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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgttccgtttagcggtgtcgctttgtccttcaccggtttagggggctgtcgtgttgatattttttttcccctctgtgctgttcgtgttgccagGCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGCGCGTCCGATCTC

Basic information

species Zea mays
transcript GRMZM2G064023_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064023_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 2
gtgagtgttccgtttagcggtgtcgctttgtccttcaccggtttagggggctgtcgtgttgatattttttttcccctctgtgctgttcgtgttgccagGCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGCGCGTCCGATCTC
||||||  |  | | | |  |      | |||| |  |   |||   | ||  | ||| ||      |      ||  | ||||  |  || |||||||| ||||||||||||||||| |||||||||||||||||||||||||||||  | || ||||| 
gtgagtagt--ggtgatccatcatcgatcgtccatgtcaatttttttgtgcatttgtggtgtggcgctgaaattccgtt-tgctcgtgttgctgccagGCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTT

upper sequence: GRMZM2G064023_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 2
gtgagtgttccgtttagcggtgtcgctttgtccttcaccggtttagggggctgtcgtgttgatat-tttttttcccctctgtgctg-ttcgtgttgccagGCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGCGCGTCCGATCTC
    |||  || |  | |  | | || |     ||  | ||     |  ||  | |  || || |    |       | |  | || || |||||| ||||| ||||||||||||||||| ||||||||| |||||||||||||||||||||| || ||||| 
----gtgagccatccaaca-tcttgcatgcctattttctggc----gatgcgtttgcatttatgtgcgctgaaaaattgttcgttgctttgtgttgtcagGCACAGGAGGCCACCACGCTTGGTGGTGTGCGATGGCTGCAGATGCAGAGCGCATCTGATCTT

upper sequence: GRMZM2G064023_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 1
-----gtgagtgttccgtttagcggtgtcgctttgtccttcaccggtttagggggctgtcgtgttgatattttttttcccctctgtgctgttcgtgttgccagGCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGCGCGTCCGATCTC
     ||||||  |  | | | |  |      | |||| |  |   |||   | ||  | ||| ||      |      ||  | ||||  |  || |||||||| ||||||||||||||||| |||||||||||||||||||||||||||||  | || ||||| 
gcatggtgagtagt--ggtgatccatcatcgatcgtccatgtcaatttttttgtgcatttgtggtgtggcgctgaaattccgtt-tgctcgtgttgctgccagGCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTT

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|149090362|gb|EE179668.2|EE179668
EST:     TGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG                         GCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATGgtgagtgttc ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGC
EST: gi|149082725|gb|EE171943.2|EE171943
EST:     TGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG                         GCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATGgtgagtgttc ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGC
EST: gi|149077813|gb|EE166538.2|EE166538
EST:     TGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG                         GCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATGgtgagtgttc ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGC
EST: gi|8103179|gb|AW927835.1|AW927835
EST:     TGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG                         GCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATGgtgagtgttc ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGC
EST: gi|211399063|gb|FL099822.1|FL099822
EST:     TGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG                         GCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATGgtgagtgttc ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGC
EST: gi|71450120|gb|DR831170.1|DR831170
EST:     TGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG                         GCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATGgtgagtgttc ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGC
EST: gi|76287895|gb|DV027463.1|DV027463
EST:     TGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG                         GCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATGgtgagtgttc ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagggggctgtcgtgttgatattttttttcccctctgtgctgttcgtgttgccagGCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGCGCGTCCGATCTC
             tgttgat  putative branch site (score: 4)
             tgttgatatttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgttccgtttagcggtgtcgctttgtccttcaccggtttagggggctgtcgtgttgatattttttttcccctctgtgctgttcgtgttgccagGCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGCGCGTCCGATCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG