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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataagtcagttgttacttattaagtgtaatgctgctgttaggctgttagttttccattataatatacatatttttctgatttggatttgaaattttgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCAC

Basic information

species Glycine max
transcript GLYMA07G34680.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G34680.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g43140.1 (Oryza sativa), 3'ss of exon 4
ataagtcagttgttacttattaagtgtaatg-ctgctgttaggctgttagttttccattataatatacatat---ttttctgatttggatttgaaattt---tgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCAC
       ||   |   |||  || | | ||| |||     |   |  ||  |    |||| ||  |     |   ||  || |||   | | |   | |   |||||||||||| ||||||||||| ||||||||||| ||||||||||||||| | || ||
-------agaaatattttaaaaaatttcatgactgtatgcattttcatatgtaaggattaaaaattggtcgtaggttccctcattaatagtcgtgttctgattgcagGGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGAC

upper sequence: GLYMA07G34680.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g09460.1 (Oryza sativa), 3'ss of exon 4
--ataagtcagttgtt--acttattaagtgtaatgctgctgttaggctgttagttttccattataatatacatatttttctgatttggatttgaaattttgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCAC
  |  |  | ||| ||  | || ||||| || | |   ||||     | ||    |      ||| ||  || ||  |  | | |  | | |  || || ||||| || |||||||||||||| |||||||||||||| |||||||||||| | || ||
ctagcatacggttttttgatttgttaagagtcaag--actgtactattcttcagatcaggccatattagtca-atagtcataactgtgctgttcaaatt-gcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGAC

upper sequence: GLYMA07G34680.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G141241_T03 (Zea mays), 3'ss of exon 2
ataagtca-gttgttacttattaagtgtaatgctgctgttaggctgtta--gttttccat-tataatatacatatttttctgatt-tggatttgaaattttgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCAC
 | | ||| |  |||  |||| | || |  | ||  ||| |||| |  |   | |  |||  || || || ||   |  |  ||| |  | ||  |  |||||||| || |||||||||||||| ||||| |||||||| |||||||||||| | || | 
-ttattcatggcgttgtttat-aggtttcctacttttgt-aggcagagaccatgtatcatgcatgatttagatcactcacaaattgtcaagtttca--tttgcagGACCTGATGACATGCCAGCACATATCAAATCATCAATGTTTGGTTGTTCCCTGAT

upper sequence: GLYMA07G34680.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G092988_T01 (Zea mays), 3'ss of exon 3
-----------------------------------------------------ataagtcagttgttacttattaagtgtaatgctgctgttaggctgttagttttccattataatatacatatttttctgatttggatttgaaattttgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCAC
                                                      |||   | |  | |||  | | ||| |    ||  |||| |      ||  | | || |     |||      |  |||||   ||  ||   || |||| || |||||||||||||| ||||||||||| || |||||||||||| | || ||
gttagttaagtctcaatcgtgttactttttgcagaatttcactgaacttttgggtaacgtattcataactactcatgtggatcattg--gttatgaaaaccgtactgctttctttgtgacaagacagtgagatttctgttctaa---ttacagGACCTGATGACATGCCAGCACATATTAAATCTTCTATGTTTGGTTGTTCCCTAAC

upper sequence: GLYMA07G34680.2 (Glycine max), 3'ss of exon 4
lower sequence: AT1G21065.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------------------------------------------ataagtcagttgttac--ttattaagtgtaatgc--tgctgttaggctgttagttttccattataatatacatatttttctgatttggatt----tgaaattttgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCAC
                                                          ||    |||||| |  ||||    || ||||   | || || |||  |   | |    | || |  |   |  |  |  |||||| |||    | ||   ||||||| || |||||||||||||||||||| || ||||| |||||||| |||  ||||||
gttagttgttggtttcatcagactaaagctaatttatatatgaacacacgataaaatcaaagatgttgttccctttatcctctgaaatgtgattctctttggcattacatctgatttcatgaattttgttgtaattagatttgaattgtgttaaataattgcagGTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAACTCAC

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|209715443|gb|BW684715.1|BW684715
EST:     GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG                         GGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
genomic: GGGTCATCTGCGCCATGGAAGCATACTCTAGAGGgttagtactt ... aattttgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
EST: gi|18692788|gb|BM521636.1|BM521636
EST:     GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG                         GGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
genomic: GGGTCATCTGCGCCATGGAAGCATACTCTAGAGGgttagtactt ... aattttgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
EST: gi|31456074|gb|CD398102.1|CD398102
EST:     GGCTCATCTGCGCCATGGAAGCATACTCTAGAGG                         GGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
genomic: GGGTCATCTGCGCCATGGAAGCATACTCTAGAGGgttagtactt ... aattttgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
EST: gi|9984433|gb|BE658541.1|BE658541
EST:     GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG                         GGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
genomic: GGGTCATCTGCGCCATGGAAGCATACTCTAGAGGgttagtactt ... aattttgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
EST: gi|31474712|gb|CD416740.1|CD416740
EST:     GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG                         GGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
genomic: GGGTCATCTGCGCCATGGAAGCATACTCTAGAGGgttagtactt ... aattttgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
EST: gi|15663182|gb|BI700553.1|BI700553
EST:     GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG                         GGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
genomic: GGGTCATCTGCGCCATGGAAGCATACTCTAGAGGgttagtactt ... aattttgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
EST: gi|23733010|gb|BU764686.1|BU764686
EST:     GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG                         GGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
genomic: GGGTCATCTGCGCCATGGAAGCATACTCTAGAGGgttagtactt ... aattttgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
EST: gi|16347696|gb|BI973291.1|BI973291
EST:     GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG                         GGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
genomic: GGGTCATCTGCGCCATGGAAGCATACTCTAGAGGgttagtactt ... aattttgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
EST: gi|7692412|gb|AW760519.1|AW760519
EST:     GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG                         GGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
genomic: GGGTCATCTGCGCCATGGAAGCATACTCTAGAGGgttagtactt ... aattttgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
EST: gi|209715444|gb|BW684716.1|BW684716
EST:     GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG                         GGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
genomic: GGGTCATCTGCGCCATGGAAGCATACTCTAGAGGgttagtactt ... aattttgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
EST: gi|31472535|gb|CD414563.1|CD414563
EST:     GGGTNATCTGCGCCATGGAAGCATACTCTAGAGG                         GGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
genomic: GGGTCATCTGCGCCATGGAAGCATACTCTAGAGGgttagtactt ... aattttgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
EST: gi|298175025|gb|HO018020.1|HO018020
EST:     GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG                         GGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
genomic: GGGTCATCTGCGCCATGGAAGCATACTCTAGAGGgttagtactt ... aattttgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
EST: gi|23733507|gb|BU764952.1|BU764952
EST:     GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG                         GGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
genomic: GGGTCATCTGCGCCATGGAAGCATACTCTAGAGGgttagtactt ... aattttgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
EST: gi|120496558|gb|EH224725.1|EH224725
EST:     GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG                         GGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
genomic: GGGTCATCTGCGCCATGGAAGCATACTCTAGAGGgttagtactt ... aattttgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
EST: gi|298172343|gb|HO019383.1|HO019383
EST:     GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG                         GGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
genomic: GGGTCATCTGCGCCATGGAAGCATACTCTAGAGGgttagtactt ... aattttgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
EST: gi|6135090|gb|AW133483.1|AW133483
EST:     GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG                         GGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGGTGTACAC
genomic: GGGTCATCTGCGCCATGGAAGCATACTCTAGAGGgttagtactt ... aattttgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
EST: gi|120496987|gb|EH225154.1|EH225154
EST:     GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG                         GGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
genomic: GGGTCATCTGCGCCATGGAAGCATACTCTAGAGGgttagtactt ... aattttgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
EST: gi|27425952|gb|CA937472.1|CA937472
EST:     GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG                         GGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC
genomic: GGGTCATCTGCGCCATGGAAGCATACTCTAGAGGgttagtactt ... aattttgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagttttccattataatatacatatttttctgatttggatttgaaattttgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCAC
                            ttctgat  putative branch site (score: 3)
          attataatatacatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataagtcagttgttacttattaagtgtaatgctgctgttaggctgttagttttccattataatatacatatttttctgatttggatttgaaattttgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA