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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacttgcaattattttatatatgaatttgaactctcaattagcacatgtgcttcacttgactacacgaagtgctgattgtaatataatgtatgtatacagGTTGAATCTACATTGGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATTCAAGATAGATATGCTGGCAATCAA

Basic information

species Glycine max
transcript GLYMA12G06920.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G06920.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g04460.t01 (Vitis vinifera), 3'ss of exon 2
---aacttgcaattattttatatatgaatttgaactctcaattagcacatgtgcttcacttgactacacgaagtgctgattgtaatataatgtatgtatacagGTTGAATCTACATTGGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATTCAAGATAGATATGCTGGCAATCAA
   ||  ||   | || |     ||     || | | |  | |    |   ||   |  |||        |  || |||   |  | |  | | |||||  |||||||||| ||| |||| |||||||||||||||||||| || |||||||||||||| ||||||   |||||||| 
agcaagatgtt-tcatgtccatcattcccatgtaatattgacttctgctgatgacactgttggtgctgttatatgatgacatt--tgttgtatttgtatgtagGTTGAATCAACACTGGCCATGCAAAATCTTCAACCAAAGATCAAGGCCATTCAAGAAAGATATAAGGGCAATCAG
















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|20815132|gb|BQ299610.1|BQ299610
EST:     TGCTCACTGTTATAGTTAAGGCAGCGACGCTTCCCCTGACAAAGCCACAG                         GTTGAATCTACATTGGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATT
genomic: TGCTCACTGTTATAGTTAAGGCAGCGACGCTTCCCCTGACAAAGCAACAGgttggtacaa ... atgtatacagGTTGAATCTACATTGGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATT
EST: gi|10847282|gb|BF071525.1|BF071525
EST:     TGCTCACTGTTATAGTTAAGGCAGCGACGCTTCCTCTGACAAAGCGACAG                         GTTGAATCTACATTGGCTATGCAAAATCTTTACCCAACA-TTAAGGCCA
genomic: TGCTCACTGTTATAGTTAAGGCAGCGACGCTTCCCCTGACAAAGCAACAGgttggtacaa ... atgtatacagGTTGAATCTACATTGGCTATGCAAAATCTTCAACCAAAAATTAAGGCCA
EST: gi|120533265|gb|EH261398.1|EH261398
EST:     TGCTCACTGTTATAGTTAAGGCAGCGACGCTTCCCCTGACAAAGCAACAG                         GTTGAATCTACATTGGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATT
genomic: TGCTCACTGTTATAGTTAAGGCAGCGACGCTTCCCCTGACAAAGCAACAGgttggtacaa ... atgtatacagGTTGAATCTACATTGGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATT
EST: gi|120533673|gb|EH261806.1|EH261806
EST:     TGCTCACTGTTATAGTTAAGGCAGCGACGCTTCCCCTGACAAAGCAACAG                         GTTGAATCTACATTGGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATT
genomic: TGCTCACTGTTATAGTTAAGGCAGCGACGCTTCCCCTGACAAAGCAACAGgttggtacaa ... atgtatacagGTTGAATCTACATTGGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATT
EST: gi|20207804|gb|BQ133893.1|BQ133893
EST:     TGCTCACTGTTATAGTTAAGGCAGCGACGCTTCCCCTGACAAAGCAACAG                         GTTGAATCTACATTGGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATT
genomic: TGCTCACTGTTATAGTTAAGGCAGCGACGCTTCCCCTGACAAAGCAACAGgttggtacaa ... atgtatacagGTTGAATCTACATTGGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATT
EST: gi|120533657|gb|EH261790.1|EH261790
EST:     TGCTCACTGTTATAGTTAAGGCAGCGACGCTTCCCCTGACAAAGCAACAG                         GTTGAATCTACATTGGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATT
genomic: TGCTCACTGTTATAGTTAAGGCAGCGACGCTTCCCCTGACAAAGCAACAGgttggtacaa ... atgtatacagGTTGAATCTACATTGGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATT
EST: gi|209720713|gb|BW677531.1|BW677531
EST:     TGCTCACTGTTATAGTTAAGGCAGCGACGCTTCCCCTGACAAAGCAACAG                         GTTGAATCTACATTGGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATT
genomic: TGCTCACTGTTATAGTTAAGGCAGCGACGCTTCCCCTGACAAAGCAACAGgttggtacaa ... atgtatacagGTTGAATCTACATTGGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATT
EST: gi|6134125|gb|AW132518.1|AW132518
EST:     TGCTCACTGTTATAGTTAAGGCAGCGACGCTTCCCCTGACAAAGCAACAG                         GTTGAATCTACATTGGCTATGCAAAATCTTCAACCAAAAATTAA
genomic: TGCTCACTGTTATAGTTAAGGCAGCGACGCTTCCCCTGACAAAGCAACAGgttggtacaa ... atgtatacagGTTGAATCTACATTGGCTATGCAAAATCTTCAACCAAAAATTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtgcttcacttgactacacgaagtgctgattgtaatataatgtatgtatacagGTTGAATCTACATTGGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATTCAAGATAGATATGCTGGCAATCAA
                         tgctgat  putative branch site (score: 3)
                              attgtaatataatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacttgcaattattttatatatgaatttgaactctcaattagcacatgtgcttcacttgactacacgaagtgctgattgtaatataatgtatgtatacagGTTGAATCTACATTGGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATTCAAGATAGATATGCTGGCAATCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- cttgcaa
- - - - - - - - - - - - - - - - - - - - - -acatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctacacg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgat