaatgtttgtttggatgatgatgatgcag

Basic information

species Glycine max
transcript GLYMA06G21080.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G21080.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os09g24540.1 (Oryza sativa), 5'ss of exon 3
GAGACCTTGGATGGTTTCCCCGAGGAAAGATGGCTGGGCCATTTCAGGAAGTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctcttgtactcttaacttttattttcctgattagcacctgtgccccttctcttcttcatttaggcagacctgctaatgtttgtttggatgatgatgatgcag
|||| ||||||||||| || || ||||| |||||||| || |||||||| ||||| || | ||||||||| ||||||||||| || || || || || |||||| | | |  |  | |||       |||||||        ||  |   |  ||| ||    ||  | | ||  |   | |  |  ||   |||      ||| | |
GAGATCTTGGATGGTTCCCGCGTGGAAAAATGGCTGGCCCTTTTCAGGATGTTGCATTTAGCACACCTGTGGGAGCTACTAGCGCACCATTTAAGTCAACgtatgtgtataattgtattactaccctttttcct--------ccaatcttcggtctattaacaatgcaagtagcgcctatgacatgagtgctgatctgtgcgataccg

upper sequence: GLYMA06G21080.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G048277_T03 (Zea mays), 5'ss of exon 3
GAGACCTTGGATGGTTTCCCCGAGGAAAGATGGCTGGGCCATTTCAGGAAGTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctcttgtactcttaacttttattttcctgattagcacctgtgccccttctcttcttcatttaggcagacctgctaatgtttgtttggatgatgatgatgcag
|||| ||||| ||||| || || || ||||||||||| || || ||||| ||||| |||||||||||||  ||| ||  ||| || || ||||| || ||||||  || |   ||| ||    ||   ||    |  ||     |||  |    | | |        | |    | |   | ||      || ||  |     ||   
GAGATCTTGGTTGGTTCCCGCGTGGCAAGATGGCTGGTCCTTTCCAGGAGGTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgcctttcacactgtttttcttccattgttcgcctattgaatgtatcatagcccatg---gcacaagtc--cttatcattgcactgctgcatttttcctgtg---

upper sequence: GLYMA06G21080.1 (Glycine max), 5'ss of exon 4
lower sequence: AT1G26550.1 (Arabidopsis thaliana), 5'ss of exon 4
GAGACCTTGGATGGTTTCCCCGAGGAAAGATGGCTGGGCCATTTCAGGAAGTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctcttgtactcttaacttttattttcctgattagcacctgtgccccttctcttcttcatttaggcagacctgctaatgtttgtttggatgatgatgatgcag
|||| ||||||||||| || |||||||||||||| || ||||| || || || ||||| || |||||||||||||  || ||||| || |||||||| |||||| ||      |      |  | |  |||| |      | | | |  |     |  |||| |||   |  ||  || | |  | |  |||  || | ||  |||||
GAGATCTTGGATGGTTCCCTCGAGGAAAGATGGCAGGTCCATTCCAAGATGTCGCCTTTAATACACCTGTTGGAGTCACCAGTGCACCCTTCAAATCAACgtatgtcc-----aaatccgatctcttctttctt------ctcttctatctgaatttatctttatt--agtgga--tgatga-atgtaattgcgtggtaat--tgcag

upper sequence: GLYMA06G21080.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv17s0000g06430.t01 (Vitis vinifera), 5'ss of exon 4
GAGACCTTGGATGGTTTCCCCGAGGAAAGATGGCTGGGCCATTTCAGGAAGTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtattt-ctcttgtactcttaacttttattttc-ctgattagcacctgtgcccct----tctcttcttcatttaggcag-----acctgctaatgtttgtttggatgatgatgatgcag
| ||||||||||||||||| || || ||||||||||| ||||||||||| |||||||||| ||||  | ||||||| || ||||| || |||||||| ||||||    ||   |     |   ||||||  ||  ||| |     ||||  | ||    |||       | |  || ||     ||  |||||   || ||| | |  |||| ||||||
GTGACCTTGGATGGTTTCCGCGTGGCAAGATGGCTGGTCCATTTCAGGATGTTGCCTTCAGCACAGTTATTGGAGCCACCAGTGCACCATTCAAATCAACgtatggattcaaatttgggtggtttttatgctcgttgagttaattctgtatctctagattcttagtactactcgggtagcttcaactagctaac-cttattttgcttttgatcatgcag

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|21888702|gb|BQ741915.1|BQ741915
EST:     GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGAC                         GCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
genomic: GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctct ... gatgatgcagGCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
EST: gi|254326762|gb|GR836371.1|GR836371
EST:     GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGAC                         GCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
genomic: GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctct ... gatgatgcagGCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
EST: gi|58019562|gb|CX706304.1|CX706304
EST:     GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGAC                         GCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
genomic: GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctct ... gatgatgcagGCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
EST: gi|15001056|gb|BI321870.1|BI321870
EST:     GTTGCCTTCAACACACCTGTGGGAGCTAGTAGTGCTCCTTTCAAATCGAC                         GCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
genomic: GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctct ... gatgatgcagGCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
EST: gi|254317146|gb|GR826091.1|GR826091
EST:     GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGAC                         GCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
genomic: GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctct ... gatgatgcagGCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
EST: gi|9257985|gb|BE346108.1|BE346108
EST:     GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCACATCGAC                         GCATGGCTACCATATTATCTTAAGTGAAGGAAGA
genomic: GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctct ... gatgatgcagGCATGGCTACCATATTATCTTAAGTGAAGGAAGA
EST: gi|209723787|gb|BW668885.1|BW668885
EST:     GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGAC                         GCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
genomic: GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctct ... gatgatgcagGCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
EST: gi|6133782|gb|AW132175.1|AW132175
EST:     GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGAC                         GCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
genomic: GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctct ... gatgatgcagGCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
EST: gi|213593108|gb|DB975355.1|DB975355
EST:     GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGAC                         GCATGGCTACCATATT-TCCTTAAGTGAAGGAAGAAAGAACTGATCCCCGA
genomic: GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctct ... gatgatgcagGCATGGCTACCATATTAT-CTTAAGTGAAGGAAGAAAGAACTGATCCCCGA
EST: gi|58021266|gb|CX708008.1|CX708008
EST:     GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGAC                         GCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
genomic: GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctct ... gatgatgcagGCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
EST: gi|254317147|gb|GR826092.1|GR826092
EST:     GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGAC                         GCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
genomic: GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctct ... gatgatgcagGCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
EST: gi|58019862|gb|CX706604.1|CX706604
EST:     GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGAC                         GCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
genomic: GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctct ... gatgatgcagGCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
EST: gi|192318789|gb|FK008001.1|FK008001
EST:     GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGAC                         GCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
genomic: GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctct ... gatgatgcagGCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
EST: gi|151400100|gb|EV269914.1|EV269914
EST:     GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGAC                         GCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
genomic: GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctct ... gatgatgcagGCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
EST: gi|254326763|gb|GR836372.1|GR836372
EST:     GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGAC                         GCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
genomic: GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctct ... gatgatgcagGCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
EST: gi|192318790|gb|FK008002.1|FK008002
EST:     GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGAC                         GCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
genomic: GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctct ... gatgatgcagGCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
EST: gi|31312264|gb|CD397467.1|CD397467
EST:     GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGAC                         GCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
genomic: GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctct ... gatgatgcagGCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
EST: gi|213614928|gb|DB957008.1|DB957008
EST:     GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGAC                         GCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
genomic: GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctct ... gatgatgcagGCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
EST: gi|151402207|gb|EV272020.1|EV272020
EST:     TTCGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGAC                         GCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAAC
genomic: TT-GCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctct ... gatgatgcagGCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAAC
EST: gi|192327814|gb|FK022079.1|FK022079
EST:     GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCCCCTTTCAAATCGAC                         GCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
genomic: GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctct ... gatgatgcagGCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
EST: gi|26057206|gb|CA800120.1|CA800120
EST:     GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGAC                         GCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
genomic: GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctct ... gatgatgcagGCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
EST: gi|192327815|gb|FK022080.1|FK022080
EST:     GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCCCCTTTCAAATCGAC                         GCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
genomic: GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctct ... gatgatgcagGCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
EST: gi|58015222|gb|CX701964.1|CX701964
EST:     GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGAC                         GCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
genomic: GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctct ... gatgatgcagGCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAGAACTGATCCCCGAA
EST: gi|10847591|gb|BF070243.1|BF070243
EST:     GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGAC                         GCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAG
genomic: GTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctct ... gatgatgcagGCATGGCTACCATATTATCTTAAGTGAAGGAAGAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGACCTTGGATGGTTTCCCCGAGGAAAGATGGCTGGGCCATTTCAGGAAGTTGCCTTCAACACACCTGTTGGAGCTACTAGTGCTCCTTTCAAATCGACgtatttctcttgtactcttaacttttattttcctgattagcacctgtgccccttctcttcttcatttaggcagacctgctaatgtttgtttggatgatgatgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT