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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACACAGATGACTGGAATTTATGATTTGGTTGCTGTATTAACCCACAAGGGTAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAAGCAAGAAAATGgttggttctgggaaacagaattgtgtttgtagtatctgactctgtcccggtctctttcaagcaataatattaatttttgttgttggcag

Basic information

species Glycine max
transcript GLYMA07G01480.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G01480.1 (Glycine max), 5'ss of exon 16
lower sequence: LOC_Os01g36930.1 (Oryza sativa), 5'ss of exon 16
ACACAGATGACTGGAATTTATGATTTGGTTGCTGTATTAACCCACAAGGGTAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAAGCAAGAAAATGgttggttctgggaaacagaattgtgtttgtagtatctgactctgtcccggtctctttcaagcaataatattaatttttgttgttggcag
| ||| ||||||| || |||||||| ||||||| || || ||||| || |||||||| || ||||| ||||||||||| ||||| |||||||| | ||| || | | | || | || | | | ||| | | | | || || | | ||| | |
AAACATTTGACTGGCATCTATGATTTAATTGCTGTTTTGACGCACAAAGGGAGAAGTGCAGACTCAGGCCATTATGTTGGCTGGGTTAAGCAAGATGACGgtagggccagctactcatgcagttaattattggagtcaactgtttatttacgatctc--actgatgattatgagctttttag-------

upper sequence: GLYMA07G01480.1 (Glycine max), 5'ss of exon 16
lower sequence: GRMZM2G017086_T03 (Zea mays), 5'ss of exon 16
ACACAGATGACTGGAATTTATGATTTGGTTGCTGTATTAACCCACAAGGGTAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAAGCAAGAAAATGgttggttctgggaaacagaattgtgtttgtagtatctgactctgtcccggtctctttcaagcaataatattaatttttgttgttggcag
| ||| | ||||| | ||||||||||||||||| || || |||||||| |||||||| || || || || |||||||| ||||| |||||||| | ||| || | | | || ||| ||| | || | | | || | || | | ||| | | | |||
AAACAATTAACTGGCGTCTATGATTTGGTTGCTGTCTTGACACACAAGGGAAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTAAAGCAAGATGACGgtcagtcaatcagtattacagcttagttacggtaatcaactgtttcactttattatt-agtcactgaaatttcatatcg--accaccag

upper sequence: GLYMA07G01480.1 (Glycine max), 5'ss of exon 16
lower sequence: GRMZM2G028733_T02 (Zea mays), 5'ss of exon 16
ACACAGATGACTGGAATTTATGATTTGGTTGCTGTATTAACCCACAAGGGTAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAAGCAAGAAAATGgttggttctgggaaacagaattgtgtttgtagtatctgactctgtcccggtctctttcaagcaataatattaatttttgttgttggcag----
| ||| | ||||| | ||||||||||||||||| || || |||||||| |||||||| || || || || |||||||| ||||| |||||||| ||||| || | | ||| || | |||| | | | | | | || | | || | || |
AAACAATTAACTGGCGTCTATGATTTGGTTGCTGTCTTGACACACAAGGGAAGAAGTGCAGACTCTGGCCACTATGTTGGCTGGGTTAAGCAAGATGATGgtcagtcaactagtattacagctcatttactataacaa---ctgtttcattttatacaggttagt--tactgaaattccatattaaccatcag

upper sequence: GLYMA07G01480.1 (Glycine max), 5'ss of exon 16
lower sequence: AT1G51710.2 (Arabidopsis thaliana), 5'ss of exon 13
ACACAGATGACTGGAATTTATGATTTGGTTGCTGTATTAACCCACAAGGGTAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAAGCAAGAAAATGgttggttctgggaaacagaattgtgtttgtagtatctgactctgtcccggtctctttcaagcaataatattaatttttgttgttggcag
|| || ||||||||||| ||||| ||||| ||||| || ||||||||||| || ||||| || || || |||||||||| |||||||||||||| | ||||| |||| | | || | | |||| || | ||| || |||| | | | |||| | || |||
ACTCACATGACTGGAATCTATGACTTGGTCGCTGTGTTGACCCACAAGGGCAGGAGTGCAGACTCTGGTCATTATGTTGCATGGGTCAAGCAAGAGAGTGgttagttccagt-----------ctctaataaactttacctctctcaca---tctctctagcatttacaacaattcacatgttttacag

upper sequence: GLYMA07G01480.1 (Glycine max), 5'ss of exon 16
lower sequence: Vv09s0002g02500.t01 (Vitis vinifera), 5'ss of exon 16
ACACAGATGACTGGAATTTATGATTTGGTTGCTGTATTAACCCACAAGGGTAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAAGCAAGAAAATGgttggttctgggaaacagaattgtgtttgtagtatctgactctgtcccggtctctttcaagcaataatattaatttttgttgttggcag
||||| ||||||||||||||||| |||||||||| || ||||||||||| || |||||||||||||| |||||||||| |||||||||||||||| |||| || || || | | | || | | | || | | || ||| || ||||||| | |
ACACACTTGACTGGAATTTATGATCTGGTTGCTGTGTTGACCCACAAGGGCAGGAGTGCTGATTCAGGGCATTATGTTGCCTGGGTCAAGCAAGAAAGTGgtcagtactctagaataaatt------------atttaatt--gttaccatagaagataaatgtaaattttgatttttggtcacag---

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|19268734|gb|BM884990.1|BM884990
EST:     TAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAAGCAAGAAAATG                         GGAAATGGATAGAGTTTGATGATGACAATCCCAAACCAAAACTAGAAGAAG
genomic: TAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAAGCAAGAAAATGgttggttctg ... ttgttggcagGGAAATGGATAGAGTTTGATGATGACAATCCCAAACCAAAACTAGAAGAAG
EST: gi|58014784|gb|CX701526.1|CX701526
EST:     TAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAAGCAAGAAAATG                         GGAAATGGATAGAGTTTGATGATGACAATCCCAAACCAAAACTAGAAGAAG
genomic: TAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAAGCAAGAAAATGgttggttctg ... ttgttggcagGGAAATGGATAGAGTTTGATGATGACAATCCCAAACCAAAACTAGAAGAAG
EST: gi|22930572|gb|BU547711.1|BU547711
EST:     TAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAAGCAAGAAAATG                         GGAAATGGATAGAGTTTGATGATGACAATCCCAAACCAAAACTAGAAGAAG
genomic: TAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAAGCAAGAAAATGgttggttctg ... ttgttggcagGGAAATGGATAGAGTTTGATGATGACAATCCCAAACCAAAACTAGAAGAAG
EST: gi|24136265|gb|BU926775.1|BU926775
EST:     TAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAAGCAAGAAAATG                         GGAAATGGATAGAGTTTGATGATGACAATCCCAAACCAAAACTAGAAGAAG
genomic: TAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAAGCAAGAAAATGgttggttctg ... ttgttggcagGGAAATGGATAGAGTTTGATGATGACAATCCCAAACCAAAACTAGAAGAAG
EST: gi|58024159|gb|CX710900.1|CX710900
EST:     TAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAAGCAAGAAAATG                         GGAAATGGATAGAGTTTGATGATGACAATCCCAAACCAAAACTAGAAGAAG
genomic: TAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAAGCAAGAAAATGgttggttctg ... ttgttggcagGGAAATGGATAGAGTTTGATGATGACAATCCCAAACCAAAACTAGAAGAAG
EST: gi|58023995|gb|CX710736.1|CX710736
EST:     TAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAAGCAAGAAAATG                         GGAAATGGATAGAGTTTGATGATGACAATCCCAAACCAAAACTAGAAGAAG
genomic: TAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAAGCAAGAAAATGgttggttctg ... ttgttggcagGGAAATGGATAGAGTTTGATGATGACAATCCCAAACCAAAACTAGAAGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACACAGATGACTGGAATTTATGATTTGGTTGCTGTATTAACCCACAAGGGTAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAAGCAAGAAAATGgttggttctgggaaacagaattgtgtttgtagtatctgactctgtcccggtctctttcaagcaataatattaatttttgttgttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA