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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagctgttcttttagtcgttcatgctttgtggtgcaaatgcttaagattaatacagtgatttcacatgctatttttgttctcttttgtggctatggacagCAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAG

Basic information

species Zea mays
transcript GRMZM2G068755_T01
intron # 49
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 49
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 48
---gtacagctgttcttttagtcgttcatgctttgtggtgcaaatgctta-agattaatacagtgatttcacatgctatttttgttctcttttgtggctatggacagCAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAG
   |||   ||| |  || | |     |   |||||      | |||||  | |||  |||||  |||    ||| | | |||  ||| | || ||  |||||  ||||||||||||||||| | |||||||||||||||||||| ||||||||||| ||||| || |||||||| || |||||||| || || ||||| |||
gtagtattactgattcttaactaacataacatttgtaa-attactgcttgcaaatttgtacagcaattg---atgttctattttgtctttcttttgattatgggtagCAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAG

upper sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 49
lower sequence: GLYMA10G35140.1 (Glycine max), 3'ss of exon 51
gtacagctgttcttttagtcgttcatgctttgtggtgcaaat-gcttaagattaatacagtgatttcacatgctatttttgttctcttttgtggctatggacagCAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAG
     | | || |||  ||  ||    | |  |  |  |  |  ||  | ||| | |   |  || | | ||    | ||  | || ||       |    |||||||||||||||||||| || ||||| ||||| || |||||||| || || ||||| || |||||||| |||||||| || ||  | |||||||||
----tgtttttatttgtgttattttgccctaatattctattttactgcaaattcaaaggctatttacccttgactctgttcctatccttaaaattaaattgcagCAAGAGCTTGCTGCTATATTTAAGAAGATTGGAGAGAAGCAAACTTGCACAATTGGTCTATATGAACTATATCGGATTACCCAATTGTACCCAAAG

upper sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 49
lower sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 50
----gtacagctgttcttttagtcgttcatgctttgtggtgcaaatgcttaagattaatacagtgatttcacatgctatttttgttctcttttgtggctatggacagCAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAG
     |  |  |||  | ||| |   | ||  | | |  | |     ||| |    |    | |        |  || ||| ||| |||   |     |     ||||||||||| |||||||| || ||||| ||||| || |||||||| || || ||||| || |||||||| ||||| || || ||  | |||||||||
ttgtttttatttgtgttattatttactaatattctattttactgcaacttcaa---aggctatttgcccttgactctgtttctgtcctcaaattaaatt----tcagCAAGAGCTGGCTGCTATATTTAAGAAGATTGGGGAGAAGCAAACTTGCACAATTGGTCTATATGAACTATATCGTATTACCCAATTGTACCCAAAG

upper sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 49
lower sequence: Vv00s0652g00030.t01 (Vitis vinifera), 3'ss of exon 20
----------------------------------------------------------gtacagctgttcttttagtcgttca---tgctttgtggtgcaaatgcttaagattaatacagtgatttcacatgctatttttgttctc--ttttgtggctatggacagCAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAG
                                                            |  | |||| | ||   | ||||   |  || ||||||   ||  | ||  | | |    |  | |  | ||  | |  |  |||   |||| |  | |    ||||| || ||||||||||| ||||||||||||||||||||||||||||| || |||||  | |||||||| || || || ||||| || ||||| |||
gtactataatgtttttattttcttcatttattgttttgaagatcatatttgaggttgttcatgggtgttatgttttgctttcaatttctttagtggtgtgtatattcaatctcattttc-tcctgttgcttgacaatgattctcttgtttttatttcaacttgcagCAGGAACTTGCTGCTATATTCAAGAAAATTGGTGACAAGCAAACATGCACTATTGGTTTATATGAACTATACCGTATTACTCAACTGTACCCCAAG

upper sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 49
lower sequence: PP1S131_18V6.1 (Physcomitrella patens), 3'ss of exon 49
--------------------gtacagctgttcttttagtcgttcatgctttgtggtgcaaatgcttaagattaataca-----gtgatttcacatgctatttttgttctcttttgtggcta-tggacagCAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAG
                     |     | | |  | | |   ||  | |  || |    | || |||       | |       | | | ||     |   | |||  |||||     | | | | |||||||||||||||||  | || ||||| || ||||| ||||| || ||||| ||||| |||||||| || ||||| || || ||||| || ||  ||
gtaagttttgcgctccttctatggtattatacgctgaattcatcggg-tcagtagacttattgtttacagcaccttcgtgttcattactgcaatccttgactgtgtattctttgacctccacttggcagCAAGAGCTTGCTGCAGTGTTTAAGAAGATCGGTGATAAGCAGACTTGTACAATTGGTCTCTATGAGCTATATCGTATCACCCAGCTATATCCTCAG

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|93014606|gb|EB640126.1|EB640126
EST:     CATCGAACAATCCAAATCCATCTACTCACTCAGCTGACGCGCAATTGAAG                         CAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACC
genomic: CATCGAACAATCCAAATCCATCTACTCACTCAGCTGACGCGCAATTGAAGgtacagctgt ... ctatggacagCAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACC
EST: gi|32834298|gb|CD973976.1|CD973976
EST:     CATCGAACAATCCAAATCCATCTACTCACTCAGCTGACGCGCAATTGAAG                         CAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGT
genomic: CATCGAACAATCCAAATCCATCTACTCACTCAGCTGACGCGCAATTGAAGgtacagctgt ... ctatggacagCAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGT
EST: gi|26456806|gb|CA828389.1|CA828389
EST:     CAATCCAAATCCATCTACTCACTCAGCTGACGCGCAATTGAAG                         CAAGAGCTTGCTGCTATTTTCAAGAAAATTGG-GACAAGCAAACATGTACC
genomic: CAATCCAAATCCATCTACTCACTCAGCTGACGCGCAATTGAAGgtacagctgt ... ctatggacagCAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACC
EST: gi|37424588|gb|CF650027.1|CF650027
EST:     CATCGAACAATCCAAATCCATCTACTCACTCAGCTGACGCGCAATTGAAG                         CAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACC
genomic: CATCGAACAATCCAAATCCATCTACTCACTCAGCTGACGCGCAATTGAAGgtacagctgt ... ctatggacagCAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACC
EST: gi|32838771|gb|CD978452.1|CD978452
EST:     CATTGAACAATCCAAATCCATCTACTCACTCAGCTGACGCGCAATTGAAG                         CAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGT
genomic: CATCGAACAATCCAAATCCATCTACTCACTCAGCTGACGCGCAATTGAAGgtacagctgt ... ctatggacagCAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGT
EST: gi|71444352|gb|DR825402.1|DR825402
EST:     CATCGAACAATCCAAATCCATCTACTCACTCAGCTGACGCGCAATTGAAG                         CAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACC
genomic: CATCGAACAATCCAAATCCATCTACTCACTCAGCTGACGCGCAATTGAAGgtacagctgt ... ctatggacagCAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACC
EST: gi|67015335|gb|CO444084.1|CO444084
EST:     CATCGAACAATCCAAATCCATCTACTCACTCAGCTGACGCGCAATTGAAG                         CAAGAGCTTGCTGCCATTTTCAAGAAAATTGGTGACAAGCAAACATGTACC
genomic: CATCGAACAATCCAAATCCATCTACTCACTCAGCTGACGCGCAATTGAAGgtacagctgt ... ctatggacagCAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACC
EST: gi|60395928|gb|DN228798.1|DN228798
EST:     CTACTCACTCAGCTGACGCGCAATTGAAG                         CAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACC
genomic: CTACTCACTCAGCTGACGCGCAATTGAAGgtacagctgt ... ctatggacagCAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACC
EST: gi|32834018|gb|CD973696.1|CD973696
EST:     CATCGAACAATCCAAATCCATCTACTCACTCAGCTGACGCGCAATTGAAG                         CAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGT
genomic: CATCGAACAATCCAAATCCATCTACTCACTCAGCTGACGCGCAATTGAAGgtacagctgt ... ctatggacagCAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGT
EST: gi|71444353|gb|DR825403.1|DR825403
EST:     CATCGAACAATCCAAATCCATCTACTCACTCAGCTGACGCGCAATTGAAG                         CAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACC
genomic: CATCGAACAATCCAAATCCATCTACTCACTCAGCTGACGCGCAATTGAAGgtacagctgt ... ctatggacagCAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattaatacagtgatttcacatgctatttttgttctcttttgtggctatggacagCAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAG
 gattaat  putative branch site (score: 3)
                        tatttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacagctgttcttttagtcgttcatgctttgtggtgcaaatgcttaagattaatacagtgatttcacatgctatttttgttctcttttgtggctatggacagCAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC