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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttttggctcattaacattgttgggatgagttgtttgccattgacattgtctcctttcctttcatcaagtcttctaaaaaggcctctacatttttgcagTGTGTCTGCAGATACCTATGGTCTGGCTGCTTCGAATTTAGTTGCTGGTAGTAATCTTGAGCAGACTATTCAACAAATTATGGACATGGGTGGTGGCAAT

Basic information

species Glycine max
transcript GLYMA07G00490.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00490.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0018g01400.t01 (Vitis vinifera), 3'ss of exon 5
tcttttggctcattaacattgttgggatgagttgtttgccattgacattgtctcctttcctttcatcaagtct---tctaaaaaggcctctacattttt---gcagTGTGTCTGCAGATACCTATGGTCTGGCTGCTTCGAATTTAGTTGCTGGTAGTAATCTTGAGCAGACTATTCAACAAATTATGGACATGGGTGGTGGCAAT
       |  || ||||| |||  || |   | |       |||| ||| |    | |  ||   | ||       |  |||   |  | |  || |||   ||||||||  ||| |||||||||||||  |||||||| ||| ||||| ||| || | |||||||||| |||||||||||||| ||||| || || ||||| |  
------tgtgcactaacaatgtgaggctttatagaaattgtttgatatttttctttgtttttagtttaaaataaaattcaaatttggttttgtatctttattgcagTGTGCTTGCTGATACCTATGGTCAAGCTGCTTCAAATATAGTTTCTGCTAATCATCTTGAGCAAACTATTCAACAAATAATGGATATAGGCGGTGGAACC
















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|8827362|gb|BE211092.1|BE211092
EST:     AGCTGCAAACAACAGTACATCTAGCACAGATGCCCCAACTACAAA                         TGTGTCTGCACATACCTATGGTCTGGCTGCTTCGAATTTAGTTGCTGGTAG
genomic: AGCTGCAAACAACAGTACATCTAGCACAGATGCCCCAACTACAAAgtatggtttt ... atttttgcagTGTGTCTGCAGATACCTATGGTCTGGCTGCTTCGAATTTAGTTGCTGGTAG
EST: gi|298188098|gb|HO032055.1|HO032055
EST:     AGCTGCAAACAACAGTACGTCTAGCACAGATGCCCCAACTACAAA                         TGTGTCTGCAGATACCTATGGTCTGGCTGCTTCGAATTTAGTTGCTGGTAG
genomic: AGCTGCAAACAACAGTACATCTAGCACAGATGCCCCAACTACAAAgtatggtttt ... atttttgcagTGTGTCTGCAGATACCTATGGTCTGGCTGCTTCGAATTTAGTTGCTGGTAG
EST: gi|213614987|gb|DB957039.1|DB957039
EST:     AGCTGCAAACAACAGTACATCTAGAACAGATGCCCCAACTACAAA                         TGTGTCTGCAGATACCTATGGTCTGGCTGCTTCGAATTTAGTTGCTGGTAG
genomic: AGCTGCAAACAACAGTACATCTAGCACAGATGCCCCAACTACAAAgtatggtttt ... atttttgcagTGTGTCTGCAGATACCTATGGTCTGGCTGCTTCGAATTTAGTTGCTGGTAG
EST: gi|298164323|gb|HO013968.1|HO013968
EST:     AGCTGCAAACAACAGTACATCTAGCACAGATGCCCCAACTACAAA                         TGTGTCTGCAGATACCTATGGTCTGGCTGCTTCG
genomic: AGCTGCAAACAACAGTACATCTAGCACAGATGCCCCAACTACAAAgtatggtttt ... atttttgcagTGTGTCTGCAGATACCTATGGTCTGGCTGCTTCG
EST: gi|213592873|gb|DB969839.1|DB969839
EST:     AGCTGCAAACAACAGTACATCTAGCACAGATGCCCCAACTACAAA                         TGTGTCTGCAGATACCTATGGTCTGGCTGCTTCGAA
genomic: AGCTGCAAACAACAGTACATCTAGCACAGATGCCCCAACTACAAAgtatggtttt ... atttttgcagTGTGTCTGCAGATACCTATGGTCTGGCTGCTTCGAA
EST: gi|27427422|gb|CA938942.1|CA938942
EST:     AGCTGCAAACAACAGTACATCTAGCACAGATGCCCCAACTACAAA                         TGTGTCTGCAGATACCTATGGTCTGGCTGCTTCGAATTTAGTTGCTGGTAG
genomic: AGCTGCAAACAACAGTACATCTAGCACAGATGCCCCAACTACAAAgtatggtttt ... atttttgcagTGTGTCTGCAGATACCTATGGTCTGGCTGCTTCGAATTTAGTTGCTGGTAG
EST: gi|23727295|gb|BU761676.1|BU761676
EST:     AGCTGCAAACAACAGTACATCTAGCACAGATGCCCCAACTACAAA                         TGTGTCTGCAGATACCTATGGTCTGGCTGCTTCGAATTTAGTTGCTGGTAG
genomic: AGCTGCAAACAACAGTACATCTAGCACAGATGCCCCAACTACAAAgtatggtttt ... atttttgcagTGTGTCTGCAGATACCTATGGTCTGGCTGCTTCGAATTTAGTTGCTGGTAG
EST: gi|298172529|gb|HO019569.1|HO019569
EST:     AGCTGCAAACAACGGTACATCTAGCACAGATGCCCCAACTACAAA                         TGTGTCTGCAGATACCTATGGTCTGGCTGCTTCG
genomic: AGCTGCAAACAACAGTACATCTAGCACAGATGCCCCAACTACAAAgtatggtttt ... atttttgcagTGTGTCTGCAGATACCTATGGTCTGGCTGCTTCG
EST: gi|33387852|gb|CA851059.1|CA851059
EST:     AGCTGCAAACAACAGTACATCTAGCACAGATGCCCCAACTACAAA                         TGTGTCTGCAGATACCTATGGTCTGGCTGCTTCGAATTTAGTTGCTGGTAG
genomic: AGCTGCAAACAACAGTACATCTAGCACAGATGCCCCAACTACAAAgtatggtttt ... atttttgcagTGTGTCTGCAGATACCTATGGTCTGGCTGCTTCGAATTTAGTTGCTGGTAG
EST: gi|15200810|gb|BI424534.1|BI424534
EST:     AGCTGCAAACAACAGTACATCTAGCACAGATGCCCCAACTACCAA                         TGTGTCTGCAGATACCTATGGTCTGGCTGCTTCGAATTTAGTTGCTGGTAG
genomic: AGCTGCAAACAACAGTACATCTAGCACAGATGCCCCAACTACAAAgtatggtttt ... atttttgcagTGTGTCTGCAGATACCTATGGTCTGGCTGCTTCGAATTTAGTTGCTGGTAG
EST: gi|15338030|gb|BI498686.1|BI498686
EST:     AGCTGCAAACAACAGTACATCTAGCACAGATGCCCCAACTACAAA                         TGTGTCTGCAGATACCTATGGTCTGGCTGCTTCGAATTTAGTTGCTGGTAG
genomic: AGCTGCAAACAACAGTACATCTAGCACAGATGCCCCAACTACAAAgtatggtttt ... atttttgcagTGTGTCTGCAGATACCTATGGTCTGGCTGCTTCGAATTTAGTTGCTGGTAG
EST: gi|298164600|gb|HO014245.1|HO014245
EST:     AGCTGCAAACAACAGTACATCTAGCACAGATGCCCCAACTACAAA                         TGTGTCTGCAGATACCTATGGTCTGGCTGCTTCG
genomic: AGCTGCAAACAACAGTACATCTAGCACAGATGCCCCAACTACAAAgtatggtttt ... atttttgcagTGTGTCTGCAGATACCTATGGTCTGGCTGCTTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgtctcctttcctttcatcaagtcttctaaaaaggcctctacatttttgcagTGTGTCTGCAGATACCTATGGTCTGGCTGCTTCGAATTTAGTTGCTGGTAGTAATCTTGAGCAGACTATTCAACAAATTATGGACATGGGTGGTGGCAAT
                           ttctaaa  putative branch site (score: 2)
                                            cattttt  putative PPT
                           ttctaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttttggctcattaacattgttgggatgagttgtttgccattgacattgtctcctttcctttcatcaagtcttctaaaaaggcctctacatttttgcagTGTGTCTGCAGATACCTATGGTCTGGCTGCTTCGAATTTAGTTGCTGGTAGTAATCTTGAGCAGACTATTCAACAAATTATGGACATGGGTGGTGGCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG