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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacgaaagtaattgatgccattcttaatttgagatataacttgcaagaatgaacttgccattgtaatattatgttattttttctgttttgttttgctcagATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTTGTGATGGAGAAGATTGAAGCTGTTGTTCAAAGCAAGCCAAAGCGCCCTG

Basic information

species Glycine max
transcript GLYMA20G19000.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G19000.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0051g00650.t01 (Vitis vinifera), 3'ss of exon 3
cacgaaagtaattga-tgccattcttaatttgagatataacttgcaagaat-gaactt--gccattgtaatattatgttattttttctgttttgttttgctcagATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTTGTGATGGAGAAGATTGAAGCTGTTGTTCAAAGCAAGCCAAAGCGCCCTG
     | ||   ||  ||| ||| |     |   |  |   | ||||  || | ||||  ||  || |   |  |  |||  |  | ||   | |      |||||||||||||| ||||| || || |||||||| ||  | ||||| |||  |||| ||||||||||||| || ||||||||||||||||||||||| ||||
---acatgtttctgcctgcaattgtacgagtattactttgttagcaatcattgtacttcagctcttttctcagca-attaagtaatttgacctctgggatgcagATTCAAGAGAATATGAAGGCTATTGATGTCATACCTCTGCTGACACCTACTGTGCTGGAGAAGATTGAGGCCGTTGTTCAAAGCAAGCCAAAGCGACCTG
















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|19936096|gb|BQ080720.1|BQ080720
EST:     CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAG                         ATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
genomic: CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAGgttagttgtc ... ttttgctcagATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
EST: gi|10253010|gb|BE820776.1|BE820776
EST:     CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAG                         ATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
genomic: CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAGgttagttgtc ... ttttgctcagATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
EST: gi|6951390|gb|AW423458.1|AW423458
EST:     AAAGGAGTCTCAG                         ATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
genomic: AAAGGAGTCTCAGgttagttgtc ... ttttgctcagATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
EST: gi|192316315|gb|FK011674.1|FK011674
EST:     CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAG                         ATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
genomic: CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAGgttagttgtc ... ttttgctcagATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
EST: gi|15203251|gb|BI426019.1|BI426019
EST:     CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAG                         ATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
genomic: CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAGgttagttgtc ... ttttgctcagATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
EST: gi|209717858|gb|BW668997.1|BW668997
EST:     CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAG                         ATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
genomic: CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAGgttagttgtc ... ttttgctcagATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
EST: gi|51341740|gb|CO983057.1|CO983057
EST:     CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAG                         ATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
genomic: CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAGgttagttgtc ... ttttgctcagATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
EST: gi|16344418|gb|BI970013.1|BI970013
EST:     CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAG                         ATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
genomic: CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAGgttagttgtc ... ttttgctcagATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
EST: gi|7924550|gb|AW830576.1|AW830576
EST:     CTTATACTAATGTCTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAG                         ATTCAAGAGAACATGAACGCAATCCATGTCATT
genomic: CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAGgttagttgtc ... ttttgctcagATTCAAGAGAACATGAAAGCAATCGATGTCATT
EST: gi|23731385|gb|BU763810.1|BU763810
EST:     CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAG                         ATTCAAGAGAACATGANAGCAATCGATGTC
genomic: CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAGgttagttgtc ... ttttgctcagATTCAAGAGAACATGAAAGCAATCGATGTC
EST: gi|208252994|gb|GE051528.1|GE051528
EST:     CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAG                         ATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
genomic: CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAGgttagttgtc ... ttttgctcagATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
EST: gi|17402081|gb|BM178863.1|BM178863
EST:     CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAG                         ATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
genomic: CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAGgttagttgtc ... ttttgctcagATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
EST: gi|9819631|gb|BE555144.1|BE555144
EST:     CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAG                         ATTCAAGAGAACATGANAGCAATCGATGTCATTCCATTACTGACTCCTGTT
genomic: CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAGgttagttgtc ... ttttgctcagATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
EST: gi|19934613|gb|BQ079643.1|BQ079643
EST:     CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAG                         ATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
genomic: CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAGgttagttgtc ... ttttgctcagATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
EST: gi|6727056|gb|AW311410.1|AW311410
EST:     CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAG                         ATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
genomic: CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAGgttagttgtc ... ttttgctcagATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
EST: gi|151413226|gb|EV283034.1|EV283034
EST:     GCTACAAAGGAGTCTCAG                         ATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
genomic: GCTACAAAGGAGTCTCAGgttagttgtc ... ttttgctcagATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
EST: gi|7029551|gb|AW459392.1|AW459392
EST:     CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAG                         ATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
genomic: CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAGgttagttgtc ... ttttgctcagATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
EST: gi|209726692|gb|BW654821.1|BW654821
EST:     CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAG                         ATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT
genomic: CTAATCCTAATGTTTCCTCGGTTATCTGTGGTGCTACAAAGGAGTCTCAGgttagttgtc ... ttttgctcagATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaatgaacttgccattgtaatattatgttattttttctgttttgttttgctcagATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTTGTGATGGAGAAGATTGAAGCTGTTGTTCAAAGCAAGCCAAAGCGCCCTG
                               ttttttctgttttgtt  CT-rich tract
              attgtaatattatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacgaaagtaattgatgccattcttaatttgagatataacttgcaagaatgaacttgccattgtaatattatgttattttttctgttttgttttgctcagATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTTGTGATGGAGAAGATTGAAGCTGTTGTTCAAAGCAAGCCAAAGCGCCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - -ccattct
- - - - - - - - - - - - - - - - - - - - -tgcaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - -cttgcca