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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcttgttgtttatgcatatcttctctggccattttactcactaaaatgcatatgtaaggttttatttaaaaatataaaacttgaggttaaacattgtttcattttcttctttgtatatagttatcatggtactgcattatttttcatttgtttcattttagattaaattattaaaatcatagtttatttgcagGCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTGGATATTAACAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTG

Basic information

species Glycine max
transcript GLYMA09G01270.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G01270.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g10310.3 (Oryza sativa), 3'ss of exon 5
gttagcttgttgtttatgcatatcttctctggccattttactcactaaaatgcatatgtaaggttttatttaaaaatataaaacttgag--gttaaacattgtttcattttcttctttgtatatagttatcatggtactg-cattatt-tttcatttgtttcattttagattaaattattaaaatcatagtttatttgcagGCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTGGATATTAACAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTG
||||| || || | | || | | | || || | || || || | | | | | | ||| ||||| ||| | || | | | || || || | || | ||| | |||| || ||| | | || | | | | || || ||||| | ||||||||||| || |||||||||||||||||| | |||||||| ||||| |||| || |||||||| || | | |||||||| |||||||
gttagtttcttacaaacctcttgactcacagtatttggtattc-ttgaactgttattgacatacctgttgcatgtttgttaaatttgagctgttggttgtcattgtggtataaaatctggccgtatgtaattagttatagatattttcatttcccctggatcaaat-atatcataacgctttgttggcttgttgctttcagGCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAATGATGCTGAAGAACATATCTTTGGCCTAATGATAATGAATGATTGGAGTG

upper sequence: GLYMA09G01270.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0187g00300.t01 (Vitis vinifera), 3'ss of exon 3
gttagcttgttgtttatgcatatcttctctggccattttactcactaaaatgcatatgtaaggttttatttaaaaatataaaacttgaggttaaacattgtttcattttcttctttgt-atatagttatcatggtactgcattatttttc--------atttgtttcattttagattaaatt-attaaaatcatagtttatttg-------cagGCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTGGATATTAACAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTG
| | | |||||| | || | ||||||| ||| | ||||| | |||| | || ||| || | || | || | ||||| | || |||| | || || || ||| | | | |||| ||| |||| || | |||||| |||||| |||| ||||| ||||| |||||||| ||||| ||||||||| |||| | ||| ||||||||||||||||||||| | ||||||||||||||||
---------------------------------------gttagttgatatgcattttta---tcctatttaagaattttaaactcatgattaattttagtatcaaattttgtcttatgatgaatttatcgt--tattgcaccagttgtcttgttgtgatatgtgttgtctctgattctatttgttaattatatggcttatttattgcacccagGCTGCTATAGTTGGTCCTGGTAATGAATTAGGAAAGCCTGTGGATGTTAATGAGGCTGCAGATCACATCTTTGGACTTGTGATCATGAATGACTGGAGTG

upper sequence: GLYMA09G01270.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0187g00340.t01 (Vitis vinifera), 3'ss of exon 6
gttagcttgttgtttatgcatatcttctctggccattttactcactaaaatgcatatgtaaggttttatttaaaaatataaaacttgaggttaaacattgtttcattttcttctttgt-atatagttatcatggtactgcattatttttc--------atttgtttcattttagattaaatt-attaaaatcatagtttatttg-------cagGCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTGGATATTAACAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTG
| | | |||||| | || | ||||||| ||| | ||||| | |||| | || ||| || | || | || | ||||| | ||||||| | || || || ||| | | | |||| ||| |||| || | |||||| |||||| |||| ||||| ||||| |||||||| ||||| ||||||||| |||| | ||| |||||| |||||||||||||| | ||||||||||||||||
---------------------------------------gttagttgatatgcattttta---tcctatttaagaattttaaactcatgattaattttagtatcaaattttgtcttatgatgaatttatcgt--tactgcaccagttgtcttgtcgtgatatgtgttgtctctgattctatttgttaattatatggcttatttattgcacccagGCTGCTATAGTTGGTCCTGGTAATGAATTAGGAAAGCCTGTGGATGTTAATGAGGCTGCAGATCATATCTTTGGACTTGTGATCATGAATGACTGGAGTG

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|208298210|gb|GE095847.1|GE095847
EST:     CTACCCCCTACTTTGGCCCTTCATTAAAGCTAGACTTTGAGTTGGAAATG                         GCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTGGATATTAAC
genomic: CTACCCCCTACTTTGGCCCTTCATTAAAGCTAGACTTTGAGTTGGAAATGgttagcttgt ... ttatttgcagGCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTGGATATTAAC
EST: gi|151405820|gb|EV275635.1|EV275635
EST:     AGTTGGAAATG                         GCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTGGATATTAAC
genomic: AGTTGGAAATGgttagcttgt ... ttatttgcagGCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTGGATATTAAC
EST: gi|254346898|gb|GR856620.1|GR856620
EST:     CTACCCCCTACTTTGGCCCTTCATTAAAGCTAGACTTTGAGTTGGAAATG                         GCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTGGAT
genomic: CTACCCCCTACTTTGGCCCTTCATTAAAGCTAGACTTTGAGTTGGAAATGgttagcttgt ... ttatttgcagGCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTGGAT
EST: gi|6567242|gb|AW234853.1|AW234853
EST:     CTACCCCCTACTTTGGCCCTTCATTAAAGCTAGACTTTGAGTTGGAAATG                         GCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTGGATATTAAC
genomic: CTACCCCCTACTTTGGCCCTTCATTAAAGCTAGACTTTGAGTTGGAAATGgttagcttgt ... ttatttgcagGCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTGGATATTAAC
EST: gi|213601975|gb|DB976222.1|DB976222
EST:     CTACCCCCTACTTTGGCCCTTCATTAAAGCTAGACTTTGAGTTGGAAATG                         GCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTGGATATTAAC
genomic: CTACCCCCTACTTTGGCCCTTCATTAAAGCTAGACTTTGAGTTGGAAATGgttagcttgt ... ttatttgcagGCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTGGATATTAAC
EST: gi|151410471|gb|EV280286.1|EV280286
EST:     CTACCCCCTACTTTGGCCCTTCATTAAAGCTAGACTTTGAGTTGGAAATG                         GCTACTATTGTTGGACCTGGAAATGAATTGGGAAA-CCTGTGGATATTAAC
genomic: CTACCCCCTACTTTGGCCCTTCATTAAAGCTAGACTTTGAGTTGGAAATGgttagcttgt ... ttatttgcagGCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTGGATATTAAC
EST: gi|7924174|gb|AW830200.1|AW830200
EST:     CTACCCGCTACTTTGGCCCTTCATTAAAGCTAGACTTTGAGTTGGAGATG                         GCTACTATTGTTGGACCT
genomic: CTACCCCCTACTTTGGCCCTTCATTAAAGCTAGACTTTGAGTTGGAAATGgttagcttgt ... ttatttgcagGCTACTATTGTTGGACCT
EST: gi|208203370|gb|GD998810.1|GD998810
EST:     CTACCCCCTACTTTGGCCCTTCATTAAAGCTAGACTTTGAGTTGGAAATG                         GCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTGGATATTAAC
genomic: CTACCCCCTACTTTGGCCCTTCATTAAAGCTAGACTTTGAGTTGGAAATGgttagcttgt ... ttatttgcagGCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTGGATATTAAC
EST: gi|192327116|gb|FK015508.1|FK015508
EST:     CTACCCCCTACTTTGGCCCTTCATTAAAGCTAGACTTTGAGTTGGAA-TG                         GCTACTATTGTTGGACCTGGAAATGAATTGGGAAA-CCTGTGGATATTA-C
genomic: CTACCCCCTACTTTGGCCCTTCATTAAAGCTAGACTTTGAGTTGGAAATGgttagcttgt ... ttatttgcagGCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTGGATATTAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttcatttgtttcattttagattaaattattaaaatcatagtttatttgcagGCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTGGATATTAACAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTG
                                            tttattt  CT-rich tract
 tttcattttagattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagcttgttgtttatgcatatcttctctggccattttactcactaaaatgcatatgtaaggttttatttaaaaatataaaacttgaggttaaacattgtttcattttcttctttgtatatagttatcatggtactgcattatttttcatttgtttcattttagattaaattattaaaatcatagtttatttgcagGCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTGGATATTAACAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA