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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ggcaagtcttttggctattttatttggtttactggacatcttatattctgagtgacaaatttcggtttgttttgaagaccttttcagtgtcttttatgttgaaaaatttaagtagtttattttcagctgattgctaacctattgtttgatggtttgatcaGGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAG

Basic information

species Glycine max
transcript GLYMA18G05730.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G05730.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 4
ggcaagtcttttggctattttatttggtttactggacatcttatattctgagtgacaaatttcggtttgttttgaagaccttttcagtgtcttttatgttgaaaaatttaagtagtttattttcagctgattgctaacctattgtttgatggtttgatcaGGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAG
                                                      |   || |   | || |||  | | ||  | |   | ||   || |  |   |||  | || |||| |||   |  ||| |||   ||   |  ||  ||    ||||| || || || ||||||||||||||||||||||| ||  | || |||||||||||  | || || ||||| ||||||||||| 
-----------------------------------------------------aattcatctgtttatgatttttataactgatgaaattattggttgctagatcctttctg-agattatattc--ttatttggtaattgatctctctat--ttc---cagGTCTGTACTGCTAAAATGAACTTGAGTGATGAGGTTGATTTGGAAGATTATGTTTCCAGACCAGATAAAATTAGTGCTGCTGAT

upper sequence: GLYMA18G05730.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G090904_T01 (Zea mays), 3'ss of exon 4
ggcaagtcttttggctattttatttggtttactggacatcttatattctgagtgacaaatttcggtttgttttgaagaccttttcagt---gtcttttatgttga-aaaatttaagtagtttattttcagctgattgctaacctattgtttgatggtttgatcaGGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAG
                                                            ||  ||||||       | || ||  ||   || || |  ||||  | | |||  ||  | | || | |     ||| |||    | | |||     ||  |||||||||||| |||||||||||| |||| |||||||| ||  | || |||||||||||  | || || || |||||||||||||| 
------------------------------------------------------------tttcgtttgtcaactcaatctgtttggtttggttttctgggttgctagattttgcgtcatctcttctta--cacttgataat---tagcttgtctaattcttcagGTTTGCACTGCCAAAATGAACCTGAGCGATGAGGTTGATTTGGAAGATTATGTTTCCAGACCGGATAAGATCAGTGCTGCTGAT

upper sequence: GLYMA18G05730.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0004g08220.t01 (Vitis vinifera), 3'ss of exon 4
ggcaagtcttttggctattttatttggtttactggacatcttatattctgagtgacaaatttcggtttgttttgaagaccttttcagtgtcttttatgttgaaaaatttaagtagtttattttcagctgattgctaacctattgtttgatggtttgatcaGGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAG
                                                      ||  | |||  ||  ||||  | |  |||||||||| ||  |  |  |  | |||| | |  |||  |     |    | |   ||||| |       |||    |||||||||| || || |||||||| || |||||||| ||| | ||||| ||||||||||| || || ||||| ||||||||||||
------------------------------------------------------acgtacttc--ttccttttctacaggttttcagtgttttggacttccagtagtttatggaaattaaatgtgttttgaag-tggtctattttccc----tttttatagGTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTATGTTTCTCGGCCAGATAAAATTAGTGCTGCTGAG

upper sequence: GLYMA18G05730.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S243_67V6.1 (Physcomitrella patens), 3'ss of exon 4
ggcaagtcttttggctattttatttggtttactggacatcttatattctgagtgacaaatttcggtttgttttgaagaccttttcagtgtcttttatgttgaaaaatttaagtagtttattttcagctgattgctaacctattgtttgatggtttgatcaGGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAG
 | | |  ||    || | || ||  | | | ||    | || || | |  |     ||| | ||| ||    ||   | |  |||||| ||||     |   |||| | | |  || | ||     || ||| |      ||   ||  | ||||| ||||| || ||||| || |||||||| ||||| || || || ||||| |||||||||||| | |||||||| || |||||||| |||
-gtacgagttacttct-tcttgttcagctgattgcg-gttttgtactttttg----gaatctgggtctg---agattgcttgctcagtggcttt----ctatcaaatatcattgcttgactt--gtttggttggtgg---gtttgatggagatttgaacagGTATGTACAGCAAAGATGAACTTAAGTGAGGAAGTTGATCTAGAAGATTATGTTTCTAGGCCTGACAAGATAAGTGCTGCCGAG

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|6454816|gb|AW185499.1|AW185499
EST:     AAAATTGAGTTCCCTTTGCCTGATANACGCCAAAAGAGGCTCGTATTTCA                         GGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTA
genomic: AAAATTGAGTTCCCTTTGCCTGATAGACGCCAAAAGAGGCTCGTATTTCAggcaagtctt ... ggtttgatcaGGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTA
EST: gi|58022279|gb|CX709020.1|CX709020
EST:     AAAATTGAG-TCCCCTTGCCTGATAGACGCCAAAAGAGGCTCGTATTTCA                         GGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTA
genomic: AAAATTGAGTTCCCTTTGCCTGATAGACGCCAAAAGAGGCTCGTATTTCAggcaagtctt ... ggtttgatcaGGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTA
EST: gi|208243697|gb|GE036996.1|GE036996
EST:     AAAATTGAGTTCCCTTTGCCTGATAGACGCCAAAAGAGGCTCGTATTTCA                         GGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTA
genomic: AAAATTGAGTTCCCTTTGCCTGATAGACGCCAAAAGAGGCTCGTATTTCAggcaagtctt ... ggtttgatcaGGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTA
EST: gi|7146493|gb|AW508415.1|AW508415
EST:     AAAATTGAGTTCCCTTTGCCTGATAGACGCCAAAAGAGGCTCGTATTTCA                         GGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTA
genomic: AAAATTGAGTTCCCTTTGCCTGATAGACGCCAAAAGAGGCTCGTATTTCAggcaagtctt ... ggtttgatcaGGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTA
EST: gi|18041397|gb|BM309691.1|BM309691
EST:     AAAATTGAGTTCCCTTTGCCTGATAGACGCCAAAAGAGGCTCGTATTTCA                         CGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTA
genomic: AAAATTGAGTTCCCTTTGCCTGATAGACGCCAAAAGAGGCTCGTATTTCAggcaagtctt ... ggtttgatcaGGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTA
EST: gi|192313767|gb|FK007639.1|FK007639
EST:     AAAATTGAGTTCCCTTTGCCTGATAGACGCCAAAAGAGGCTCGTATTTCA                         GGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTA
genomic: AAAATTGAGTTCCCTTTGCCTGATAGACGCCAAAAGAGGCTCGTATTTCAggcaagtctt ... ggtttgatcaGGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTA
EST: gi|6848666|gb|AW350956.1|AW350956
EST:     AAAGAGGCTCGTATTTCA                         GGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTA
genomic: AAAGAGGCTCGTATTTCAggcaagtctt ... ggtttgatcaGGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTA
EST: gi|192312053|gb|FK003844.1|FK003844
EST:     AAAATTGAGTTCCCTTTGCCTGATAGACGCCAAAAGAGGCTCGTATTTCA                         GGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTA
genomic: AAAATTGAGTTCCCTTTGCCTGATAGACGCCAAAAGAGGCTCGTATTTCAggcaagtctt ... ggtttgatcaGGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTA
EST: gi|4396236|gb|AI495233.1|AI495233
EST:     AAAGAGGCTCGTATTTCA                         GGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTA
genomic: AAAGAGGCTCGTATTTCAggcaagtctt ... ggtttgatcaGGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTA
EST: gi|192313766|gb|FK007638.1|FK007638
EST:     AAAATTGAGTTCCCTTTGCCTGATAGACGCCAAAAGAGGCTCGTATTTCA                         GGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTA
genomic: AAAATTGAGTTCCCTTTGCCTGATAGACGCCAAAAGAGGCTCGTATTTCAggcaagtctt ... ggtttgatcaGGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTA
EST: gi|16342518|gb|BI968113.1|BI968113
EST:     AAAATTGAGTTCCCTTTGCCTGATAGACGCCAAAAGAGGCTCGTATTTCA                         GGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTA
genomic: AAAATTGAGTTCCCTTTGCCTGATAGACGCCAAAAGAGGCTCGTATTTCAggcaagtctt ... ggtttgatcaGGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTA
EST: gi|17401263|gb|BM178045.1|BM178045
EST:     AAAATTGAGTTCCCTTTGCCTGATAGACGCCAAAAGAGGCTCGTATTTCA                         GGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTA
genomic: AAAATTGAGTTCCCTTTGCCTGATAGACGCCAAAAGAGGCTCGTATTTCAggcaagtctt ... ggtttgatcaGGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTA
EST: gi|208106009|gb|GD904222.1|GD904222
EST:     AAAATTGAGTTCCCTTTGCCTGATAGACGCCAAAAGAGGCTCGTATTTCA                         GGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTA
genomic: AAAATTGAGTTCCCTTTGCCTGATAGACGCCAAAAGAGGCTCGTATTTCAggcaagtctt ... ggtttgatcaGGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttaagtagtttattttcagctgattgctaacctattgtttgatggtttgatcaGGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAG
       tagtttatttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggcaagtcttttggctattttatttggtttactggacatcttatattctgagtgacaaatttcggtttgttttgaagaccttttcagtgtcttttatgttgaaaaatttaagtagtttattttcagctgattgctaacctattgtttgatggtttgatcaGGTTTGCACAGCCAAAATGAACTTGAGTGATGAGGTAGACCTAGAGGATTATGTTTCTCGTCCTGACAAAATCAGTGCTGCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT