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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgggcaatatacatgatgatgttcattggtcttattgtgtattgtgaacctagcaaatggccttacaatgtctttttcttggttgataaattgaacagGTGCACCTAGGAGATACTCCCCATAACTTGGCTGAAAGTGATTTCGAACATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT

Basic information

species Glycine max
transcript GLYMA12G09300.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G09300.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0080g00160.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------gcatgggcaatatacatgatga-tgttcattggtcttattgtgtattgtgaacctagcaaatggccttacaatgtctttttcttgg---ttgataaa-ttgaacagGTGCACCTAGGAGATACTCCCCATAACTTGGCTGAAAGTGATTTCGAACATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT
                              |     |||  |    || | |  |   || |   | | ||  ||      | ||    |    |||   |    |||| |||    ||| |||| ||| | ||||||| || ||||||||||| || |||||| ||||||||||||| |||   || ||||  |||||||| |||||||| |||||||||||  |||| |||
gtactggaacttgttcttgattttttccttacaaataattcaataaataaataataggtgatgcaactctgctttacagtgccagtgtctctttttaatgtccaattttgttgtgccttggtaaacttgcaaagGTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGCTTAGCTCAGAAGACAGAAGGGTTTTCTGGTTCAGATATTGCTGTTTGT
















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|51338581|gb|CO982447.1|CO982447
EST:     GTATATACATACCCCTACCTGATTTAAAGGCTCGCCAACACATGTTCAAG                         GTGCACCTAGGAGATACTCCCCATAACTTGGCTGAAAGTGATTTCGAACAT
genomic: GTATATACATACCCCTACCTGATTTAAAGGCTCGCCAACACATGTTCAAGgcatgggcaa ... aattgaacagGTGCACCTAGGAGATACTCCCCATAACTTGGCTGAAAGTGATTTCGAACAT
EST: gi|208248007|gb|GE048601.1|GE048601
EST:     CCCTACCTGATTTAAAGGCTCGCCAACACATGTTCAAG                         GTGCACCTAGGAGATACTCCCCATAACTTGGCTGAAAGTGATTTCGAACAT
genomic: CCCTACCTGATTTAAAGGCTCGCCAACACATGTTCAAGgcatgggcaa ... aattgaacagGTGCACCTAGGAGATACTCCCCATAACTTGGCTGAAAGTGATTTCGAACAT
EST: gi|57575390|gb|CX548365.1|CX548365
EST:     GTATATACATACCCCTACCTGATTTAAAGGCTCGCCAACACATGTTCAAG                         GTGCACCTAGGAGATACTCCCCATAACTTGGCTGAAAGTGATTTCGAACAT
genomic: GTATATACATACCCCTACCTGATTTAAAGGCTCGCCAACACATGTTCAAGgcatgggcaa ... aattgaacagGTGCACCTAGGAGATACTCCCCATAACTTGGCTGAAAGTGATTTCGAACAT
EST: gi|193360519|gb|FK328117.1|FK328117
EST:     GTATATACATACCCCTACCTGATTTAAAGGCTCGCCAACACATGTTCAAG                         GTACACCTAGGAGATACTCCCCATAACTTGGCTGAAAGT
genomic: GTATATACATACCCCTACCTGATTTAAAGGCTCGCCAACACATGTTCAAGgcatgggcaa ... aattgaacagGTGCACCTAGGAGATACTCCCCATAACTTGGCTGAAAGT
EST: gi|18721136|gb|BM523322.1|BM523322
EST:     GTATATACATACCCCTACCTGATTTAAAGGCTCGCCAACACATGTTCAAG                         GTGCACCTAGGAGATACTCCCCATAACTTGGCTGAAAGTGATTTCGAACAT
genomic: GTATATACATACCCCTACCTGATTTAAAGGCTCGCCAACACATGTTCAAGgcatgggcaa ... aattgaacagGTGCACCTAGGAGATACTCCCCATAACTTGGCTGAAAGTGATTTCGAACAT
EST: gi|58014504|gb|CX701246.1|CX701246
EST:     GTATATACATACCCCTACCTGATTTAAAGGCTCGCCAACACATGTTCAAG                         GTGCACCTAGGAGATACTCCCCATAACTTGGCTGAAAGTGATTTCGAACAT
genomic: GTATATACATACCCCTACCTGATTTAAAGGCTCGCCAACACATGTTCAAGgcatgggcaa ... aattgaacagGTGCACCTAGGAGATACTCCCCATAACTTGGCTGAAAGTGATTTCGAACAT
EST: gi|58023445|gb|CX710186.1|CX710186
EST:     GTATATACATACCCCTACCTGATTTAAAGGCTCGCCAACACATGTTCAAG                         GTGCACCTAGGAGATACTCCCCATAACTTGGCTGAAAGTGATTTCGAACAT
genomic: GTATATACATACCCCTACCTGATTTAAAGGCTCGCCAACACATGTTCAAGgcatgggcaa ... aattgaacagGTGCACCTAGGAGATACTCCCCATAACTTGGCTGAAAGTGATTTCGAACAT
EST: gi|13252419|gb|BG363322.1|BG363322
EST:     GTATATACATACCCCTACCTGATTTAAAGGCTCGCCAACACATGTTCAAG                         GTGCACCTAGGAGATACTCCCCATAACTTGGCTGAAAGTGATTTCGAACAT
genomic: GTATATACATACCCCTACCTGATTTAAAGGCTCGCCAACACATGTTCAAGgcatgggcaa ... aattgaacagGTGCACCTAGGAGATACTCCCCATAACTTGGCTGAAAGTGATTTCGAACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgaacctagcaaatggccttacaatgtctttttcttggttgataaattgaacagGTGCACCTAGGAGATACTCCCCATAACTTGGCTGAAAGTGATTTCGAACATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT
                                       ttgataaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgggcaatatacatgatgatgttcattggtcttattgtgtattgtgaacctagcaaatggccttacaatgtctttttcttggttgataaattgaacagGTGCACCTAGGAGATACTCCCCATAACTTGGCTGAAAGTGATTTCGAACATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT

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