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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCCTTGTTTACAACATCAAATACACAAGGAACAATCGTGGATTCAGGAACAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCGgtgagtttcatatggtacacaatcttttccttatagtggccatacacagtgcgtctacatttcttactaattctgtgacgtgatcattaactgtctttgttcatacctgcag

Basic information

species Zea mays
transcript GRMZM2G133029_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133029_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g56930.2 (Oryza sativa), 5'ss of exon 5
CTCCTTGTTTACAACATCAAATACACAAGGAACAATCGTGGATTCAGGAACAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCGgtgagtttcatatggtacac----aatctt--ttccttatagtggccatacacagtgcgtctacatttcttactaattctgtgacgtgatcattaactgtctttgttcatacctgcag
|||||||||||| ||||||||||||||||||||||| ||||| ||||||||||| || ||||| ||||||||||| || || ||||||||||||| ||||||||| |||||| ||  |||    | |  |  || ||   | |  ||||| |   |  | ||||  |  | | ||||  ||| || ||||  |||    || |  ||  |   |||||
CTCCTTGTTTACGACATCAAATACACAAGGAACAATTGTGGACTCAGGAACAACTTTAGCATATCTTGCAGATGGGGCATATGATCCATTTGTTAATGCGgtgagcttcatagggcccacttatagttctattttctggaattccccatatatgataagcctacgatagtaattaatcttgttacatgattgttagtcctcatattttgtttttgcag

upper sequence: GRMZM2G133029_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA12G08870.1 (Glycine max), 5'ss of exon 5
CTCCTTGTTTACAACATCAAATACACAAGGAACAATCGTGGATTCAGGAACAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCGgtgagtttcatatggtacacaatcttttccttatag--tggccatacacagtgcgtctacatttcttactaattctgtgacgtgatcattaactgtctttgttc--atacctgcag-------------------------------
  |  | ||| | |||||||| |    ||| || || || ||||| |||||||| ||||||||||||||||| |  || ||| |||| ||||| | |||||||||||   |  ||||     | ||   |  || |       ||| | | | | |  |   ||| |      |  |  |      |||||  | |  || ||   | |  ||                                  
TGCAGTTTTTGCTACATCAAACAACAGAGGTACCATTGTTGATTCTGGAACAACTTTGGCATACCTTGCAGAAGAGGCTTACAATCCCTTTGTCAATGCGgtgagttctgttaggtaatttcttttcatccaattgatcaataatagataattctttgattcttcatgtgtgattagcaatagtgacattattttttctttttaggaaatttgtcaataattaacagcaaaattattgttgatgcag
















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|32928121|gb|CF032933.1|CF032933
EST:     CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCG                         ATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
genomic: CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCGgtgagtttca ... atacctgcagATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
EST: gi|14203670|gb|BG837347.1|BG837347
EST:     CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCG                         ATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
genomic: CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCGgtgagtttca ... atacctgcagATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
EST: gi|32928510|gb|CF033322.1|CF033322
EST:     CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCG                         ATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
genomic: CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCGgtgagtttca ... atacctgcagATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
EST: gi|32919740|gb|CF024552.1|CF024552
EST:     CAACATTGGCATACCTTGCAGATGGGGCCTACGATCCATTTGTTAGTGCG                         ATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
genomic: CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCGgtgagtttca ... atacctgcagATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
EST: gi|84976772|gb|DW475194.1|DW475194
EST:     CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCG                         ATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
genomic: CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCGgtgagtttca ... atacctgcagATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
EST: gi|211449625|gb|FL035069.1|FL035069
EST:     CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCG                         ATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
genomic: CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCGgtgagtttca ... atacctgcagATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
EST: gi|74234970|gb|DT642884.1|DT642884
EST:     CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCG                         ATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
genomic: CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCGgtgagtttca ... atacctgcagATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
EST: gi|148940876|gb|EC885709.2|EC885709
EST:     CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCG                         ATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
genomic: CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCGgtgagtttca ... atacctgcagATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
EST: gi|32928535|gb|CF033347.1|CF033347
EST:     AACATTGGCATACCTTGCAGATGGAGCCTACGATCNCATTTGTTAGTGCG                         ATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
genomic: AACATTGGCATACCTTGCAGATGGAGCCTACGATC-CATTTGTTAGTGCGgtgagtttca ... atacctgcagATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
EST: gi|32929051|gb|CF033863.1|CF033863
EST:     CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCG                         ATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
genomic: CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCGgtgagtttca ... atacctgcagATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
EST: gi|60339993|gb|DN206966.1|DN206966
EST:     CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCG                         ATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCT
genomic: CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCGgtgagtttca ... atacctgcagATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCT
EST: gi|74234969|gb|DT642883.1|DT642883
EST:     CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCG                         ATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
genomic: CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCGgtgagtttca ... atacctgcagATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
EST: gi|211449627|gb|FL035071.1|FL035071
EST:     CAACATTGGCATACCTTGCAGATGGAGCCTAYGATCCATTTGTTAGTGCG                         ATAGCTGCTGCAGTCTCTCYATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
genomic: CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCGgtgagtttca ... atacctgcagATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
EST: gi|113702354|gb|EE679858.1|EE679858
EST:     CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCG                         ATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
genomic: CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCGgtgagtttca ... atacctgcagATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
EST: gi|32931524|gb|CF036336.1|CF036336
EST:     CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCG                         ATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
genomic: CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCGgtgagtttca ... atacctgcagATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
EST: gi|33100162|gb|CF060122.1|CF060122
EST:     CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCG                         ATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
genomic: CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCGgtgagtttca ... atacctgcagATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
EST: gi|33095406|gb|CF055400.1|CF055400
EST:     CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCG                         ATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
genomic: CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCGgtgagtttca ... atacctgcagATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
EST: gi|211449626|gb|FL035070.1|FL035070
EST:     AACATTGGCATACCTTGCAGATGGAGCCTACGATCCCATTTGT-AGTGCG                         ATAGCTGCTGCAG
genomic: AACATTGGCATACCTTGCAGATGGAGCCTACGATCC-ATTTGTTAGTGCGgtgagtttca ... atacctgcagATAGCTGCTGCAG
EST: gi|148983004|gb|EE028899.2|EE028899
EST:     CCATTTGTTAGTGCG                         ATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
genomic: CCATTTGTTAGTGCGgtgagtttca ... atacctgcagATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
EST: gi|33099546|gb|CF059506.1|CF059506
EST:     CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCG                         ATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC
genomic: CAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCGgtgagtttca ... atacctgcagATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCCTTGTTTACAACATCAAATACACAAGGAACAATCGTGGATTCAGGAACAACATTGGCATACCTTGCAGATGGAGCCTACGATCCATTTGTTAGTGCGgtgagtttcatatggtacacaatcttttccttatagtggccatacacagtgcgtctacatttcttactaattctgtgacgtgatcattaactgtctttgttcatacctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA