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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGAGGGATTTTAAAAGATTGCAACAAGATCCTCCTGCTGGCATCAGTGGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGGgtgtgtaggagtatataaatcatgaaatttttgttttcttaagtgtgtgtttctctttactttgtggttttggatgatttaaggtatgataacaatctaattgtgcttttcttggttctttttttccag

Basic information

species Glycine max
transcript GLYMA18G16160.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G16160.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os05g08960.2 (Oryza sativa), 5'ss of exon 2
TGATGAGGGATTTTAAAAGATTGCAACAAGATCCTCCTGCTGGCATCAGTGGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGGgtgtgtaggagtatataaatcatgaaatttttgttttcttaagtgtgtgtttctctttactttgtggttttggatgatttaaggtatgataacaatctaattgtgcttttcttggttctttttttccag
||||||||||||| ||| || ||   || |||||||| |||||||| |||||||| || || ||||| ||||| ||||||||||||||||| || |||||||  |  |    |  |||   || |  ||||  |  | |    | | | ||  ||  |  |   | ||| |  || || |   || |   |                                      
TGATGAGGGATTTCAAACGACTGATGCAGGATCCTCCAGCTGGCATAAGTGGGGCCCCACAGGACAACAATATAATGCTTTGGAATGCTGTAATTTTTGGgtaaggtgttagacttaagagat-atgttttattcctttcggttttattttgatccattatacttagttgtcaattatgtcttgttttgcag-------------------------------------

upper sequence: GLYMA18G16160.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv01s0026g01770.t01 (Vitis vinifera), 5'ss of exon 3
TGATGAGGGATTTTAAAAGATTGCAACAAGATCCTCCTGCTGGCATCAGTGGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGGgtgtgtaggagtatataaatcatgaaatttttgttttcttaagtgtgtgtttctctttactttgtggttttggatgatttaaggtatgataacaatctaattgtgc-ttttcttggttctttttttccag
| ||||||||||| || || |||||||| ||||| ||||| ||||||||||| ||||| ||||||||||| |||||||| |||||||||||||| ||||||| ||  ||   | ||  |||||    | ||| || | |           || | | || ||||||   |||| || || ||| | |||      |  | || | |   |||||||||   ||       
TCATGAGGGATTTCAAGAGGTTGCAACAGGATCCACCTGCAGGCATCAGTGGTGCTCCTCAAGACAATAACATTATGCTCTGGAATGCTGTTATATTTGGgtatgctggg--aaatgcatcat----tgtttattctttc----------ttttgtatagtttgtg---ttgggtg-ttaaagatctgaatcagttgcacttatacgccttcttggttgaattgcag---

upper sequence: GLYMA18G16160.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S219_106V6.1 (Physcomitrella patens), 5'ss of exon 1
TGATGAGGGATTTTAAAAGATTGCAACAAGATCCTCCTGCTGGCATCAGTGGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGGgtgtgtaggagtatataaatcatgaaatttttgttttcttaagtgtgtgtttctctttactttgtggttttggatgatttaaggtatgataacaatctaattgtgcttttcttggttctttttttccag
||||| | || || ||  | |||||||| |||||||| || |||||||| || ||||| || ||||| ||||| ||||| ||||||||||| || || ||||    | | |  |      | ||   |  || |||  | || |||||    |   |     || ||  || |  |      || | |   ||     | |   | ||||                   
TGATGCGTGACTTCAAGCGCTTGCAACATGATCCTCCGGCCGGCATCAGCGGCGCTCCGCAGGACAACAATATCATGCTGTGGAATGCTGTGATATTCGGgtaacgaagtgcct-----ccctggtttcgttttttgttcaattgtgt----ccggtcgtggtgcggaattcgccgggc-gtgggaggcgcacgtcggagtgtcggtttt-------------------

upper sequence: GLYMA18G16160.1 (Glycine max), 5'ss of exon 3
lower sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 1
TGATGAGGGATTTTAAAAGATTGCAACAAGATCCTCCTGCTGGCATCAGTGGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGGgtgtgtaggagtatataaatcatgaaatttttgttttcttaagtgtgtgtttctctttactttgtggttttggatgatttaaggtatgataacaatctaattgtgcttttcttggttctttttttccag
||||| | ||||| ||  |  | || || |||||||| || |||||||| || ||||| || ||||| ||||| ||| | ||||||||||| ||||| ||||| ||    |     ||| | |    | || |  || || | |||  |||  |  ||||                                                                     
TGATGCGAGATTTCAAGCGCCTACAGCATGATCCTCCGGCAGGCATCAGCGGCGCTCCACAGGACAACAATATCATGTTGTGGAATGCTGTGATCTTCGGgtgagttctcgcg---aaacctt----tcttagggtttttgaatgtcggttctttcttacag-------------------------------------------------------------------

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|208327169|gb|GE118485.1|GE118485
EST:     GGGCTCCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGG                         ACCAGATGACACCCCTTGGGATGGAG
genomic: GGGCT-CCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGGgtgtgtagga ... ttttttccagACCAGATGACACCCCTTGGGATGGAG
EST: gi|209728174|gb|BW651609.1|BW651609
EST:     GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGG                         ACCAGATGACACCCCTTGGGATGGAG
genomic: GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGGgtgtgtagga ... ttttttccagACCAGATGACACCCCTTGGGATGGAG
EST: gi|9986725|gb|BE660833.1|BE660833
EST:     GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGG                         ACCAGATGACACCCCTTGGGATGGAG
genomic: GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGGgtgtgtagga ... ttttttccagACCAGATGACACCCCTTGGGATGGAG
EST: gi|22926835|gb|BU543974.1|BU543974
EST:     GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGG                         ACCAGATGACACCCCTTGGGATGGAG
genomic: GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGGgtgtgtagga ... ttttttccagACCAGATGACACCCCTTGGGATGGAG
EST: gi|193570531|gb|FK524958.1|FK524958
EST:     GGCTCCCCAAGACAATTAATTATTATGCTTTGGAATGCTGTTATCTTTGG                         ACCAGATGACACCCCTTGGGATGGAG
genomic: GGCTCCCCAAGACAA-TAA-TATTATGCTTTGGAATGCTGTTATCTTTGGgtgtgtagga ... ttttttccagACCAGATGACACCCCTTGGGATGGAG
EST: gi|13311395|gb|BG405046.1|BG405046
EST:     GTTATCTTTGG                         ACCAGATGACACCCCTTGGGATGGAG
genomic: GTTATCTTTGGgtgtgtagga ... ttttttccagACCAGATGACACCCCTTGGGATGGAG
EST: gi|21255605|gb|BQ452493.1|BQ452493
EST:     GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGG                         ACCAGATGACACCCCTTGGGATGGAG
genomic: GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGGgtgtgtagga ... ttttttccagACCAGATGACACCCCTTGGGATGGAG
EST: gi|13480716|gb|BG510059.1|BG510059
EST:     GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGG                         ACCAGATGACACCCCTTGGGATGGAG
genomic: GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGGgtgtgtagga ... ttttttccagACCAGATGACACCCCTTGGGATGGAG
EST: gi|254333697|gb|GR848615.1|GR848615
EST:     GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGG                         ACCAGATGACACCCCTTGGGATGGAG
genomic: GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGGgtgtgtagga ... ttttttccagACCAGATGACACCCCTTGGGATGGAG
EST: gi|17518903|gb|BM187945.1|BM187945
EST:     TGTTATCTTTGG                         ACCAGATGACACCCCTTGGGATGGAG
genomic: TGTTATCTTTGGgtgtgtagga ... ttttttccagACCAGATGACACCCCTTGGGATGGAG
EST: gi|192294426|gb|FG987355.1|FG987355
EST:     GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGG                         ACCAGATGACACCCCTTGGGATGGAG
genomic: GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGGgtgtgtagga ... ttttttccagACCAGATGACACCCCTTGGGATGGAG
EST: gi|4292045|gb|AI437706.1|AI437706
EST:     GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGG                         ACCAGATGACACCCCTTGGGATGGAG
genomic: GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGGgtgtgtagga ... ttttttccagACCAGATGACACCCCTTGGGATGGAG
EST: gi|254333698|gb|GR848616.1|GR848616
EST:     GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGG                         ACCAGATGACACCCCTTGGGATGGAG
genomic: GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGGgtgtgtagga ... ttttttccagACCAGATGACACCCCTTGGGATGGAG
EST: gi|192305566|gb|FG998322.1|FG998322
EST:     GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGG                         ACCAGATGACACCCCTTGGGATGGAG
genomic: GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGGgtgtgtagga ... ttttttccagACCAGATGACACCCCTTGGGATGGAG
EST: gi|26269575|gb|CA820638.1|CA820638
EST:     GGGGCTCCCCAACACAATAATATTATGCTTTGGAATGCTGTTATCTTTGG                         ACCAGATGACACCCCTTGGGATGGAG
genomic: GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGGgtgtgtagga ... ttttttccagACCAGATGACACCCCTTGGGATGGAG
EST: gi|254320629|gb|GR827078.1|GR827078
EST:     GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGG                         ACCAGATGACACCCCTTGGGATGGAG
genomic: GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGGgtgtgtagga ... ttttttccagACCAGATGACACCCCTTGGGATGGAG
EST: gi|193369402|gb|FK336664.1|FK336664
EST:     GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGG                         CCCAGATGACACCCCTTGGGATGGAG
genomic: GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGGgtgtgtagga ... ttttttccagACCAGATGACACCCCTTGGGATGGAG
EST: gi|15812366|gb|BI784641.1|BI784641
EST:     CCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGG                         ACCAGATGACACCCCTTGGGATGGAG
genomic: CCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGGgtgtgtagga ... ttttttccagACCAGATGACACCCCTTGGGATGGAG
EST: gi|22926846|gb|BU543985.1|BU543985
EST:     AATAATATTATGCTTTGGAATGCTGTTATCTTTGG                         ACCAGATGACACCCCTTGGGATGGAG
genomic: AATAATATTATGCTTTGGAATGCTGTTATCTTTGGgtgtgtagga ... ttttttccagACCAGATGACACCCCTTGGGATGGAG
EST: gi|4295885|gb|AI442396.1|AI442396
EST:     GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGG                         ACCAGATGACACCCCTTGGGATGGAG
genomic: GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGGgtgtgtagga ... ttttttccagACCAGATGACACCCCTTGGGATGGAG
EST: gi|192296666|gb|FG991234.1|FG991234
EST:     GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGG                         ACCAGATGACACCCCTTGGGATGGAG
genomic: GGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGGgtgtgtagga ... ttttttccagACCAGATGACACCCCTTGGGATGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGAGGGATTTTAAAAGATTGCAACAAGATCCTCCTGCTGGCATCAGTGGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGGgtgtgtaggagtatataaatcatgaaatttttgttttcttaagtgtgtgtttctctttactttgtggttttggatgatttaaggtatgataacaatctaattgtgcttttcttggttctttttttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT