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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgacacatagaattgtatttttgagttgtgatagtctggtagataattgaaaccattcttactctagctttagaagcatgcaattagctatctgcatttttcaattatgtcaatatctccctcattttttttgagtacgcccttttataattagttttgcttatgttgctcctctttgaaatcgcagAAAGATTAAAGATAGACCGAGAGATCTTGCCAAGTGGGATGAGATAGCTGATGTTGTGTCAGCGCTGTCAATTCCAGTTATAGCTAATGGAGATGTCTTT

Basic information

species Zea mays
transcript GRMZM2G468693_T06
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G468693_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g44890.1 (Oryza sativa), 3'ss of exon 5
gtaatgacacatagaattgtatttttgagttgtgatagtctggtagataattgaaaccattcttactctagctttagaagcatgcaattagctatctgcatttttcaattatgtcaatatctccctcattttttttgagtacgcccttttataattagttttgcttatgttgctcctctttgaaatcgcagAAAGATTAAAGATAGACCGAGAGATCTTGCCAAGTGGGATGAGATAGCTGATGTTGTGTCAGCGCTGTCAATTCCAGTTATAGCTAATGGAGATGTCTTT
                                                                           ||||  |||  ||     || |  | | | || ||   ||||| | ||||| || | | ||          |||  |||||  |||  || ||||||     ||||  |   |||||||| | ||||| ||||| ||||||| ||| |||||||||||||| || ||||||||||| || |||||||||||||||||||||||||||||||| |||
--------------------------------------------------------------------------cagaataatgtcat-----atatcaactctccattt---tcaatct-tccctaatatgtctt--------tttttgttaattgatttccctgatgttggattcctttacacatgcagAAAGGTCAAAGACAGACCAAGAGATCCTGCTAAGTGGGATGAGATTGCAGATGTTGTGTCTGCACTGTCAATTCCAGTTATAGCTAATGGAGATGTATTT

upper sequence: GRMZM2G468693_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G36840.1 (Glycine max), 3'ss of exon 5
gtaatgacacatagaattgtatttttgagttgtgatagtctggtagataattgaaaccattcttactctagctttagaagcatgcaattagctatctgcatttttcaattatgtcaatatctccctcattttttttgagtacgcccttttataattagttttgcttatgttgctcctctttgaaatcgcagAAAGATTAAAGATAGACCGAGAGATCTTGCCAAGTGGGATGAGATAGCTGATGTTGTGTCAGCGCTGTCAATTCCAGTTATAGCTAATGGAGATGTCTTT
                                                                                 || |  |   |||| | |  | |||||||   |  | ||| |    |||  | ||  ||          ||  | | ||||     ||||| ||   ||        ||||||  |   |||||| || ||||||| ||| |||||| |||| || |||||||||||||||||  | || |||||||||||||  ||||| ||||| |||
--------------------------------------------------------------------------------aattctttctcctattttc--tgttcaatttcattta-atcactagtattaatctttggt-tattaacacatgctcacttttttccttgttgatctattt-------acagAAAAGTCCCAGATAGGCCCAGAGATCCTGCTAAGTGGAATGAAATCGCTGATGTTGTGTCAGCATTATCTATTCCAGTTATAGAAAATGGTGATGTTTTT

upper sequence: GRMZM2G468693_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA01G23820.3 (Glycine max), 3'ss of exon 5
gtaatgacacatagaattgtatttttgagttgtgatagtctggtagataattgaaaccattcttactctagctttagaagcatgcaattagctatctgcatttttcaattatgtcaatatctccctcattttttttgagtacgcccttttataattagttt-tgcttatgttgctcctctttga---aatcgcagAAAGATTAAAGATAGACCGAGAGATCTTGCCAAGTGGGATGAGATAGCTGATGTTGTGTCAGCGCTGTCAATTCCAGTTATAGCTAATGGAGATGTCTTT
                                                                                            ||  |   | |   | || |||  | || ||  | | |   |   | ||    ||||  | ||||     || | |  ||  ||||  ||||   | |  ||||||  |   |||||| || ||||||| ||| |||||| |||| || |||||||||||||||||  | || |||||||||||||| ||||| ||||| |||
--------------------------------------------------------------------------------------------taattctctctcctatttctgttca-atttcatttaatcactaatattaa--tctttggttattaacacatgttcacttttttccttgttgatctatttacagAAAAGTCCCAGATAGGCCCAGAGATCCTGCTAAGTGGAATGAAATCGCTGATGTTGTGTCAGCATTATCTATTCCAGTTATAGCAAATGGTGATGTTTTT

upper sequence: GRMZM2G468693_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ08104 (Selaginella moellendorffii), 3'ss of exon 5
gtaatgacacatagaattgtatttttgagttgtgatagtctggtagataattgaaaccattcttactctagctttagaagcatgcaatt-agctatctgcatttttcaattatgtcaatatctccctcattttttttgagtacgcccttttataattagttttgcttatgttgctcctctttgaaatcgcagAAAGATTAAAGATAGACCGAGAGATCTTGCCAAGTGGGATGAGATAGCTGATGTTGTGTCAGCGCTGTCAATTCCAGTTATAGCTAATGGAGATGTCTTT
                                                                          |      | |  ||| |  |   ||  |  || ||    |  ||||| |      |||| ||      | | ||| | |  | |     |   |  ||| |  |||||       ||| |  |||   |||||||| | ||||| ||||||||||||||  || || ||||| ||||| |||||||||||||| || ||||||||||| ||||| || 
-------------------------------------------------------------------------gtgatgctacgggattgaaatgcatgtttcctttaacc--gctaatatgt-----gttttctt------ctcacttgttttctcaaacacgtacaatttgtttttcttt-----tccagGAGAATTCCCGATAGACCAAAAGATCGTGCCAAGTGGGATGGAATCGCGGATGTGGTGTCTGCGCTGTCAATTCCTGTCATAGCTAATGGGGATGTTTTC

upper sequence: GRMZM2G468693_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ24692 (Selaginella moellendorffii), 3'ss of exon 5
gtaatgacacatagaattgtatttttgagttgtgatagtctggtagataattgaaaccattcttactctagctttagaagcatgcaattagctatctgcatttttcaattatgtcaatatctccctcattttttttgagtacgcccttttataattagttttgcttatgttgctcctctttgaaatcgcagAAAGATTAAAGATAGACCGAGAGATCTTGCCAAGTGGGATGAGATAGCTGATGTTGTGTCAGCGCTGTCAATTCCAGTTATAGCTAATGGAGATGTCTTT
                                                                                                    |  | | |     |  | ||     |   ||||      ||   | ||||    |     ||| || | || |   | |||    |  ||| |  ||    |||||||| | ||||| ||||||||||||||  || || ||||| ||||| |||||||||||||| || ||||||||||| ||||| || 
---------------------------------------------------------------------------------------------------gtgatgctacgggattgagatgcatgtttcttttaaccgctaattcgtttttccttctcacttgttt-tcttacaaattttttt--ttccagGAGAATCCCCGATAGACCAAAAGATCGTGCCAAGTGGGATGGAATCGCGGATGTGGTGTCTGCGCTGTCAATTCCTGTCATAGCTAATGGGGATGTTTTC

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|18963977|gb|BM660737.1|BM660737
EST:     GCACGCCGGATTGAGAAAACTGGTGTTCCTGCTCTTGCTGTCCATGGAAG                         AAAGATTAAAGA
genomic: GCACGCCGGATTGAGAAAACTGGTGTTCCTGCTCTTGCTGTCCATGGAAGgtaatgacac ... gaaatcgcagAAAGATTAAAGA
EST: gi|78022286|gb|DV490673.1|DV490673
EST:     GCACGCCGGATTGAGAAAACTGGTGTTCCTGCTCTTGCTGTCCATGGAAG                         AAAGATTAAAGATAGACCGAGAGATCTTGCCAAGTGGGATGAGATAGCTGA
genomic: GCACGCCGGATTGAGAAAACTGGTGTTCCTGCTCTTGCTGTCCATGGAAGgtaatgacac ... gaaatcgcagAAAGATTAAAGATAGACCGAGAGATCTTGCCAAGTGGGATGAGATAGCTGA
EST: gi|87153475|gb|DY398264.1|DY398264
EST:     GCACGCCGGATTGAGAAAACTGGTGTTCCTGCTCTTGCTGTCCATGGAAG                         AAAGATTAAAGA
genomic: GCACGCCGGATTGAGAAAACTGGTGTTCCTGCTCTTGCTGTCCATGGAAGgtaatgacac ... gaaatcgcagAAAGATTAAAGA
EST: gi|76922868|gb|DV169214.1|DV169214
EST:     GCACGCCGGATTGAGAAAACTGGTGTTCCTGCTCTTGCTGTCCATGGAAG                         AAAGATTAAAGATAGACCGAGAGATCTTGCCAAGTGGGATGAGATAGCTGA
genomic: GCACGCCGGATTGAGAAAACTGGTGTTCCTGCTCTTGCTGTCCATGGAAGgtaatgacac ... gaaatcgcagAAAGATTAAAGATAGACCGAGAGATCTTGCCAAGTGGGATGAGATAGCTGA
EST: gi|76015755|gb|DT942925.1|DT942925
EST:     GCACGCCGGATTGAGAAAACTGGTGTTCCTGCTCTTGCTGTCCATGGAAG                         AAAGATTAAAGATAGACCGAGAGATCTTGCCAAGTGGGATGAGATAGCTGA
genomic: GCACGCCGGATTGAGAAAACTGGTGTTCCTGCTCTTGCTGTCCATGGAAGgtaatgacac ... gaaatcgcagAAAGATTAAAGATAGACCGAGAGATCTTGCCAAGTGGGATGAGATAGCTGA
EST: gi|5915492|gb|AW053133.1|AW053133
EST:     GCACGCCGGATTGAGAAAACTGGTGTTCCTGCTCTTGCTGTCCATGGAAG                         AAAGATTAAAGATAGACCGAGAGATCTTGCCAAGTGGGATGAGATAGCTGA
genomic: GCACGCCGGATTGAGAAAACTGGTGTTCCTGCTCTTGCTGTCCATGGAAGgtaatgacac ... gaaatcgcagAAAGATTAAAGATAGACCGAGAGATCTTGCCAAGTGGGATGAGATAGCTGA
EST: gi|89762291|gb|DY689959.1|DY689959
EST:     GCACGCCGGATTGAGAAAACTGGTGTTCCTGCTCTTGCTGTCCATGGAAG                         AAAGATTAAAGATAGAC
genomic: GCACGCCGGATTGAGAAAACTGGTGTTCCTGCTCTTGCTGTCCATGGAAGgtaatgacac ... gaaatcgcagAAAGATTAAAGATAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtacgcccttttataattagttttgcttatgttgctcctctttgaaatcgcagAAAGATTAAAGATAGACCGAGAGATCTTGCCAAGTGGGATGAGATAGCTGATGTTGTGTCAGCGCTGTCAATTCCAGTTATAGCTAATGGAGATGTCTTT
                                    ctcctctttg  CT-rich tract
          ttttataattagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgacacatagaattgtatttttgagttgtgatagtctggtagataattgaaaccattcttactctagctttagaagcatgcaattagctatctgcatttttcaattatgtcaatatctccctcattttttttgagtacgcccttttataattagttttgcttatgttgctcctctttgaaatcgcagAAAGATTAAAGATAGACCGAGAGATCTTGCCAAGTGGGATGAGATAGCTGATGTTGTGTCAGCGCTGTCAATTCCAGTTATAGCTAATGGAGATGTCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG