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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagacccaaacagccgaaaatctttagcctgcctgcgtgcgtgcctgcctgcatgttttaactgaaagatttgcacattttttgggggtatatacatacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGG

Basic information

species Zea mays
transcript GRMZM2G470499_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G470499_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g54700.1 (Oryza sativa), 3'ss of exon 4
gtagacccaaacagccgaaaatctttagcctgcctgcgtgcgtgcctgcctgcatgttttaactgaaagatttgcacattttttgggggtatatacatacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGG
        |||  || |||||| |  | |||||     |   || |    | |  || || |  |  |                 || | | | |  |   | |||||||||||||| ||||||||||| ||||||||  ||||    ||| ||||||| ||||| || || ||||| || ||
------gtaaatcgc-gaaaatttggaacctgca---ataattgacgttatacgcgtatttatcgcgaa----------------ggtgcacacatgtttgtacagGTTGCAGATTTTGGGTTGGCCAAGTACCAAGCCACTGAGCAGACCGCTGTTTCGACGCGCGTAATGGGAACTTTTGG
















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|101381709|gb|EB812912.1|EB812912
EST:     GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG                         GTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
genomic: GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
EST: gi|148995866|gb|EE035102.2|EE035102
EST:     GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG                         GTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
genomic: GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
EST: gi|71436076|gb|DR817126.1|DR817126
EST:     GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG                         GTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
genomic: GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
EST: gi|149104235|gb|EE289671.2|EE289671
EST:     GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG                         GTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
genomic: GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
EST: gi|89249349|gb|DY621135.1|DY621135
EST:     GTGACATCAAAGCGGGGAGCATCCTTCTGGATTACCATTACGAGCCAAAG                         GTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
genomic: GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
EST: gi|94477995|gb|EB706953.1|EB706953
EST:     GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG                         GTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
genomic: GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
EST: gi|88750189|gb|DY534330.1|DY534330
EST:     TGACATCAAAGCGGCGAAACATCCTTTTGGATTACCATTACGAGCCAAAG                         GTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
genomic: TGACATCAAAGCGGCG-AACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
EST: gi|37422946|gb|CF649190.1|CF649190
EST:     GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG                         GTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
genomic: GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
EST: gi|71771807|gb|DR969744.1|DR969744
EST:     GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG                         GTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
genomic: GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
EST: gi|148959212|gb|EE010655.2|EE010655
EST:     GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG                         GTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
genomic: GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
EST: gi|76914139|gb|DV165421.1|DV165421
EST:     GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG                         GTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
genomic: GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
EST: gi|110215668|gb|EC897566.1|EC897566
EST:     GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG                         GTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
genomic: GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
EST: gi|148952461|gb|EC898287.2|EC898287
EST:     CATCAAAGCGGCGAACATCCTTCTGGATTACCAATACGAGCCAAAG                         GTTGCAGATTTCGGGTTGGCCAAAATACCAAGCAGCTGAAGTCACCCCTGT
genomic: CATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCC-AAATACCAAGCAGCTGAAGTCACCCCTGT
EST: gi|71316884|gb|DR795129.1|DR795129
EST:     GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG                         GTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
genomic: GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
EST: gi|148963688|gb|EE014752.2|EE014752
EST:     GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG                         GTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
genomic: GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
EST: gi|148987250|gb|EE031085.2|EE031085
EST:     GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG                         GTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
genomic: GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
EST: gi|94474665|gb|EB703623.1|EB703623
EST:     GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG                         GTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
genomic: GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
EST: gi|78087049|gb|DV515442.1|DV515442
EST:     GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG                         GTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
genomic: GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
EST: gi|71763339|gb|DR961276.1|DR961276
EST:     GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG                         GTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
genomic: GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
EST: gi|101384403|gb|EB814246.1|EB814246
EST:     GGGACATCAAAGCGGCGAACATCTTTCTGGATTACCATTACGAGCCAAAG                         GTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCGGAAGTCACCCCTGTT
genomic: GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
EST: gi|50334733|gb|CO529859.1|CO529859
EST:     GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG                         GTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
genomic: GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
EST: gi|148987251|gb|EE031086.2|EE031086
EST:     GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG                         GTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
genomic: GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
EST: gi|148959211|gb|EC905317.2|EC905317
EST:     GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG                         GTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
genomic: GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
EST: gi|78124341|gb|DV542725.1|DV542725
EST:     GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG                         GTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
genomic: GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
EST: gi|71423642|gb|DR806109.1|DR806109
EST:     GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG                         GTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT
genomic: GTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAGgtagacccaa ... atacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatgttttaactgaaagatttgcacattttttgggggtatatacatacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGG
     ttttaac  putative branch site (score: 2)
                                      tatatacatacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagacccaaacagccgaaaatctttagcctgcctgcgtgcgtgcctgcctgcatgttttaactgaaagatttgcacattttttgggggtatatacatacattcagGTTGCAGATTTCGGGTTGGCCAAATACCAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG