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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAAGACAGGACTTCCGCCTGCGTTTCCGCAACATGTCTCCTGGCGCAGTCGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAGgtacctgccttcatgcaagtcactttattagtggtggcttaactataaactcaaagaccttttttttcatatgcag

Basic information

species Zea mays
transcript GRMZM2G127141_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G127141_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os10g38950.1 (Oryza sativa), 5'ss of exon 5
CCAAGACAGGACTTCCGCCTGCGTTTCCGCAACATGTCTCCTGGCGCAGTCGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAGgtac-ctgccttcatgcaagtcactttattagtggtggcttaactataaactcaaagaccttttttttcatatgcag
||||| |||||||||||| |||| ||||||||||||||| |||| ||||||||| |||| || |  ||||| |||||||| |||||||||||||| || |||||  || ||| |  | |   |||  | |  || || ||| ||| |||| | ||    | || ||||   ||||||
CCAAGGCAGGACTTCCGCTTGCGCTTCCGCAACATGTCTGCTGGTGCAGTCGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTGgtacattgactttacaccaactactccacttttgttgcctttactgtaaattgaa----cattatttttccatgcag

upper sequence: GRMZM2G127141_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA18G47140.1 (Glycine max), 5'ss of exon 5
CCAAGACAGGACTTCCGCCTGCGTTTCCGCAACATGTCTCCTGGCGCAGTCGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAGgta------cctgccttcatgcaagtcactttattagtggtggcttaactata--aactcaaagaccttttttttca---tatgcag--------------
 |||| ||  | ||        | ||||  |  ||||||||||| || || |||||||| || | ||||||||| ||||||||||  || || ||||||||||      | |   ||        |  |||| |  ||     |||    ||   |  | | | |      |||| |    ||| ||              
-CAAGGCAACAATTTGCTACTAGATTCCCAAGTATGTCTCCTGGTGCTGTTGATTTGTTAGAGAAGATGCTTGTCTTTGATCCAAATAGGCGCATTACAGGtaaaatgacataatttttcttctctttctttttgggtacaacctttgtaattttattttataaattgcccttttaaatccatgtagagtttgctgacctc

upper sequence: GRMZM2G127141_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT4G01370.1 (Arabidopsis thaliana), 5'ss of exon 5
CCAAGACAGGACTTCCGCCTGCGTTTCCGCAACATGTCTCCTGGCGCAGTCGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAGgtacctgccttcatgcaagtcactttattagtggtggcttaactataaactcaaagaccttttttttcatatgcag
|| |||||| ||||        | ||||  ||||||||  |||| |||||||||||| |||| |  |||||||| ||||||||||||||||| || ||||||    |   |  |  |  | |||   |   || |   |   ||||    ||  |     ||||||   | || ||
CCTAGACAGAACTTTGCTGCTAGATTCCCAAACATGTCGGCTGGTGCAGTCGATTTGCTGGAGAAAATGCTTGTTTTTGATCCAAGCAGACGCATCACAGgtga--gttatattttatataactgcttctctgtttcttcggctat--tttctgaacatgttttttgtgtgtgtag

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|19436217|gb|BM952627.1|BM952627
EST:     CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAG                         TTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
genomic: CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAGgtacctgcct ... tcatatgcagTTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
EST: gi|76010905|gb|DT938075.1|DT938075
EST:     CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAG                         TTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
genomic: CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAGgtacctgcct ... tcatatgcagTTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
EST: gi|32933341|gb|CF038153.1|CF038153
EST:     CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAG                         TTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
genomic: CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAGgtacctgcct ... tcatatgcagTTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
EST: gi|149042023|gb|EE046997.2|EE046997
EST:     CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAG                         TTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
genomic: CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAGgtacctgcct ... tcatatgcagTTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
EST: gi|60356919|gb|DN223892.1|DN223892
EST:     CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAG                         TTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
genomic: CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAGgtacctgcct ... tcatatgcagTTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
EST: gi|78023551|gb|DV491938.1|DV491938
EST:     CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAG                         TTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
genomic: CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAGgtacctgcct ... tcatatgcagTTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
EST: gi|211219872|gb|FL299417.1|FL299417
EST:     TGTGTTTGATCCAAGCAGACGGATTACAG                         TTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
genomic: TGTGTTTGATCCAAGCAGACGGATTACAGgtacctgcct ... tcatatgcagTTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
EST: gi|74241511|gb|DT649425.1|DT649425
EST:     CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAG                         TTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
genomic: CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAGgtacctgcct ... tcatatgcagTTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
EST: gi|60399358|gb|DN232172.1|DN232172
EST:     CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAG                         TTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
genomic: CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAGgtacctgcct ... tcatatgcagTTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
EST: gi|71771177|gb|DR969114.1|DR969114
EST:     CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAG                         TTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
genomic: CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAGgtacctgcct ... tcatatgcagTTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
EST: gi|110223138|gb|EC905036.1|EC905036
EST:     CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAG                         TTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
genomic: CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAGgtacctgcct ... tcatatgcagTTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
EST: gi|76917704|gb|DV166966.1|DV166966
EST:     CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAG                         TTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
genomic: CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAGgtacctgcct ... tcatatgcagTTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
EST: gi|50338933|gb|CO534059.1|CO534059
EST:     CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAG                         TTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
genomic: CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAGgtacctgcct ... tcatatgcagTTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
EST: gi|28986239|gb|CB351038.1|CB351038
EST:     AGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAG                         TTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
genomic: AGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAGgtacctgcct ... tcatatgcagTTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
EST: gi|60359685|gb|DN226658.1|DN226658
EST:     CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAG                         TTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
genomic: CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAGgtacctgcct ... tcatatgcagTTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
EST: gi|78091136|gb|DV519510.1|DV519510
EST:     CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAG                         TTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
genomic: CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAGgtacctgcct ... tcatatgcagTTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
EST: gi|17932520|gb|BM269480.1|BM269480
EST:     CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAG                         TTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG
genomic: CGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAGgtacctgcct ... tcatatgcagTTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAAGACAGGACTTCCGCCTGCGTTTCCGCAACATGTCTCCTGGCGCAGTCGATTTGTTGGAAAGGATGCTTGTGTTTGATCCAAGCAGACGGATTACAGgtacctgccttcatgcaagtcactttattagtggtggcttaactataaactcaaagaccttttttttcatatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG