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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGGGCTATCTGCCCAATGACCGCTCGCTGTGGGAGCAGGAGCTGGCAAAGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgctgcacattcaggtcatacctatggtatcttgattgcagtttttgttgcacatatatttacctagtttatggccaccaatgcctggctaaatcctctcccgaaaatagaggttctgaatcctgaatttgctaggtaggtag

Basic information

species Zea mays
transcript GRMZM2G068392_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068392_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g68010.1 (Oryza sativa), 5'ss of exon 3
ACTGGGCTATCTGCCCAATGACCGCTCGCTGTGGGAGCAGGAGCTGGCAAAGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgctgcacattcaggtcat--acctatggtatcttgattgcagttttt-gttgcacatatatt----tacctagtttatggccaccaatgcctggctaaatcctctcccgaaaatagaggttctgaatcctgaatttgctaggtaggtag
 ||||||||| |||| | ||| ||  | ||||||||||||||| ||||||||||||||   |||||||| || || ||||| || |||||||  ||||||||| | | || || |||||| |     || |    ||| ||||||| | ||||  | | ||| |    |    ||       |  |  | |   |  || | || | |||| |   ||||||||| | |||||| || | | || |||||||    
GCTGGGCTATTTGCCGAGTGATCGTGCCCTGTGGGAGCAGGAGTTGGCAAAGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgccccttcagattcagatttgtgactttctctattttgattgtaattttaagatacacgtgcggtgtagtatagtacctgagatccctttttgcttgttaga-cctcactacaaaatagagatcctgaattctaattctgttaggtag----
















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|78076514|gb|DV504948.1|DV504948
EST:     GAAGAGAGGGCAGTACGCTGCTTTTCAA-GATGAGTTCCTTACCAACCCT                         G
genomic: GAAGAGAGGGCAGTACGCTGCTTT-CAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... aggtaggtag-
EST: gi|78076514|gb|DV504948.1|DV504948
EST:     GAAGAGAGGGCAGTACGCTGCTTTTCAA-GATGAGTTCCTTACCAACCCT                         G
genomic: GAAGAGAGGGCAGTACGCTGCTTT-CAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... aggtaggtag-
EST: gi|78076514|gb|DV504948.1|DV504948
EST:     GAAGAGAGGGCAGTACGCTGCTTTTCAA-GATGAGTTCCTTACCAACCCT                         G
genomic: GAAGAGAGGGCAGTACGCTGCTTT-CAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... aggtaggtag-
EST: gi|211170254|gb|FL097983.1|FL097983
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCT                         G
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... aggtaggtag-
EST: gi|211170254|gb|FL097983.1|FL097983
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCT                         G
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... aggtaggtag-
EST: gi|211170254|gb|FL097983.1|FL097983
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCT                         G
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... aggtaggtag-
EST: gi|44681890|gb|CK786938.1|CK786938
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCT                         G
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... aggtaggtag-
EST: gi|44681890|gb|CK786938.1|CK786938
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCT                         G
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... aggtaggtag-
EST: gi|44681890|gb|CK786938.1|CK786938
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCT                         G
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... aggtaggtag-
EST: gi|50324142|gb|CO519268.1|CO519268
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTGT                        
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCC--Tgtaagtcgct ... aggtaggta
EST: gi|50324142|gb|CO519268.1|CO519268
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTGT                        
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCC--Tgtaagtcgct ... aggtaggta
EST: gi|50324142|gb|CO519268.1|CO519268
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTGT                        
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCC--Tgtaagtcgct ... aggtaggta
EST: gi|50331308|gb|CO526434.1|CO526434
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTGT                        
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCC--Tgtaagtcgct ... aggtaggta
EST: gi|50331308|gb|CO526434.1|CO526434
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTGT                        
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCC--Tgtaagtcgct ... aggtaggta
EST: gi|50331308|gb|CO526434.1|CO526434
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTGT                        
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCC--Tgtaagtcgct ... aggtaggta
EST: gi|71433967|gb|DR815017.1|DR815017
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTGT                        
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCC--Tgtaagtcgct ... aggtaggta
EST: gi|71433967|gb|DR815017.1|DR815017
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTGT                        
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCC--Tgtaagtcgct ... aggtaggta
EST: gi|71433967|gb|DR815017.1|DR815017
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTGT                        
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCC--Tgtaagtcgct ... aggtaggta
EST: gi|211166904|gb|FL097963.1|FL097963
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCT                         G
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... aggtaggtag-
EST: gi|211166904|gb|FL097963.1|FL097963
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCT                         G
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... aggtaggtag-
EST: gi|211166904|gb|FL097963.1|FL097963
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCT                         G
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... aggtaggtag-
EST: gi|148935027|gb|EC879068.2|EC879068
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTGTAGGT                    
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCC------Tgtaagtcgct ... aggta
EST: gi|148935027|gb|EC879068.2|EC879068
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTGTAGGT                    
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCC------Tgtaagtcgct ... aggta
EST: gi|148935027|gb|EC879068.2|EC879068
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTGTAGGT                    
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCC------Tgtaagtcgct ... aggta
EST: gi|50331565|gb|CO526691.1|CO526691
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCT                         G
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... aggtaggtag-
EST: gi|50331565|gb|CO526691.1|CO526691
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCT                         G
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... aggtaggtag-
EST: gi|50331565|gb|CO526691.1|CO526691
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCT                         G
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... aggtaggtag-
EST: gi|38502614|gb|CF972474.1|CF972474
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCT                         G
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... aggtaggtag-
EST: gi|38502614|gb|CF972474.1|CF972474
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCT                         G
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... aggtaggtag-
EST: gi|38502614|gb|CF972474.1|CF972474
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCT                         G
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... aggtaggtag-

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGGGCTATCTGCCCAATGACCGCTCGCTGTGGGAGCAGGAGCTGGCAAAGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgctgcacattcaggtcatacctatggtatcttgattgcagtttttgttgcacatatatttacctagtttatggccaccaatgcctggctaaatcctctcccgaaaatagaggttctgaatcctgaatttgctaggtaggtag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG