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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGAAATCACAGTAACAAAGTTGCTTTTGAAATCATACTATGACATTGTCAGGAAAAATGTTGAGGATCTTGTCCCCAAAGCAATTATGCACTTCTTGgtactttatattcttcttctaggctttgctaaattgtttttcaattagatgccccaaatgatgaatattagacaaataatctgctttcaatttccaaatt...

Basic information

species Glycine max
transcript GLYMA08G07160.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G07160.1 (Glycine max), 5'ss of exon 17
lower sequence: GRMZM2G129155_T01 (Zea mays), 5'ss of exon 17
TGTTGAAATCACAGTAACAAAGTTGCTTTTGAAATCATACTATGACATTGTCAGGAAAAATGTTGAGGATCTTGTCCCCAAAGCAATTATGCACTTCTTGgtactttatattcttcttctaggctttgc--taaattgtttttcaattagatgccccaa-atgatgaatattagacaaataatctgctttcaatttccaaatt
  |||||||  |  | ||||||||||| ||||| ||||| ||  | ||||||||||||||||| |||||  |  | || |||||| ||||||| |||||||||  | ||     ||   | | | || |  ||     | |||    ||  |        ||| |     |||||        ||      ||    | |   
GCTTGAAATAGCGATCACAAAGTTGCTATTGAAGTCATATTACAATATTGTCAGGAAAAATGTGGAGGACTTAATACCAAAAGCAGTTATGCATTTCTTGgtatgtgattcatatccgattgtcctttcggtatgcaatctttgtgctatttttaatggcatggtaggctttagatgtcggtgctaaagctaaacagcta---

upper sequence: GLYMA08G07160.1 (Glycine max), 5'ss of exon 17
lower sequence: GRMZM2G180335_T03 (Zea mays), 5'ss of exon 9
TGTTGAAATCACAGTAACAAAGTTGCTTTTGAAATCATACTATGACATTGTCAGGAAAAATGTTGAGGATCTTGTCCCCAAAGCAATTATGCACTTCTTGgtactttatattcttcttctaggctttgctaaattgtttttcaat---tagatgc--cccaaatgatgaatattagacaaataatctgctttcaatttccaaatt
  |||||||  || | ||||||||||| ||||| ||||| ||  | ||||||||||||||||| |||||  |  | || |||||||||||||| ||| |||||    | |||||| | | |   |    ||  |     ||| ||   |  ||||   ||   || | | | |||     ||  |  ||||  |  |  ||    
ACTTGAAATAGCAATTACAAAGTTGCTATTGAAGTCATATTACAATATTGTCAGGAAAAATGTGGAGGACTTCATACCAAAAGCAATTATGCATTTCCTGgtatgagagattcttatccaattgtcctttatgtgcgcattccatctctgtatgcaatccttgtgct-acttttaatggcatggtaggctt--agatgtcagt--

upper sequence: GLYMA08G07160.1 (Glycine max), 5'ss of exon 17
lower sequence: AT2G14120.3 (Arabidopsis thaliana), 5'ss of exon 18
TGTTGAAATCACAGTAACAAAGTTGCTTTTGAAATCATACTATGACATTGTCAGGAAAAATGTTGAGGATCTTGTCCCCAAAGCAATTATGCACTTCTTGgt--actttatattcttct-----tctag--gctttgctaaattgtttttcaatta--gatgccccaaatgatgaat--att----------agacaaataatctgctttca---atttccaaatt--------
 ||||| ||     |||||||| |  | |||||||| |||||||||||||| ||||| ||||| |||||  | ||||| |||||||| ||||| ||  ||||     ||  | ||||||     |||    |  | || |||   | ||    | |  |||| | |  |   ||  |  |||           ||| |||||     || ||   | ||   |||         
AGTTGAGATTGAGATAACAAAGCTATTATTGAAATCCTACTATGACATTGTAAGGAAGAATGTCGAGGACTTGGTCCCAAAAGCAATCATGCATTTTCTGgttagtgttccactcttctagtcttctgattgtctagccaaac-atcttatggtcattgatgacacttagtgtgggtcgattctttgtgaggggactaataactctattccatataattgtgaataaaacacag

upper sequence: GLYMA08G07160.1 (Glycine max), 5'ss of exon 17
lower sequence: Vv03s0038g00970.t01 (Vitis vinifera), 5'ss of exon 18
TGTTGAAATCACAGTAACAAAGTTGCTTTTGAAATCATACTATGACATTGTCAGGAAAAATGTTGAGGATCTTGTCCCCAAAGCAATTATGCACTTCTTGgtactttatattcttct-tctaggctttgctaaattgtttttcaattagatgccccaaatgatgaatattagacaaataatctgcttt-caatttccaaatt--
  |||||||  |||| || ||  ||||  |   |||||| ||||||||||||||||| ||| ||||||||  ||| || ||||| || ||||||||| ||||| ||  | |  | || |||   |     |   |  | |||   ||  |||  |    || |  |  | | | ||||  |    ||    |  |||   |   
AATTGAAATTTCAGTCACTAAACTGCTGCTACGATCATATTATGACATTGTCAGGAAGAATATTGAGGATGCTGTACCTAAAGCCATCATGCACTTCCTGgtaattgttttaatcctatctgctcaccattttctgttcttttcttttcatgttc----tgttatacctaaaaaaaatgttgaagttcatgagatcctgctgta

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|15285978|gb|BI469869.1|BI469869
EST:     TCAGGAAAAATGTTGAGGATCTTGTCCCCAAAGCAATTATGCACTTCTTG                         GTAAATAACACAAAGAGAGAGCTTCACAATGTCTTCATTGAAAAACTATAC
genomic: TCAGGAAAAATGTTGAGGATCTTGTCCCCAAAGCAATTATGCACTTCTTGgtactttata ... tcataactagGTAAATAACACAAAGAGAGAGCTTCACAATGTCTTCATTGAAAAACTATAC
EST: gi|9440008|gb|BE440519.1|BE440519
EST:     TCAGGAAAAATGTTGAGGATCTTGTCCCCAAAGCAATTATGCACTTCTTG                         GTAAATAACACAAAGAGAGAGCTTCACAATGTCTTCATTGAAAAACTATAC
genomic: TCAGGAAAAATGTTGAGGATCTTGTCCCCAAAGCAATTATGCACTTCTTGgtactttata ... tcataactagGTAAATAACACAAAGAGAGAGCTTCACAATGTCTTCATTGAAAAACTATAC
EST: gi|16349201|gb|BI974796.1|BI974796
EST:     TCAGGAAAAATGTTGAGGATCTTGTCCCCAAAGCAATTATGCACTTCTTG                         GTAAATAACACAAAGAGAGAGCTTCACAATGTCTTCATTGAAAAACTATAC
genomic: TCAGGAAAAATGTTGAGGATCTTGTCCCCAAAGCAATTATGCACTTCTTGgtactttata ... tcataactagGTAAATAACACAAAGAGAGAGCTTCACAATGTCTTCATTGAAAAACTATAC
EST: gi|16347149|gb|BI972744.1|BI972744
EST:     TCAGGAAAAATGTTGAGGATCTTGTCCCCAAAGCAATTATGCACTTCTTG                         GTAAATAACACAAAGAGAGAGCTTCACAATGTCTTCATTGAAAAACTATAC
genomic: TCAGGAAAAATGTTGAGGATCTTGTCCCCAAAGCAATTATGCACTTCTTGgtactttata ... tcataactagGTAAATAACACAAAGAGAGAGCTTCACAATGTCTTCATTGAAAAACTATAC
EST: gi|21887251|gb|BQ740464.1|BQ740464
EST:     TCAGGAAAAATGTTGAGGATCTTGTCCCCAAAGCAATTATGCACTTCTTG                         GTAAATAACACAAAGAGAGAGCTTCACAATGTCTTCATTGAAAAACTATAC
genomic: TCAGGAAAAATGTTGAGGATCTTGTCCCCAAAGCAATTATGCACTTCTTGgtactttata ... tcataactagGTAAATAACACAAAGAGAGAGCTTCACAATGTCTTCATTGAAAAACTATAC
EST: gi|7588935|gb|AW704720.1|AW704720
EST:     AAAAATGTTGAGGATCTTGTCCCCAAAGCAATTATGCACTTCTTG                         GTAAATAACACAAAGAGAGAGCTTCACAATGTCTTCATTGAAAAACTATAC
genomic: AAAAATGTTGAGGATCTTGTCCCCAAAGCAATTATGCACTTCTTGgtactttata ... tcataactagGTAAATAACACAAAGAGAGAGCTTCACAATGTCTTCATTGAAAAACTATAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGAAATCACAGTAACAAAGTTGCTTTTGAAATCATACTATGACATTGTCAGGAAAAATGTTGAGGATCTTGTCCCCAAAGCAATTATGCACTTCTTGgtactttatattcttcttctaggctttgctaaattgtttttcaattagatgccccaaatgatgaatattagacaaataatctgctttcaatttccaaatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA