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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataatttctaacatgctgaaaacataaaattcttaaattaactatacttagtttctgaaccatgccataattaaacacgagtcttaattaatttatgcagGTGAACCCTGATGATGTTGTGTTTGGGGGATGGGATATCAGTAACTTGAACCTGGCTGATGCCATGGCCAGGGCCAAGGTGTTTGATATCGACCTGCAGA

Basic information

species Glycine max
transcript GLYMA08G14670.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G14670.3 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 3
ataatttctaaca-tgctgaaaacataaaattcttaaattaactatacttag-tttctgaaccatgccataattaaacacgagtcttaattaatttatgcagGTGAACCCTGATGATGTTGTGTTTGGGGGATGGGATATCAGTAACTTGAACCTGGCTGATGCCATGGCCAGGGCCAAGGTGTTTGATATCGACCTGCAGA
  |  ||   ||| || |  |    |  ||| | |  |  ||   |  | || |||    | | ||   |          ||   |||   ||   || |||||||||||||||||  ||||||| ||||| ||||| || || ||| |||||||||||||||| ||| ||||||| |||||  |||| || || |||||||
--atctttggacaatgattgatctgttgaatacatccacaaatagttttcagatttgcagaacctgtttttccgttttctgatggttatgaaaaaaattcagGTGAACCCTGATGACCTTGTGTTCGGGGGCTGGGACATTAGCAACATGAACCTGGCTGATGCTATGACCAGGGCAAAGGTACTTGACATTGATCTGCAGA

upper sequence: GLYMA08G14670.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 3
--ataatttctaacatgctgaaaacataaaattcttaaattaactatacttagtttctgaaccatg---ccataattaaacacgagtcttaattaatttatgcagGTGAACCCTGATGATGTTGTGTTTGGGGGATGGGATATCAGTAACTTGAACCTGGCTGATGCCATGGCCAGGGCCAAGGTGTTTGATATCGACCTGCAGA
     | | || |||  | |        || |  ||    ||| |   |  | |||      | ||    ||| |  ||     | | || |     || | ||||||||||| || ||  |||||||||| || ||||| ||||| | | |||||||||| ||||||||| |||||||||||||| | || || ||||||||||
tgggcagtactgacagac-ggtggtgctaactggttg---taaatcctcaaacttttgaggtcttgttttcatgaccaagttgaactattgaactggtttt-cagGTGAACCCAGACGACCTTGTGTTTGGAGGCTGGGACATCAGCAGCATGAACCTGGCAGATGCCATGACCAGGGCCAAGGTGCTGGACATTGACCTGCAGA

upper sequence: GLYMA08G14670.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 1
--ataatttctaacatgctgaaaacataaaattcttaaattaactatacttagtttctgaaccatg---ccataattaaacacgagtcttaattaatttatgcagGTGAACCCTGATGATGTTGTGTTTGGGGGATGGGATATCAGTAACTTGAACCTGGCTGATGCCATGGCCAGGGCCAAGGTGTTTGATATCGACCTGCAGA
     | | || || ||  |        || |  ||    ||| |   |  | |||      | ||    ||| |  ||     | | || |     || | ||||||||| |||| ||  |||||||||| || ||||| ||||| | | ||||| |||| ||||||||| |||||||||||||| | || || ||||| ||||
tgggcagtactgac-tgacggtggtgctaactggttg---taaatcctcaaacttttgaggtcttgttttcatgaccaagttgaactattgaactggtttt-cagGTGAACACTGACGACCTTGTGTTTGGAGGCTGGGACATCAGCATCATGAACTTGGCAGATGCCATGACCAGGGCCAAGGTGCTGGACATTGACCTACAGA

upper sequence: GLYMA08G14670.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 3
ataatt-tctaacat-gctgaaaacataaaat--tcttaaattaactatacttagtttctgaaccatgccataattaaacacgagtcttaattaatttatgcagGTGAACCCTGATGATGTTGTGTTTGGGGGATGGGATATCAGTAACTTGAACCTGGCTGATGCCATGGCCAGGGCCAAGGTGTTTGATATCGACCTGCAGA
| | |  |  |  || |  ||       || |  |   | |||  | | |||  || | ||     | |  |   | | || | || | || |  |||   ||||||||||| || ||  ||||||| || || ||||| || || ||| |||||||||| ||  ||||| |||||||||||||| | ||||| ||||||||||
acactcgtgcagtattgacgatggtgctaactggttgcagattcgc-agactcggtgtttgttatcttcttttcatgaccaagtgt-tgaactggtttt--cagGTGAACCCAGACGACATTGTGTTCGGAGGCTGGGACATTAGCAACATGAACCTGGCCGACTCCATGACCAGGGCCAAGGTGCTGGATATTGACCTGCAGA

upper sequence: GLYMA08G14670.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G177461_T01 (Zea mays), 3'ss of exon 3
-------ataatttctaacatgctgaaaacataaaattcttaaattaactatacttagtttctgaaccatgccataattaaacacgagtcttaattaatttatgcagGTGAACCCTGATGATGTTGTGTTTGGGGGATGGGATATCAGTAACTTGAACCTGGCTGATGCCATGGCCAGGGCCAAGGTGTTTGATATCGACCTGCAGA
       || | || |||  || ||  |   ||  |  ||    | |     | ||||||  |    ||     || |   |     || ||  || | | |||||||| |||||  |   | | || ||||| || ||||| ||||||||| ||||| |||| || ||||||||||||||| ||||  | || ||  |||| ||||
aaaaactatcagttttaatttgttgcgacactagtacactactgtgatacccagttagttctttcttca----gtagtggcatt---gtattgcttgaatcatgcagGTTAACCCCAACACTATCGTCTTTGGTGGGTGGGACATCAGTAACCTGAACATGGCCGACGCCATGGCCAGGGCCCAGGTCCTAGACATTCACCTTCAGA

upper sequence: GLYMA08G14670.3 (Glycine max), 3'ss of exon 2
lower sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 3
-ataatttctaacatgctgaaaacataaaattcttaaattaactatacttagtttctgaaccatgccataattaaacacgagtctta-attaatttatgcagGTGAACCCTGATGATGTTGTGTTTGGGGGATGGGATATCAGTAACTTGAACCTGGCTGATGCCATGGCCAGGGCCAAGGTGTTTGATATCGACCTGCAGA
  |  |   || |  |||   || | ||| || | | |      |   ||  ||  | ||   ||   |||||        ||  |     |||  |  |||||||| || ||||||||||||||||| ||||||||||| ||| || ||||| | || ||||||||||| || |||| |||  ||||||||||| ||||||
gttggtgattagctagcttttaa-acaaatttttgagac-----aggttttcttcttaaagtgtgttttaattttgggatcgttgtgtggaaataaaaacagGTGAATCCGGATGATGTTGTGTTTGGAGGATGGGATATAAGTGACATGAACTTAGCAGATGCCATGGCTAGAGCCAGGGTTCTTGATATCGACTTGCAGA

upper sequence: GLYMA08G14670.3 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 3'ss of exon 3
ataatttc-taacatgctgaaaacataaaattcttaaattaactatacttagtttctgaaccatgccataattaaacacgagtcttaattaatttatgcagGTGAACCCTGATGATGTTGTGTTTGGGGGATGGGATATCAGTAACTTGAACCTGGCTGATGCCATGGCCAGGGCCAAGGTGTTTGATATCGACCTGCAGA
 ||| ||  ||||    |   |    |||||  ||  ||       |   | | | |||   ||   ||| |   | |  | |  || |  | | || ||||||||||| |||||  |||| |||||||||||||| |||||| || |||||||||| ||||| ||||||||||| |||||  | || || || |||||||
gtaagttagtaactcaatttcattg-aaaatatttgcatgtgtggaaagcattatttgatttat-ttatagtatgatataatttatattataatgat-cagGTGAACCCAGATGACATTGTTTTTGGGGGATGGGACATCAGTGACATGAACCTGGCAGATGCAATGGCCAGGGCTAAGGTCCTGGACATTGATCTGCAGA

upper sequence: GLYMA08G14670.3 (Glycine max), 3'ss of exon 2
lower sequence: EFJ37320 (Selaginella moellendorffii), 3'ss of exon 3
ataatttctaacatgctgaaaacataaaattcttaaattaactatacttagtttctgaaccatgccataattaaacacgagtcttaattaatttatgcagGTGAACCCTGATGATGTTGTGTTTGGGGGATGGGATATCAGTAACTTGAACCTGGCTGATGCCATGGCCAGGGCCAAGGTGTTTGATATCGACCTGCAGA
                                            ||  ||    |      |     |  || |      || |    ||     |||||||||| || || ||||||||  ||||||||||||||||||  ||| ||||||| || ||||||||||   | || || || || || || ||||| ||||
-------------------------------------------gtaactaacaacaatcaaagatggttcttgagttttggtttcttgtatcacttgcagGTGAATCCCGACGATGTTGTTCTTGGGGGATGGGATATCAACAACATGAACCTCGCAGATGCCATGGAGCGAGCGAAAGTTTTGGACATGGACCTCCAGA

upper sequence: GLYMA08G14670.3 (Glycine max), 3'ss of exon 2
lower sequence: EFJ27629 (Selaginella moellendorffii), 3'ss of exon 3
ataatttctaacatgctgaaaacataaaattcttaaattaactatacttagtttctgaaccatgccataattaaacacgagtcttaattaatttatgcagGTGAACCCTGATGATGTTGTGTTTGGGGGATGGGATATCAGTAACTTGAACCTGGCTGATGCCATGGCCAGGGCCAAGGTGTTTGATATCGACCTGCAGA
                                            ||  ||    |      |     |  || |      || |    ||     |||||||||| ||||| ||||||||  ||||||||||||||||||  ||| ||||||| || ||||||||||   | || || || || || || ||||| ||||
-------------------------------------------gtaactaacaacaatcaaagatggttcttgagttttggtttcttgtatcacttgcagGTGAATCCTGACGATGTTGTTCTTGGGGGATGGGATATCAACAACATGAACCTCGCAGATGCCATGGAGCGAGCGAAAGTTTTGGACATGGACCTCCAGA

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|14011639|gb|BG726561.1|BG726561
EST:     GGGAAGAAATATATGCTCCATTCAAGAGCCTGCTT-CATATG                         GTGAACCCTGATGATGTTGTGTTTGGGGGATGGGATATCAGTAACTTGAA
genomic: GGGAAGAAATATATGCTCCATTCAAGAGCCTGCTTCCA-ATGgtatactacc ... atttatgcagGTGAACCCTGATGATGTTGTGTTTGGGGGATGGGATATCAGTAACTTGAA
EST: gi|9901531|gb|BE610499.1|BE610499
EST:     CTTTCCAAGGGGAAGAAATATATGCTCCATTCAAGAGCCTGCTTCCAATG                         GTGAACCCTGATGATGTTGTGTTTGGGGGATGGGATATCAGTAACTTGAAC
genomic: CTTTCCAAGGGGAAGAAATATATGCTCCATTCAAGAGCCTGCTTCCAATGgtatactacc ... atttatgcagGTGAACCCTGATGATGTTGTGTTTGGGGGATGGGATATCAGTAACTTGAAC
EST: gi|31561688|gb|CD487526.1|CD487526
EST:     CTTTCCAAGGGGAAGAAATATATGCTCCATTCAAGAGCCTGCTTCCAATG                         GTGAACCCTGATGATGTTGTGTTTGGGGGATGGGATATCAGTAACTTGAAC
genomic: CTTTCCAAGGGGAAGAAATATATGCTCCATTCAAGAGCCTGCTTCCAATGgtatactacc ... atttatgcagGTGAACCCTGATGATGTTGTGTTTGGGGGATGGGATATCAGTAACTTGAAC
EST: gi|22523311|gb|BU082122.1|BU082122
EST:     CTTTCCAAGGGGAAGAAATATATGCTCCATTCAAGAGCCTGCTTCCAATG                         GTGAACCCTGATGATGTTGTGTTTGGGGGATGGGATATCAGTAACTTGAAC
genomic: CTTTCCAAGGGGAAGAAATATATGCTCCATTCAAGAGCCTGCTTCCAATGgtatactacc ... atttatgcagGTGAACCCTGATGATGTTGTGTTTGGGGGATGGGATATCAGTAACTTGAAC
EST: gi|15284727|gb|BI468618.1|BI468618
EST:     CTTTCCAAGGGGAAG-AATATATGCTCCATTCAAGAGCCTGCTTCCAATG                         GTGAACCCTGATGATGTTGTGTTTGGGGGATGGGATATCAGTAACTTGAAC
genomic: CTTTCCAAGGGGAAGAAATATATGCTCCATTCAAGAGCCTGCTTCCAATGgtatactacc ... atttatgcagGTGAACCCTGATGATGTTGTGTTTGGGGGATGGGATATCAGTAACTTGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttagtttctgaaccatgccataattaaacacgagtcttaattaatttatgcagGTGAACCCTGATGATGTTGTGTTTGGGGGATGGGATATCAGTAACTTGAACCTGGCTGATGCCATGGCCAGGGCCAAGGTGTTTGATATCGACCTGCAGA
                                        aattaat  putative branch site (score: 3)
                                  agtcttaattaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataatttctaacatgctgaaaacataaaattcttaaattaactatacttagtttctgaaccatgccataattaaacacgagtcttaattaatttatgcagGTGAACCCTGATGATGTTGTGTTTGGGGGATGGGATATCAGTAACTTGAACCTGGCTGATGCCATGGCCAGGGCCAAGGTGTTTGATATCGACCTGCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG