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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattcctgtacgtggtcaatgctgcatgtaacagtttctggccaattcatatccaaagttggaatggtttgacaactctaaatgcatgatttgtcggcagATCTTCGGGATGATAAGCAATTTTTTATGGACCATCCTGGTGCAGTGCCAATTACTACAGCACAG

Basic information

species Glycine max
transcript GLYMA04G02530.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G02530.3 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 4
aattcctgtacgtggtcaatgctgcatgtaacagtttct--ggccaattcatatccaaagttggaatggtttgacaactctaaatgcatgatttgtcggcagATCTTCGGGATGATAAGCAATTTTTTATGGACCATCCTGGTGCAGTGCCAATTACTACAGCACAG
|| |    | |    ||| | || ||  ||| |    ||  | ||  |  | ||||||   | |     ||  |    ||  | ||  |  |     |||||||||||| ||||| ||||| |||||| |||||||||||||||| || || || || || || |||
aaattaaattc-caatcatt-ctacagataatatccccttcgacctgtaaagatccaactgtagcccacttacatttttcacattgtttattgcactggcagATCTTCGAGATGACAAGCAGTTTTTTGTGGACCATCCTGGTGCTGTTCCTATCACCACTGCTCAG

upper sequence: GLYMA04G02530.3 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 4
aattcctgtacgtggtcaatgctgcatgtaacagtttctggccaattcatatccaaagttggaatggtttgacaactcta-aatgcatgatttgtcggcagATCTTCGGGATGATAAGCAATTTTTTATGGACCATCCTGGTGCAGTGCCAATTACTACAGCACAG
|| |  ||  | |      | |   |    ||   |   |   |                 | |     | | | ||  | ||||||   |||   | |||||||||| ||||| ||||| || ||| |||||||||||||||| || || || ||||| || |||
aactagtg-gcataacttgtacacaaacccacgcctagagtaaagcctcaggttgctagcagcacatccttatatcttcacaatgcacattttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG

upper sequence: GLYMA04G02530.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g14670.t01 (Vitis vinifera), 3'ss of exon 4
aattcctgtacgtggtcaatgctgcatgtaacagtttctggcca-attcatatccaaagttggaatggtttgacaactctaaatgcatgatttgtcggcagATCTTCGGGATGATAAGCAATTTTTTATGGACCATCCTGGTGCAGTGCCAATTACTACAGCACAG
| ||      |    | ||   ||| | |  || |    | ||  |  | | |||      | |||       ||  | |||        |   || |||||||||||||||||||||||||| ||| | ||||| |||||||||||||| ||||||||||| |||
acttatcactcaaatttaagcttgcct-tctcattagtagtccttaaccttctcccctcgcgaaatataccctcagttttaataatcctttacatctgcagATCTTCGGGATGATAAGCAATTCTTTGTAGACCACCCTGGTGCAGTGCCTATTACTACAGCTCAG

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|58014216|gb|CX700958.1|CX700958
EST:     AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAG                         ATCTTCGGGATGATAAGCAATTTTTTATGGACCATCCTGGTGCAGTGCCAA
genomic: AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAGgtaggtgttt ... ttgtcggcagATCTTCGGGATGATAAGCAATTTTTTATGGACCATCCTGGTGCAGTGCCAA
EST: gi|14258618|gb|BG881526.1|BG881526
EST:     AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAG                         ATCTTCGGGATGATAAGCAATTTTTTATGGACCATCCTGGTGCAGTG
genomic: AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAGgtaggtgttt ... ttgtcggcagATCTTCGGGATGATAAGCAATTTTTTATGGACCATCCTGGTGCAGTG
EST: gi|9563948|gb|BE473457.1|BE473457
EST:     AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAG                         ATCTTCGGGATGATAAGCGATTTTTTATGGACCATCCTGGTGCAGTGGCAA
genomic: AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAGgtaggtgttt ... ttgtcggcagATCTTCGGGATGATAAGCAATTTTTTATGGACCATCCTGGTGCAGTGCCAA
EST: gi|192331824|gb|FK024928.1|FK024928
EST:     AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAG                         ATTTTCGGGATGATAAGCAATTTTTTATGGACCATCCTGGTGCAGTGCCAA
genomic: AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAGgtaggtgttt ... ttgtcggcagATCTTCGGGATGATAAGCAATTTTTTATGGACCATCCTGGTGCAGTGCCAA
EST: gi|193696036|gb|FK637504.1|FK637504
EST:     AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAG                         ATCTTCGGGATGATAAGCAATTTTTTATGGACCATCCTGGTGCAGTGCCAA
genomic: AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAGgtaggtgttt ... ttgtcggcagATCTTCGGGATGATAAGCAATTTTTTATGGACCATCCTGGTGCAGTGCCAA
EST: gi|58024705|gb|CX711446.1|CX711446
EST:     AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAG                         ATCTTCGGGATGATAAGCAATTTTTTATGGACCATCCTGGTGCAGTGCCAA
genomic: AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAGgtaggtgttt ... ttgtcggcagATCTTCGGGATGATAAGCAATTTTTTATGGACCATCCTGGTGCAGTGCCAA
EST: gi|58021086|gb|CX707828.1|CX707828
EST:     AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAG                         ATCTTCGGGATGATAAGCAATTTTTTATGGACCATCCTGGTGCAGTGCCAA
genomic: AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAGgtaggtgttt ... ttgtcggcagATCTTCGGGATGATAAGCAATTTTTTATGGACCATCCTGGTGCAGTGCCAA
EST: gi|151393592|gb|EV263467.1|EV263467
EST:     AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAG                         ATCTTCGGGATGATAAGCAATTTTTTATGGACCATCCTGGTGCAGTGCCAA
genomic: AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAGgtaggtgttt ... ttgtcggcagATCTTCGGGATGATAAGCAATTTTTTATGGACCATCCTGGTGCAGTGCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatatccaaagttggaatggtttgacaactctaaatgcatgatttgtcggcagATCTTCGGGATGATAAGCAATTTTTTATGGACCATCCTGGTGCAGTGCCAATTACTACAGCACAG
                              ctctaaa  putative branch site (score: 3)
                               tctaaat  TA-rich tract