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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatttctggtcatttcagaatgatttatttttggatgcagcagtttatataatttatcactcactttgtgaattgctgatgtcttgggatatctcacagATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGCCACGGCCTACATGGCATGCTCCTTGGAAGAACTATCGG

Basic information

species Zea mays
transcript GRMZM2G017089_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017089_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g21990.1 (Oryza sativa), 3'ss of exon 6
tgatttctggtcatttcaga-atgatttatttttggatgcagcagtttatataatttatcactcactt----tgtgaattgctgatgtcttgggatatctcacagATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGCCACGGCCTACATGGCATGCTCCTTGGAAGAACTATCGG
      || |  |    | | ||    |  |||  |||  | ||| ||  | | ||| |   | |  |    | |||||| |||||| |||        |  |||||| |||||||| |||||||||||||||||||| ||||||||||||||||||   |||||||||||||||||||| ||| ||
-----actagcaagcgtatatattccatcctttatgatagaacaggttgaaaattttctagtttaactgaaatatgaatttctgatggcttatatctcatttcagATTCTCTACATCTGCACTGATGGAAAGGATACCAAGTAGATGGCCACGGCCTGTCTGGCATGCTCCTTGGAAGAATTATAGG

upper sequence: GRMZM2G017089_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA15G15960.2 (Glycine max), 3'ss of exon 5
---tgatttctggtcatttcagaatg-atttatttttggatgcagcagtttatataatttatcactcactttg--tgaattgctgatgtcttgggatatctcacagATTT-TCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGCCACGGCCTACATGGCATGCTCCTTGGAAGAACTATCGG
   ||  || ||   || |  || || |||||| |||   |      ||   | |  |  | ||  || ||||  | || ||||    | |    | |   || | |||| || ||||| ||  |||||||||| || || |||| ||||||||| |||  ||||||||| || |||||||||||  ||
ttatgcattttgccaatgtaggattgtatttatgtttt--taggattgtcactctcttggaacaaacattttgactaaactgctatgatttc--aacactacagAAATTTATCAACATCTGCTTTGATGGAAAGAATGCCAAGTAAATGGCCACGTCCTGTATGGCATGCACCATGGAAGAACTACAGG
















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|76013838|gb|DT941008.1|DT941008
EST:     ACCATACCTGGCAAAAATACAACTCTGTCAATTCCTGGATCATCTGACAG                         ATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGCCACGGCC
genomic: ACCATACCTGGCAAAAATACAACTCTGTCAATTCCTGGATCATCTGACAGgtttattccc ... tatctcacagATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGCCACGGCC
EST: gi|211485186|gb|FL175528.1|FL175528
EST:     ACCATACCTGGCAAAAATACA-CTCTGTCAATTCCTGGATCATCTGACAG                         ATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGGCACGGCC
genomic: ACCATACCTGGCAAAAATACAACTCTGTCAATTCCTGGATCATCTGACAGgtttattccc ... tatctcacagATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGCCACGGCC
EST: gi|76013076|gb|DT940246.1|DT940246
EST:     ACCATACCTGGCAAAAATACAACTCTGTCAATTCCTGGATCATCTGACAG                         ATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGCCACGGC
genomic: ACCATACCTGGCAAAAATACAACTCTGTCAATTCCTGGATCATCTGACAGgtttattccc ... tatctcacagATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGCCACGGC
EST: gi|78085590|gb|DV513983.1|DV513983
EST:     ACCATACCTGGCAAAAATACAACTCTGTCAATTCCTGGATCATCTGACAG                         ATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGCCACGGCC
genomic: ACCATACCTGGCAAAAATACAACTCTGTCAATTCCTGGATCATCTGACAGgtttattccc ... tatctcacagATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGCCACGGCC
EST: gi|78087205|gb|DV515598.1|DV515598
EST:     ACCATACCTGGCAAAAATACAACTCTGTCAATTCCTGGATCATCTGACAG                         ATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGCCACGGCC
genomic: ACCATACCTGGCAAAAATACAACTCTGTCAATTCCTGGATCATCTGACAGgtttattccc ... tatctcacagATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGCCACGGCC
EST: gi|211104567|gb|FL375458.1|FL375458
EST:     ACCATACCTGGCAAAAATACAACTCTGTCAATTCCTGGATCATCTGACAG                         ATTTTCTACATCCGCACTGATGGAAAGG
genomic: ACCATACCTGGCAAAAATACAACTCTGTCAATTCCTGGATCATCTGACAGgtttattccc ... tatctcacagATTTTCTACATCCGCACTGATGGAAAGG
EST: gi|6021220|gb|AW066148.1|AW066148
EST:     ACCATACCTGGCAAAAA-ACAACTCTGTCAATTCCTGGATCATCTGACAG                         ATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGCCACGGCC
genomic: ACCATACCTGGCAAAAATACAACTCTGTCAATTCCTGGATCATCTGACAGgtttattccc ... tatctcacagATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGCCACGGCC
EST: gi|211482306|gb|FL175513.1|FL175513
EST:     ACCATACCTGGCAAAAATACA-CTCTGTCAATTCCTGGATCATCTGACAG                         ATTT-CTACATC-GCACTGATGGAAAGGATAC-TAGTAGATGGC-ACGGNC
genomic: ACCATACCTGGCAAAAATACAACTCTGTCAATTCCTGGATCATCTGACAGgtttattccc ... tatctcacagATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGCCACGGCC
EST: gi|78089068|gb|DV517459.1|DV517459
EST:     ACCATACCTGGCAAAAATACAACTCTGTCAATTCCTGGATCATCTGACAG                         ATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGGCACGGCC
genomic: ACCATACCTGGCAAAAATACAACTCTGTCAATTCCTGGATCATCTGACAGgtttattccc ... tatctcacagATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGCCACGGCC
EST: gi|148951460|gb|EC897185.2|EC897185
EST:     ACCATACCTGGCAAAAATACAACTCTGTCAATTCCTGGATCATCTGACAG                         ATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGAAGGGCACGGCC
genomic: ACCATACCTGGCAAAAATACAACTCTGTCAATTCCTGGATCATCTGACAGgtttattccc ... tatctcacagATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGCCACGGCC
EST: gi|211479425|gb|FL175508.1|FL175508
EST:     ACCATACCTGGCAAAAATACAACTCTGTCAATTCCTGGATCATCTGACAG                         ATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGAATG-CCACGGC
genomic: ACCATACCTGGCAAAAATACAACTCTGTCAATTCCTGGATCATCTGACAGgtttattccc ... tatctcacagATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGA-TGGCCACGGC
EST: gi|94478034|gb|EB706992.1|EB706992
EST:     ACCATACCTGGCAAAAATACAACTCTGTCAATTCCTGGATCATCTGACAG                         ATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGCCACGGCC
genomic: ACCATACCTGGCAAAAATACAACTCTGTCAATTCCTGGATCATCTGACAGgtttattccc ... tatctcacagATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGCCACGGCC
EST: gi|149079798|gb|EE168796.2|EE168796
EST:     CATACCTGGCAAAAAATACA-CTCTGTNCA-TTCCTGGATCATCTGACAG                         ATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGCCACGGCC
genomic: CATACCTGGCAAAAA-TACAACTCTGT-CAATTCCTGGATCATCTGACAGgtttattccc ... tatctcacagATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGCCACGGCC
EST: gi|148950913|gb|EC896543.2|EC896543
EST:     ACCATACCTGGCAAAAATACAACTCTGTCAATTCCTGGATCATCTGACAG                         ATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGCCACGGCC
genomic: ACCATACCTGGCAAAAATACAACTCTGTCAATTCCTGGATCATCTGACAGgtttattccc ... tatctcacagATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGCCACGGCC
EST: gi|148962621|gb|EE013511.2|EE013511
EST:     ACCATACCTGGCAAAAATACAACTCTGTCAATTCCTGGATCATCTGACAG                         ATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGCCACGGCC
genomic: ACCATACCTGGCAAAAATACAACTCTGTCAATTCCTGGATCATCTGACAGgtttattccc ... tatctcacagATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGCCACGGCC
EST: gi|76019935|gb|DT947105.1|DT947105
EST:     ACCATACCTGGCAAAAATACAACTCTGTCAATTCCTGGATCATCTGACAG                         ATTTTCTACATCCGCACTGATGGAAAGGATACCTAGT
genomic: ACCATACCTGGCAAAAATACAACTCTGTCAATTCCTGGATCATCTGACAGgtttattccc ... tatctcacagATTTTCTACATCCGCACTGATGGAAAGGATACCTAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatataatttatcactcactttgtgaattgctgatgtcttgggatatctcacagATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGCCACGGCCTACATGGCATGCTCCTTGGAAGAACTATCGG
     taatttatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatttctggtcatttcagaatgatttatttttggatgcagcagtttatataatttatcactcactttgtgaattgctgatgtcttgggatatctcacagATTTTCTACATCCGCACTGATGGAAAGGATACCTAGTAGATGGCCACGGCCTACATGGCATGCTCCTTGGAAGAACTATCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC