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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttacttctatatggaattactggtttcattaatcttatacttaatgaatcttaagtaaaaagtttttggacctcctcttcagGTAAAGGATGTGTTATTTGAACCTGTTCGCAAAACCCAAGATGCAATGTTCTTCTTGAAGAATCCCGAGGGTATGTGGATCCCGTGTGGACCAAAGCAAC

Basic information

species Glycine max
transcript GLYMA12G30910.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G30910.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g04814.3 (Oryza sativa), 3'ss of exon 6
gtaagttttacttctatatggaattactggtttcattaatcttatacttaatgaatcttaagtaaaaagtttttggacctcctcttcagGTAAAGGATGTGTTATTTGAACCTGTTCGCAAAACCCAAGATGCAATGTTCTTCTTGAAGAATCCCGAGGGTATGTGGATCCCGTGTGGACCAAAGCAAC
||||||| |  ||||  |   | |  |  || ||  |  |||  ||    ||    || || |        | |        ||  ||||||||||||||||||||||||||||| |||||||| || ||||| ||||||||||| |||  |   |  | ||||||||| || ||||||||||||||| 
gtaagttgt-tttctgca-acattctcatgtatccatgctctgttagcatata---ctgaaatctcgttgctcttttttctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTCTTCTTTAAGGCTGATGGTGATATGTGGATGCCTTGTGGACCAAAGCAAT

upper sequence: GLYMA12G30910.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G126860_T01 (Zea mays), 3'ss of exon 6
----gtaagttttacttct---atatggaattactg-gtttca----ttaatcttatacttaatgaatcttaagtaaaaagtttttggacctcctcttcagGTAAAGGATGTGTTATTTGAACCTGTTCGCAAAACCCAAGATGCAATGTTCTTCTTGAAGAATCCCGAGGGTATGTGGATCCCGTGTGGACCAAAGCAAC
    | || |||    |||   || ||  ||||||  | | ||    | | ||| ||   |  |       || | ||     |       || ||  ||||| |||||||| |||||||||||||| |||||||| || ||||| ||||||||||| |||     ||  |  |||||||| || ||||||||||| ||||
gtaagcaattttggactcttgaatctgtcattactatgctccacagttcagtctcatctatcttactatgcaatttaatctgatacttgtttcttcaacagGTTAAGGATGTCTTATTTGAACCTGTGCGCAAAACACAGGATGCCATGTTCTTCTTCAAGGCAGACGGTGACATGTGGATGCCATGTGGACCAAAACAAC

upper sequence: GLYMA12G30910.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G088834_T01 (Zea mays), 3'ss of exon 6
----gtaagtttt--acttctatat--ggaattactg-gtttcatt----aatcttatacttaatgaatc--ttaagtaaaaagtttttggacctcctct-tcagGTAAAGGATGTGTTATTTGAACCTGTTCGCAAAACCCAAGATGCAATGTTCTTCTTGAAGAATCCCGAGGGTATGTGGATCCCGTGTGGACCAAAGCAAC
    |||| || |  |||| |  ||  |  || |||  | |||| |    | ||| | | |  |  || |  | || |   |    |||      ||||   ||||| ||||| |||||||||||||| || |||||||| || || || ||||||||||| |||     ||  |  |||||||| || |||||||| |||||||
gtaagtaatttctgaacttgtgcatctgtcatcactatgcttcactgctcagtctcacattgtactaagcaatgaaatctgatacattttttttccctcgaccagGTTAAGGACGTGTTATTTGAACCCGTGCGCAAAACGCAGGACGCCATGTTCTTCTTCAAGGCGGACGGTGACATGTGGATGCCATGTGGACCGAAGCAAC

upper sequence: GLYMA12G30910.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G27600.1 (Arabidopsis thaliana), 3'ss of exon 6
------------gtaagttttacttctatatggaattactggtttcat-taatcttatacttaatgaatcttaagtaaaaagtttttggacctcctcttcagGTAAAGGATGTGTTATTTGAACCTGTTCGCAAAACCCAAGATGCAATGTTCTTCTTGAAGAATCCCGAGGGTATGTGGATCCCGTGTGGACCAAAGCAAC
            |   |  ||| ||||   ||   ||| |     | | |  |  ||||  ||   || | |  ||    ||  | |      |   | |||||||| |||||  | |||||||||||||| ||||| ||||||||||||||||| || |||  ||| || ||||  ||||| || ||||| || | ||| |
gtacgtaacttggcctgagttatttcttattgtccttaatttccccctatgttgctatagatagataagcctttgtcttgagaatctttttggctcttgcagGTAAAAGATGTTCTGTTTGAACCTGTTCGTAAAACACAAGATGCAATGTTCTTTTTCAAGTCTCCTGATGGTACATGGATGCCATGTGGGCCTAGGCACC

upper sequence: GLYMA12G30910.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0080g00160.t01 (Vitis vinifera), 3'ss of exon 6
-------------------------------------------gtaagttttacttctatatggaattactggtttcattaatcttatacttaatgaatcttaagtaaaaagtttttgg-acctcctcttcagGTAAAGGATGTGTTATTTGAACCTGTTCGCAAAACCCAAGATGCAATGTTCTTCTTGAAGAATCCCGAGGGTATGTGGATCCCGTGTGGACCAAAGCAAC
                                            | || ||| | ||  ||      |    | |     |   |  ||   |||   |  | |        |||||||     ||| | ||||| || |||||  | |||||||||||||| |||||||||||||||||||| ||| | || | |||  | | ||||||| | |||||||||||||||||||
gtaagtgcgagtgctatatcagatgctcaactaaattctccctttgagcttt-cctcagtagtatggtttaaggtgggacagaatagtagaaaatagcttatcatcttgctttttttggtgtaccctttgcagGTTAAAGATGTACTGTTTGAACCTGTTCGTAAAACCCAAGATGCAATGTTTTTCATTAATACTCCAAATGATATGTGGGTACCGTGTGGACCAAAGCAAC

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|16104773|gb|BI892513.1|BI892513
EST:     ACTTGGCTAGCAGGACAGAGGGGTTTTCTGGTTCAGACATATCTGTCTGT                         GTAAAGGATGTGTTATTTGAACCTGTTCGCAAAACCCAAGATGCAATGTTC
genomic: ACTTGGCTAGCAGGACAGAGGGGTTTTCTGGTTCAGACATATCTGTCTGTgtaagtttta ... tcctcttcagGTAAAGGATGTGTTATTTGAACCTGTTCGCAAAACCCAAGATGCAATGTTC
EST: gi|208067302|gb|GD866916.1|GD866916
EST:     ACTTGGCTAGCAGGACAGAGGGGTTTTCTGGTTCAGACATATCTGTCTGT                         GTAAAGGATGTGTTATTTGAACCTGTTCGCAAAACCCAAGATGCAATGTTC
genomic: ACTTGGCTAGCAGGACAGAGGGGTTTTCTGGTTCAGACATATCTGTCTGTgtaagtttta ... tcctcttcagGTAAAGGATGTGTTATTTGAACCTGTTCGCAAAACCCAAGATGCAATGTTC
EST: gi|207762929|gb|GD733874.1|GD733874
EST:     ACTTGGCTAGCAGGACAGAGGGGTTTTCTGGTTCAGACATATCTGTCTGT                         GTAAAGGATGTGTTATTTGAACCTGTTCGCAAAACCCAAGATGCAATGTTC
genomic: ACTTGGCTAGCAGGACAGAGGGGTTTTCTGGTTCAGACATATCTGTCTGTgtaagtttta ... tcctcttcagGTAAAGGATGTGTTATTTGAACCTGTTCGCAAAACCCAAGATGCAATGTTC
EST: gi|193479837|gb|FK447198.1|FK447198
EST:     ACTTGGCTAGCAGGACAGAGGGGTTTTCTGGTTCAGACATATCTGTCTGT                         GTAAAGGATGTGTTATTTGAACCTGTTCGCAAAACCCAAGATGCAATGTTC
genomic: ACTTGGCTAGCAGGACAGAGGGGTTTTCTGGTTCAGACATATCTGTCTGTgtaagtttta ... tcctcttcagGTAAAGGATGTGTTATTTGAACCTGTTCGCAAAACCCAAGATGCAATGTTC
EST: gi|207788052|gb|GD760156.1|GD760156
EST:     ACTTGGCTAGCAGGACAGAGGGGTTTTCTGGTTCAGACATATCTGTCTGT                         GTAAAGGATGTGTTATTTGAACCTGTTCGCAAAACCCAAGATGCAATGTTC
genomic: ACTTGGCTAGCAGGACAGAGGGGTTTTCTGGTTCAGACATATCTGTCTGTgtaagtttta ... tcctcttcagGTAAAGGATGTGTTATTTGAACCTGTTCGCAAAACCCAAGATGCAATGTTC
EST: gi|22931002|gb|BU548141.1|BU548141
EST:     ACTTGGCTAGCAGGACAGAGGGGTTTTCTGGTTCAGACATATCTGTCTGT                         GTAAAGGATGTGTTATTTGAACCTGTTCGCAAAACCCAAGATGCAATGTTC
genomic: ACTTGGCTAGCAGGACAGAGGGGTTTTCTGGTTCAGACATATCTGTCTGTgtaagtttta ... tcctcttcagGTAAAGGATGTGTTATTTGAACCTGTTCGCAAAACCCAAGATGCAATGTTC
EST: gi|254331393|gb|GR843405.1|GR843405
EST:     AC-TGGCTAGCAGGACAGA-GGG-TTTCTGGTTCAGACATATCTGTCTGT                         GTAAAGGATGTGTTATTTGAACCTGTTCGCAAAACCCAAGATGCAATGTTC
genomic: ACTTGGCTAGCAGGACAGAGGGGTTTTCTGGTTCAGACATATCTGTCTGTgtaagtttta ... tcctcttcagGTAAAGGATGTGTTATTTGAACCTGTTCGCAAAACCCAAGATGCAATGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaatcttatacttaatgaatcttaagtaaaaagtttttggacctcctcttcagGTAAAGGATGTGTTATTTGAACCTGTTCGCAAAACCCAAGATGCAATGTTCTTCTTGAAGAATCCCGAGGGTATGTGGATCCCGTGTGGACCAAAGCAAC
                                           cctcctcttc  CT-rich tract
       ttatacttaatgaatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttttacttctatatggaattactggtttcattaatcttatacttaatgaatcttaagtaaaaagtttttggacctcctcttcagGTAAAGGATGTGTTATTTGAACCTGTTCGCAAAACCCAAGATGCAATGTTCTTCTTGAAGAATCCCGAGGGTATGTGGATCCCGTGTGGACCAAAGCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA