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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaacagcagtcatcagtaatgtattgaagaacgcaataatactattgcttatagttgtaattttgatacttaatttgtttgtttatttactatttgcagACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCTAAGGGCCGAATTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTTATCTATGCTGATACG

Basic information

species Glycine max
transcript GLYMA02G04120.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G04120.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv01s0127g00260.t01 (Vitis vinifera), 3'ss of exon 9
---ctaacagcagtcatcagtaatgtattgaagaacgcaataatactattgcttatagttgtaattttgatacttaatttgtttgtttatttactatttgcagACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCTAAGGGCCGAATTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTTATCTATGCTGATACG
| | || || || | || | | | | | || || | | | || || | || || || | | |||||||||||||| || || || |||||||| ||||||| ||||| || |||||||| |||||||| || |||||||| ||||| |||||||| ||||||
acatttttgagattccccaa-aaaggatcacatgtcttttcagtgggtatcctcat--tcatgaggatgttattaaactttacaagttgtcatattcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGGACTATGGTAGCAGGAGGAGGTGCAAGTGTCATCTATGCAGATACG

upper sequence: GLYMA02G04120.2 (Glycine max), 3'ss of exon 8
lower sequence: PP1S63_54V6.2 (Physcomitrella patens), 3'ss of exon 9
-------------------ctaacagcagtcatcagtaa-----tgtattgaagaacgcaataat---actattgcttatagttgtaattttgatacttaatttgtttgtttatttac-tatttgcagACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCTAAGGGCCGAATTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTTATCTATGCTGATACG
|||| | || || | || | | | ||| || || | | ||| || | |||| |||| | | | |||| | ||||||| |||| || | ||||| || | |||| || |||||||| |||||||||||||| ||||| || ||||| ||||| || || ||||||||
gtgtgattgattcatttatctaatacaagacactaccaaattcttccactccagactttaaccatcgcaattccacttcacgtgatcatttctatacagggtcttaagtagtgtttatgtggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGGACAATGGTTGCTGGAGGTGGTGCCAGTGTCATTTACGCTGATACT

upper sequence: GLYMA02G04120.2 (Glycine max), 3'ss of exon 8
lower sequence: PP1S7_156V6.1 (Physcomitrella patens), 3'ss of exon 9
---------------------------------ctaacagcagtcatcagtaatgtattgaagaacgcaataatactattgcttatagttgtaattttga-tacttaatttgtttgtttatttact-atttgcagACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCTAAGGGCCGAATTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTTATCTATGCTGATACG
|| | | | || | | | | | | || || | | | || | ||| | |||||| | || | | |||||||| |||| ||||| ||||| ||| | ||||||||| | |||||||| ||||| ||||| |||||||||||||| ||||||||||| ||||||||
gtatgcggcactgctctgatagtttgaggcgggctctctggtactaccaaaaccatgccgcatg-tacgagctccctgtt-cgtttgtttccagtttagggcttttaattgacatagctacatgtttgattgcagACCGGTGCCTCCTTGAAATTGACAATCTTGAACCCTGAAGGCCGAATCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG

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|18735196|gb|BM528624.1|BM528624
EST:     GAAGGGTTATGAGTGCCACCGAGTCTTTCATTCATGGATTAGATGAAAAG                         ACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCAAAGGGCCGAATTTGG
genomic: GAAGGGTTATGAGTGCCACCGAGTCTTTCATTCATGGATTAGATGAAAAGgtgcacaaat ... ctatttgcagACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCTAAGGGCCGAATTTGG
EST: gi|57575455|gb|CX548430.1|CX548430
EST:     GAAGGGTTATGAGTGCCACCGAGTCTTTCATTCATGGATTAGATGAAAAG                         ACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCTAAGGGCCGAATTTGG
genomic: GAAGGGTTATGAGTGCCACCGAGTCTTTCATTCATGGATTAGATGAAAAGgtgcacaaat ... ctatttgcagACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCTAAGGGCCGAATTTGG
EST: gi|6134722|gb|AW133115.1|AW133115
EST:     GAAGGGTTATGAGTGCCACCGAGTCTTTCATTCATGGATTAGATGAAAAG                         ACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCTAAGGGCCGAATTTGG
genomic: GAAGGGTTATGAGTGCCACCGAGTCTTTCATTCATGGATTAGATGAAAAGgtgcacaaat ... ctatttgcagACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCTAAGGGCCGAATTTGG
EST: gi|58016426|gb|CX703168.1|CX703168
EST:     GAAGGGTTATGAGTGCCACCGAGTCTTTCATTCATGGATTAGATGAAAAG                         ACAAGTGCATCCTTAAAATTCACAGTGTTGAACCTTAAGGGCCGAATTTGG
genomic: GAAGGGTTATGAGTGCCACCGAGTCTTTCATTCATGGATTAGATGAAAAGgtgcacaaat ... ctatttgcagACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCTAAGGGCCGAATTTGG
EST: gi|16346050|gb|BI971645.1|BI971645
EST:     GAAGGGTTATGAGTGCCACCGAGTCTTTCATTCATGGATTAGATGAAAAG                         ACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCTAAGGGCCGAATTTGG
genomic: GAAGGGTTATGAGTGCCACCGAGTCTTTCATTCATGGATTAGATGAAAAGgtgcacaaat ... ctatttgcagACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCTAAGGGCCGAATTTGG
EST: gi|19453151|gb|BM954561.1|BM954561
EST:     GAAGGGTTATGAGTGCCACCGAGTCTTTCATTCATGGATTAGATGAAAAG                         ACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCTAAGGGCCGAATTTGG
genomic: GAAGGGTTATGAGTGCCACCGAGTCTTTCATTCATGGATTAGATGAAAAGgtgcacaaat ... ctatttgcagACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCTAAGGGCCGAATTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcttatagttgtaattttgatacttaatttgtttgtttatttactatttgcagACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCTAAGGGCCGAATTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTTATCTATGCTGATACG
                       acttaat  putative branch site (score: 4)
 taattttgatacttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaacagcagtcatcagtaatgtattgaagaacgcaataatactattgcttatagttgtaattttgatacttaatttgtttgtttatttactatttgcagACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCTAAGGGCCGAATTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTTATCTATGCTGATACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - gcagtca
- - - - - - - - - - - - - - -gaacgca
- - - - - - - - - - - - - - - - - - - - - ctattgc