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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatcgttctgtgatgttggcagggcacacactcaccaattcgcccacatacagcataacctgctgacgcatattctaagactgaatttctgttgtcttttgtttttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGACGTCTTCTCCTTCGGTGTGATGCTGCTGGAGCTCATCACCGGGAGGAAA

Basic information

species Zea mays
transcript GRMZM2G470499_T03
intron # 4
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 4
lower sequence: LOC_Os01g54700.1 (Oryza sativa), 3'ss of exon 5
gtaaatcgttctgtgatgttggcagggcacacactcaccaattcgcccacatacagcataacctgct-gacgcatattcta---agactgaa-tttctgttgtcttttgtttttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGACGTCTTCTCCTTCGGTGTGATGCTGCTGGAGCTCATCACCGGGAGGAAA
|||||    ||           ||   ||  || | ||  | | || | | |||  || ||  | ||    |||    | |    |||| || ||| || ||||      || | ||  ||||||| | ||||||||||| |||||||| |||||| | | |||||| |||||||||||||| ||||| |||||||| |||||||| |||||||||| ||| 
gtaaacacatcaccatcacaaccacaacaatcaattac--acttgcactcgtacgtcaaaagttcctcagtgcacgcaccacgcggactaaactttgtgctgtcaacaacttgtatctccagATATTTAGCTCCAGAGTATGCTGCCACGGGCAAAGTGAACGACCGTTCCGACGTCTTCTCATTCGGCGTGATGCTCCTGGAGCTGATCACCGGGAAGAAG
















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:     CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGG                         ATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
genomic: CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGgtaaatcgtt ... ttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
EST: gi|148995866|gb|EE035102.2|EE035102
EST:     CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGG                         ATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
genomic: CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGgtaaatcgtt ... ttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
EST: gi|71436076|gb|DR817126.1|DR817126
EST:     CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGG                         ATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
genomic: CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGgtaaatcgtt ... ttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
EST: gi|149104235|gb|EE289671.2|EE289671
EST:     CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGG                         ATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
genomic: CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGgtaaatcgtt ... ttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
EST: gi|89249349|gb|DY621135.1|DY621135
EST:     CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGG                         ATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
genomic: CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGgtaaatcgtt ... ttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
EST: gi|94477995|gb|EB706953.1|EB706953
EST:     CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGG                         ATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
genomic: CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGgtaaatcgtt ... ttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
EST: gi|88750189|gb|DY534330.1|DY534330
EST:     CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGG                         ATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
genomic: CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGgtaaatcgtt ... ttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
EST: gi|37422946|gb|CF649190.1|CF649190
EST:     CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGG                         ATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
genomic: CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGgtaaatcgtt ... ttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
EST: gi|71771807|gb|DR969744.1|DR969744
EST:     CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGG                         ATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
genomic: CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGgtaaatcgtt ... ttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
EST: gi|148959212|gb|EE010655.2|EE010655
EST:     AAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGGACCTTCCGG                         ATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAA
genomic: AAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTC-GGgtaaatcgtt ... ttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAA
EST: gi|76914139|gb|DV165421.1|DV165421
EST:     CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGG                         ATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
genomic: CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGgtaaatcgtt ... ttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
EST: gi|110215668|gb|EC897566.1|EC897566
EST:     CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGG                         ATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
genomic: CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGgtaaatcgtt ... ttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
EST: gi|148952461|gb|EC898287.2|EC898287
EST:     CAAGCAGCTGAAGTCACCCCTGTTTTTACGCGTGTGATAGGAACCTTCGG                         ATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
genomic: CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGgtaaatcgtt ... ttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
EST: gi|71316884|gb|DR795129.1|DR795129
EST:     CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGG                         ATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
genomic: CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGgtaaatcgtt ... ttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
EST: gi|148963688|gb|EE014752.2|EE014752
EST:     CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGG                         ATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
genomic: CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGgtaaatcgtt ... ttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
EST: gi|148987250|gb|EE031085.2|EE031085
EST:     CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGG                         ATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
genomic: CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGgtaaatcgtt ... ttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
EST: gi|94474665|gb|EB703623.1|EB703623
EST:     CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGG                         ATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
genomic: CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGgtaaatcgtt ... ttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
EST: gi|78087049|gb|DV515442.1|DV515442
EST:     CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGG                         ATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
genomic: CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGgtaaatcgtt ... ttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
EST: gi|71763339|gb|DR961276.1|DR961276
EST:     CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGG                         ATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
genomic: CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGgtaaatcgtt ... ttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
EST: gi|101384403|gb|EB814246.1|EB814246
EST:     CAAGCAGCGGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGG                         ATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
genomic: CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGgtaaatcgtt ... ttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
EST: gi|50334733|gb|CO529859.1|CO529859
EST:     CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGG                         ATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
genomic: CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGgtaaatcgtt ... ttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
EST: gi|148987251|gb|EE031086.2|EE031086
EST:     CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGG                         ATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
genomic: CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGgtaaatcgtt ... ttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
EST: gi|148959211|gb|EC905317.2|EC905317
EST:     CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGG                         ATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
genomic: CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGgtaaatcgtt ... ttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
EST: gi|78124341|gb|DV542725.1|DV542725
EST:     CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGG                         ATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
genomic: CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGgtaaatcgtt ... ttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
EST: gi|71423642|gb|DR806109.1|DR806109
EST:     CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGG                         ATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA
genomic: CAAGCAGCTGAAGTCACCCCTGTTTCTACGCGTGTGATAGGAACCTTCGGgtaaatcgtt ... ttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgctgacgcatattctaagactgaatttctgttgtcttttgtttttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGACGTCTTCTCCTTCGGTGTGATGCTGCTGGAGCTCATCACCGGGAGGAAA
 tgctgac  putative branch site (score: 2)
                          tttctgttgtcttttg  putative PPT
                                     ttttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatcgttctgtgatgttggcagggcacacactcaccaattcgcccacatacagcataacctgctgacgcatattctaagactgaatttctgttgtcttttgtttttgtccgcagATATCTGGCTCCAGAGTACGCTGCCACAGGCAAAATTAGCGACCGGTCCGACGTCTTCTCCTTCGGTGTGATGCTGCTGGAGCTCATCACCGGGAGGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA