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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgtgtgaattttaaatgtgtgatggattttattatgtacctttggtttttgtatgtctctagtaattgaaattagctatcagttgacttacatgattggtttccttaacagGTGGAAACTTTTGGCGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAA

Basic information

species Glycine max
transcript GLYMA06G15330.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G15330.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G64760.2 (Arabidopsis thaliana), 3'ss of exon 4
gtccgtgtgaattttaaatgtgtgatggattttattatgtacctttggtttttgtatgtctctagtaattgaaattagctatcagttgacttacatgattggtttccttaacagGTGGAAACTTTTGGCGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAA
              |||   | |  |    | || | |  | |||| ||     |   | | || | |||  | |    ||||| |   | |  ||  |   | |   | | ||||||| || ||||| || ||||| |||||||||||||| || |||||||||||||||
-------------gtaagcttttctt--cctctactttccaactttcgtggaaatcgttttttatttatttta-tagtttatcaatgtgcattgattgtgattatgaattatagGTGGAGACATTTGGTGCTATGGCAAAAACTGAGAAAATTGCTTTCATTCTTGAACAA

upper sequence: GLYMA06G15330.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G09900.2 (Arabidopsis thaliana), 3'ss of exon 4
gtccgtgtgaattttaaatgtgtgatggattttattatgtacctttggtttttgtatgtctctagtaattgaaattagctatcagttgacttacatgattggtt---tccttaacagGTGGAAACTTTTGGCGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAA
                             |   ||| ||| | ||||| | ||  || || || | ||||    ||        ||| ||       ||| | |   |  |||||||||||| || ||||| || ||||| |||||||||||||| ||||| || |||||||||
----------------------------gtaagattttgtgcatttggctattaaatctc-ctggaaatt----ttcttcccttgttaacccctgcaatttgataaataattaacagGTGGAGACATTTGGTGCTATGGCAAAAACTGAGAAAATTGCATTTATCCTTGAACAA

upper sequence: GLYMA06G15330.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 4
gtccgtgtgaattttaaatgtgtgatggattttattatgtacctttggtttttgta-----tgtctctagtaattgaaattagctatcagttgacttacatgattggt-ttccttaa---cagGTGGAAACTTTTGGCGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAA
      || | ||  ||||  | | |    |    | | ||  |||||| || | |     |  | |   |  |||   |||  ||| |   ||      || ||| | || |||||   ||||||||||| ||||| || ||||| |||||||| ||||| ||||||||||||||||||
------gtcagttaaaaata-gagttaccatgggctttttatttttggtattagaaaacactaaccccgttgtttgttttta--tattacacgagcactttggttgatgttacttaatcacagGTGGAAACATTTGGTGCAATGGCAAAAACTGAAAAAATTGCATTCATTCTTGAACAA

upper sequence: GLYMA06G15330.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S257_89V6.2 (Physcomitrella patens), 3'ss of exon 4
--------------------------gtccgtgtgaatttta--aatgtgtgatgg--attttattatgtacctttggtttttgtatgtctctagtaattgaa--attagctatcag----ttgacttacatgattggtttccttaacagGTGGAAACTTTTGGCGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAA
                           ||  |   |   |||  ||  ||| |||   ||  | |     || ||| | |  |    |  |  |     ||    |||   |||  |     ||| |   ||    | |||  |   ||||||||||||||||| |||||||| ||||||||||| || || |||||||||||||||
gtatgtgatattgcttcgtgctgttgatcaattcaacggttagtaacatgtaatgttcatggtgtggaagacattttggtgctactagagtgcacagggtggtgtattgaatattggagccctgattcgtatcggcg-tttggtcttcagGTGGAAACTTTTGGTGCCATGGCAAAAACTGAGAAGATTGCTTTCATTCTTGAACAA

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|41146268|gb|CK606479.1|CK606479
EST:     AAGAACAGGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACTTTTGGCGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
genomic: AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtccgtgtga ... tccttaacagGTGGAAACTTTTGGCGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
EST: gi|7692920|gb|AW761019.1|AW761019
EST:     AAGAACAAGGACTTATAGCTGAAGCTGCTGATTGGATGCAGGAAATTGCG                         GTGGAAACGTTTGGCGCCATGGCTAAGACTGAGAAAATCGCATTCATTCTT
genomic: AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtccgtgtga ... tccttaacagGTGGAAACTTTTGGCGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
EST: gi|26048081|gb|CA784677.1|CA784677
EST:     AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACTTTTGGCGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
genomic: AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtccgtgtga ... tccttaacagGTGGAAACTTTTGGCGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
EST: gi|26048108|gb|CA784697.1|CA784697
EST:     AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACTTTTGGCGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT
genomic: AAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtccgtgtga ... tccttaacagGTGGAAACTTTTGGCGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctagtaattgaaattagctatcagttgacttacatgattggtttccttaacagGTGGAAACTTTTGGCGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAA
                            gacttac  putative branch site (score: 2)
                                           tttcctt  putative PPT
      taattgaaatta  TA-rich tract