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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatacattttgttggagccatcgacttggcgttttatgtgctagctgctaaatcatctttggtaatcacacacgtgcctcctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAG

Basic information

species Zea mays
transcript GRMZM2G030784_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030784_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g05490.2 (Oryza sativa), 3'ss of exon 6
-------------------------gtacatacattttgttggagccatcgacttggcgttttatgtgctagctgctaaatcatctttg-gtaatcacacacgtgcctcctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAG
                         | ||| ||| |||      |    |      ||   ||| | |  | |||         ||     | ||     || ||  |  ||||||||| || ||||||| |||||||||||| ||||| |||||| |||||||||| ||||||||||| |||||||| ||||| ||||||
gtataaatctacagtatattttcttgaacaaacactttacgattgattgcacaagtgcaccttaggcgacaactgtcctggtgcctggacatgattgtttacatgattt-tgctacagGTTCCGTAACTGGTGCGAACTGCAAGGAGCTGGCAGCAAAGCCTGATGTTGATGGTTTTCTCGTCGGTGGTGCTTCATTGAAG
















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|71325325|gb|DR799341.1|DR799341
EST:     GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAG                         GCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
genomic: GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
EST: gi|19437215|gb|BM953625.1|BM953625
EST:     GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAG                         GCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
genomic: GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
EST: gi|213178228|gb|FM191284.1|FM191284
EST:     GACCAATGCCAGCCCTNNNNNNNCTGAATCTACTANNATCATCTACGGAG                         GCTCTGTAACTGCTGCGAACTGCNNNGAGCTAGCAGCACAGC
genomic: GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGC
EST: gi|71323015|gb|DR798174.1|DR798174
EST:     GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAG                         GCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGTCTGATGTCG
genomic: GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
EST: gi|67026065|gb|CO454814.1|CO454814
EST:     GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAG                         GCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
genomic: GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
EST: gi|67024324|gb|CO453073.1|CO453073
EST:     GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAG                         GCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
genomic: GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
EST: gi|71433477|gb|DR814527.1|DR814527
EST:     GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAG                         GCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
genomic: GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
EST: gi|31355717|gb|CD440074.1|CD440074
EST:     GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAG                         GCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
genomic: GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
EST: gi|67021074|gb|CO449823.1|CO449823
EST:     CCAATGCCAGCCCCTGAG-TTGCTGAATCTACTANGATCATCTACGGGAG                         -CTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCAC
genomic: CCAATGCCAGCCC-TGAGGTTGCTGAATCTACTAGGATCATCTACGG-AGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCAC
EST: gi|67034586|gb|CO463136.1|CO463136
EST:     GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTANGATCATCTACGGAG                         GCTCTGTAACTGCTGCGAACTGCNAAGAGCTAGCAGCACAGCCTGATGTCG
genomic: GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
EST: gi|67016932|gb|CO445681.1|CO445681
EST:     ACCAATGCCAGCCCTTGAG-TTGCTGAATCTACTAGGATCATCTACGGAG                         GCTCTGTNACTGCTGCGAACTGCANAGAGCTAGCAGCACAGCCTGATGTCG
genomic: ACCAATGCCAGCCCT-GAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
EST: gi|84980759|gb|DW531108.1|DW531108
EST:     ACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACNGGAG                         -CTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAG
genomic: ACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTAC-GGAGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAG
EST: gi|211324557|gb|FL104648.1|FL104648
EST:     GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAR                         GCTCTGTAACTGCTGCGAACTGCAAAG
genomic: GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAG
EST: gi|38502719|gb|CF972579.1|CF972579
EST:     GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAG                         GCTCTGTAACTGCTGCGAACTGCAAGGAGCTAGCAGCACAGCCTGATGTCG
genomic: GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
EST: gi|38502545|gb|CF972405.1|CF972405
EST:     GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAG                         GCTCTGTAACTGCTGCGAACTGCAAA-AGCTACCAGCACAGCCTGATGTC
genomic: GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTC
EST: gi|67012349|gb|CO441098.1|CO441098
EST:     GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAG                         GCTCTGTAACTGCTGCGAACTGCAAAGAGCTACCAGCACAGCCTGATGTCA
genomic: GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
EST: gi|211405979|gb|FL414494.1|FL414494
EST:     GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAG                         GCTCTGTAACTGCTGCGAACTGCAA-GAGCTAGCAGCACAGCCTG
genomic: GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTG
EST: gi|18384965|gb|BM418164.1|BM418164
EST:     GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAG                         GCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGAT
genomic: GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGAT
EST: gi|83278900|gb|DV942908.1|DV942908
EST:     GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAG                         GCTCTGTTACTGCTGCGAACTGCAAAGAGCTA
genomic: GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTA
EST: gi|67017841|gb|CO446590.1|CO446590
EST:     ACCAATGCCAGCCCCTGAG-TTGCTGAATCTACTANGATCATCTACGGAG                         GCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
genomic: ACCAATGCCAGCCC-TGAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
EST: gi|31350868|gb|CD435225.1|CD435225
EST:     GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAG                         GCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
genomic: GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
EST: gi|31355497|gb|CD439854.1|CD439854
EST:     GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAG                         GCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
genomic: GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
EST: gi|29544034|gb|CB604414.1|CB604414
EST:     GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAG                         GCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
genomic: GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
EST: gi|67020170|gb|CO448919.1|CO448919
EST:     ACCAATGCCAGCCCCTGAGGT-GCTGAATCTACTAGGATCATCTACGGAG                         GCTCTGNTA-CTGCTGCGAACTGCANAGAGCTAGCAGCACAGCCTGATGTC
genomic: ACCAATGCCAGCCC-TGAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTG-TAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTC
EST: gi|67020068|gb|CO448817.1|CO448817
EST:     CCAATGCCAGCCCTGNAG-TTGCTGAATCTACTANGATCATCTACGGGAG                         -CTCTGTTACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTC
genomic: CCAATGCCAGCCCTG-AGGTTGCTGAATCTACTAGGATCATCTACGG-AGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTC
EST: gi|31354917|gb|CD439274.1|CD439274
EST:     GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAG                         GCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
genomic: GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
EST: gi|18384001|gb|BM417201.1|BM417201
EST:     GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAG                         GCTCTGNAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGAT
genomic: GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGAT
EST: gi|71332087|gb|DR802949.1|DR802949
EST:     GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAG                         GCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
genomic: GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
EST: gi|93283118|gb|EB675382.1|EB675382
EST:     GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAG                         GCTCTGTAACTGCTGCGAACT
genomic: GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACT
EST: gi|67035472|gb|CO464005.1|CO464005
EST:     GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAG                         GCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
genomic: GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
EST: gi|31355762|gb|CD440119.1|CD440119
EST:     GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAG                         GCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
genomic: GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCG
EST: gi|67024408|gb|CO453157.1|CO453157
EST:     GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTANGATCATCTACGGAG                         GCTCTGNTA-CTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTC
genomic: GACCAATGCCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAGgtacatacat ... cctgctacagGCTCTG-TAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtgctagctgctaaatcatctttggtaatcacacacgtgcctcctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAG
           tgctaaa  putative branch site (score: 2)
                                          cctcctgct  putative PPT
              taaatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatacattttgttggagccatcgacttggcgttttatgtgctagctgctaaatcatctttggtaatcacacacgtgcctcctgctacagGCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG