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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaacatagaatccccttatctagtcttttagctatgcttaattggtaatagcatcagagaatatgtgtttcctggtatgcctactactatgcagcaaaattttgaccgagtttttctcctgttggtatccagCTAACAAGATTCGTCTTTGGAACAAGGGTGTTGATTCTGAAAAATTCCATCCCAAATACCGCTCCCATGAAATGCGATTAAGACTAAG

Basic information

species Glycine max
transcript GLYMA07G17680.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G17680.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g01030.1 (Oryza sativa), 3'ss of exon 6
gtgaacatagaatccccttatctagtcttttagctatgcttaattggtaatagcatcagagaatatgtgtttcctggtatgcctactactatgcagcaaaattttgaccgagtttttctcctgttggtatccagCTAACAAGATTCGTCTTTGGAACAAGGGTGTTGATTCTGAAAAATTCCATCCCAAATACCGCTCCCATGAAATGCGATTAAGACTAAG
||   ||| |     | |  | | || ||||   ||   |||     | ||     || ||  |     | |  || |||   ||| | | |        ||| |||  |        || | ||    |||||| || ||||| || ||||||||||||||||||||||| ||||  |||||||||   | |||     | ||||||||   ||| |||| 
gttgtcatggctatacatagttttgttttttt-ttacctttaccatcttattctgacatagtttcaccttcttttgctat---taccaattt--------attatgatggg-------tcatatt----tccagCCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAAC

upper sequence: GLYMA07G17680.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g15840.1 (Oryza sativa), 3'ss of exon 7
gtgaacatagaatccccttatctagtcttttagctatgcttaattggtaatagcatcaga-gaatatgtgtttcctggtatgcctactactatgcagcaaaattttgaccgagtttttctcctgttggtatccagCTAACAAGATTCGTCTTTGGAACAAGGGTGTTGATTCTGAAAAATTCCATCCCAAATACCGCTCCCATGAAATGCGATTAAGACTAAG
                                             | |||     | |||  ||| | | |||| |  | |   | || | || || ||      | ||||   ||| ||  | |     | |||| || |   |||| ||||||||||| ||||||||||||||||  |||||||| ||||  ||    |||||||||||  | | | | ||
---------------------------------------------gttaaacaattaagataaatctatatttcttcatttcattccttc-atccatca------taaccgtagtttccttgtctc----ttcagCAAATAGAGTTCGGCTTTGGAACAAAGGTGTTGATTCTGAAAGTTTCCATCCTAAATTTCGGAAGCATGAAATGCGCATTAAATTGAG

upper sequence: GLYMA07G17680.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0007g01940.t01 (Vitis vinifera), 3'ss of exon 7
gtgaacatagaatccccttatctagtcttttagctatgcttaattggtaatagcatcagagaatatgtgtttcctggtatgcctactactatgcagcaaaattttgaccgagtttttctcctgttggtatccagCTAACAAGATTCGTCTTTGGAACAAGGGTGTTGATTCTGAAAAATTCCATCCCAAATACCGCTCCCATGAAATGCGATTAAGACTAAG
                            |  |   |||   | |  | ||  |   || | |  |  |||        ||| | |    |    |   |||  |  |  |    ||| ||   ||| | | |||||||||  |||||||||||||| ||||| ||||| |||||||  ||||||||    |||   || || |||||||| |||||||||||
---------------------------gtgcatggatgtccattgtgcaactgttgcaaaaacaaattgta----atgatgtcaatggatcaatattgaaaactaaattg---ctttatctctttgctttgcagCTAACAGAATTCGTCTTTGGAATAAGGGGGTTGACTCTGAAAGTTTCCATCCTCGTTACTATTCTCACGAAATGCGTTTAAGACTAAG

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|208179722|gb|GD973641.1|GD973641
EST:     CGGGGGATCTTCCTTAGCAGCTAGAGTCACAGCAG                         CTAACAAGATTCGTCTTTGGAACAAGGGTGTTGATTCTGAAAAATTCCATC
genomic: CGGGGGATC-TCC-TAGCAGCTAGAGTCACAGCAGgtgaacatag ... tggtatccagCTAACAAGATTCGTCTTTGGAACAAGGGTGTTGATTCTGAAAAATTCCATC
EST: gi|193701460|gb|FK638219.1|FK638219
EST:     CGGGGGATCTCCTAGCAGCTAGAGTCACAGCAG                         CTAACAAGATTCGTCTTTGGAACAAGGGTGTTGATTCTGAAAAATTCCATC
genomic: CGGGGGATCTCCTAGCAGCTAGAGTCACAGCAGgtgaacatag ... tggtatccagCTAACAAGATTCGTCTTTGGAACAAGGGTGTTGATTCTGAAAAATTCCATC
EST: gi|7590070|gb|AW705831.1|AW705831
EST:     GCCATCTGCTGCCATTGCGGGGGATCTCCTAGCAGCTAGAGTCACAGCAG                         CTAACAAGATTCGTCTTTGGAACAAGGGTGTTGATTCTGAAAAATTCCATC
genomic: GCCATCTGCTGCCATTGCGGGGGATCTCCTAGCAGCTAGAGTCACAGCAGgtgaacatag ... tggtatccagCTAACAAGATTCGTCTTTGGAACAAGGGTGTTGATTCTGAAAAATTCCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcctactactatgcagcaaaattttgaccgagtttttctcctgttggtatccagCTAACAAGATTCGTCTTTGGAACAAGGGTGTTGATTCTGAAAAATTCCATCCCAAATACCGCTCCCATGAAATGCGATTAAGACTAAG
                      ttttgac  putative branch site (score: 3)
                                 tttttctcctgtt  putative PPT
                  aaaattttga  TA-rich tract