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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagttttctgtgctctttacatgtgtgtgtcttttaattaatttacctaaatcattgctgtagtcgctgttttttaattgtcatatgttgtctcatgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG

Basic information

species Glycine max
transcript GLYMA13G31550.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g58090.1 (Oryza sativa), 3'ss of exon 6
------aagttttctgtgctctttaca----tgtgtgtgtcttttaattaatttacctaaatcattgctgtagtcgctgttttttaattgtcatatgttgtctcatgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG
         || |||    |||||       |   || | | |   |  |  |||| | |     || ||| ||    |  ||||| ||   |  |  | | |  | ||||| ||||||||||| ||||||||||| ||| |||||||||||||  ||||||| ||||||||||||||||| || ||||||||||||||||||
gtaacttgattatctcgattcttttaggcttttcttgggacatgataccagcttactttaggagctg-tgtggtgctcgaattttattta--aatttctttttttttcagGCATATATTGAGAAGGAGGATAGTAAAAAGTTGAAACAAAAGCAGCGGGAGCGTATGCAACCAAAAATGGGCAAGATGGATATAGATTATCAG

upper sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G121354_T01 (Zea mays), 3'ss of exon 2
-----------------------------------------aagttttctgtgctctttacatgt-gtgtgtcttttaattaatttacctaaatcattgctgtagtcgct-gttttttaattgtcatatgttgtctcatgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG
                                            | |||  |  | |||   ||| | | |      || || |    | |  |   |||  |  ||    | |   ||||||   | |        |  ||||| |||||||||||||||||||| |||||| ||||||| || ||  ||||||||||||| || |||||||| |||||||||||||||||||||
gtaacttgcttcttgtatctcagtaatttacttctttctctgcttattcatttttttttctttgtagagcgctgcggaactattcattccagtttggtgccatgatcatgagctacctaattgatttctaaatgtgtacacagGCGTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGGGAGCGCATGCAGCCCAAAATGGGCAAAATGGATATAGATTATCAG

upper sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G132060_T01 (Zea mays), 3'ss of exon 5
--------------------------------------------aagttttctgtgctctttacatgtgtgtgtcttttaattaatttacctaaatc-attgctgtagtcgctg-ttttttaattgtcatatgttgtctcatgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG
                                               || ||     | |||    |||     ||    |   ||| |  | | |    ||   ||  |          | ||||   | |        |  |||||||||||||||||||||||||| |||||| ||||||| || ||  | ||||| ||||| || || ||||| |||||||||||||||||||||
gtaacttgcttctggtatctcagtaatctacctctccctctctctgcttatccaatttttttcttggtggaacactgcagaactattgatatcagtttggtggcataaacatgaaccgcctgattgatttctaaatgtatacacagGCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAG

upper sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 6
lower sequence: AT4G21660.1 (Arabidopsis thaliana), 3'ss of exon 5
aagttttctgtgctctttacatgtgtgtgtcttttaat-taatttacctaaatcattgc-tgtagtcgctgttttttaattgtcatatgttgtctcatgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG
                 || | ||   | ||| | ||| |||  | |  || ||  |   ||      ||||    ||||| |  | || | ||| ||| ||||||| ||||||||||| ||| |||||||  |||| ||||||||| ||||| | ||||||||||||||||| || ||||| || || || |||
----------------gtaaaagttattctctatcaatataaggtgc--aagtcgctaaatgcttctactgtcagctaattcttgtgtggt-tcttatgtagGCTTACATTGAGAAAGAAGATGGTAAGAAATTGAAGCAAAAGCAACGGGAGAGAATGCAACCAAAAATGGGAAAGATGGACATTGACTACCAG

upper sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 6
lower sequence: PP1S505_13V6.1 (Physcomitrella patens), 3'ss of exon 6
--aagttttctgtgctctttacatgtgt-gtgtcttttaattaatttacctaaatcattgctgtagtcgctgttttttaattgtcatatgttgtctcatgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG
   |  |||      ||  |         |  |||||  |   |    ||  | |   || | |   |  ||| ||| |  | | || |  ||    || |||||||||||||| || || || || |||||||| || |||||||| |||||    ||||| ||||| |||||||| ||||| ||||||||||||
tctatatttggaaattcaatctggactcagcatctttagacataacggccctactttgtgttatg--ccatgtatttaatattttatcttatgggctat-cagGCTTATATTGAAAAGGAAGACAGCAAGAAGCTTAAGCAAAAGCAGAGGGAAAAGATGCAGCCAAAGATGGGGAAGATGGACATAGATTATCAG

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|7234841|gb|AW570174.1|AW570174
EST:     TTCAGCTTCCTGATTTCATTGCTGCCACTGGAATTGAGAAAATCAGACAG                         GCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCGAAGGGAG
genomic: TTCAGCTTCCTGATTTCATTGCTGCCACTGGAATTGAGAAAATCAGACAGgtaatatgat ... tctcatgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAG
EST: gi|23725417|gb|BU760662.1|BU760662
EST:     TTCAGCTTCCTGATTTCATTGCTGCCACTGGAATTGAGAAAATCAGACAG                         GCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAG
genomic: TTCAGCTTCCTGATTTCATTGCTGCCACTGGAATTGAGAAAATCAGACAGgtaatatgat ... tctcatgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctaaatcattgctgtagtcgctgttttttaattgtcatatgttgtctcatgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG
                          ttttaat  putative branch site (score: 3)
                                          ttgtctc  putative PPT
                        ttttttaattgtcata  TA-rich tract