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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtgagctgatctcctctcagttctcactcagatccctatctgctaatgcgcattctaatcgcgaccgtgtttcttcgcttaataacaacctgtgcttgatcagATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTG

Basic information

species Zea mays
transcript GRMZM2G136831_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G136831_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g12740.1 (Oryza sativa), 3'ss of exon 1
--gtgcgtgagctgatctcctctcagtt---ctcactcagatccctat-ctgctaatgcgcattctaatcgcgaccgtgtttcttcgcttaataacaacc---tgtgcttgatc-agATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTG
  | ||  ||| | ||| | | |   ||   |   | | ||| |   | |||||  ||    ||    |   ||  || |||||  | ||  |     |    |  | |||| | |||||||||||||| || |  || |||||||||||  |||| ||||||||||||||
gtgagcaagagataatcacgtttagtttagccatgcgctgatgctgctgctgctcctgatgctttggctaatgattgtttttctgggtttgttggttgctaaattcggttgacccagATGGGATCTCCCCGGTGGGGCATACGACAGGACAAGAGGAAACAGGAGGAACTG
















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|101386485|gb|EB815259.1|EB815259
EST:     GTCTACGCCGTCTTCTGGCGCATCCTGCCCCGGAACTACCCGCCCCCCAA                         ATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAA
genomic: GTCTACGCCGTCTTCTGGCGCATCCTGCCCCGGAACTACCCGCCCCCCAAgtgcgtgagc ... gcttgatcagATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAA
EST: gi|76933211|gb|DV173372.1|DV173372
EST:     GTCTACGCCGTCTTCTGGCGCATCCTGCCCCGGAACTACCCGCCCCCTAA                         ATGGGATCTCCCTGGCGCCGCGTACGACAGGACCAGAGGGAACA
genomic: GTCTACGCCGTCTTCTGGCGCATCCTGCCCCGGAACTACCCGCCCCCCAAgtgcgtgagc ... gcttgatcagATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACA
EST: gi|149070786|gb|EE159197.2|EE159197
EST:     GTCTACGCCGTCTTCTGGCGCATCCTGCCCCGGAACTACCCGCCCCCCAA                         ATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAA
genomic: GTCTACGCCGTCTTCTGGCGCATCCTGCCCCGGAACTACCCGCCCCCCAAgtgcgtgagc ... gcttgatcagATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAA
EST: gi|74238082|gb|DT645996.1|DT645996
EST:     GTCTACGCCGTCTTCTGGCGCATCCTGCCCCGGAACTACCCGCCCCCCAA                         ATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAA
genomic: GTCTACGCCGTCTTCTGGCGCATCCTGCCCCGGAACTACCCGCCCCCCAAgtgcgtgagc ... gcttgatcagATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAA
EST: gi|148980599|gb|EE027224.2|EE027224
EST:     GTCTACGCCGTCTTCTGGCGCATCCTGCCCCGGAACTACCCGCCCCCCAA                         ATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAA
genomic: GTCTACGCCGTCTTCTGGCGCATCCTGCCCCGGAACTACCCGCCCCCCAAgtgcgtgagc ... gcttgatcagATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAA
EST: gi|71435285|gb|DR816335.1|DR816335
EST:     GTCTACGCCGTCTTCTGGCGCATCCTGCCCCGGAACTACCCGCCCCCCAA                         ATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAA
genomic: GTCTACGCCGTCTTCTGGCGCATCCTGCCCCGGAACTACCCGCCCCCCAAgtgcgtgagc ... gcttgatcagATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAA
EST: gi|71429782|gb|DR810832.1|DR810832
EST:     GTCTACGCCGTCTTCTGGCGCATCCTGCCCCGGAACTACCCGCCCCCCAA                         ATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAA
genomic: GTCTACGCCGTCTTCTGGCGCATCCTGCCCCGGAACTACCCGCCCCCCAAgtgcgtgagc ... gcttgatcagATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAA
EST: gi|76287078|gb|DV026646.1|DV026646
EST:     GTCTACGCCGTCTTCTGGCGCATCCTGCCCCGGAACTACCCGCCCCCCAA                         ATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAA
genomic: GTCTACGCCGTCTTCTGGCGCATCCTGCCCCGGAACTACCCGCCCCCCAAgtgcgtgagc ... gcttgatcagATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAA
EST: gi|149104906|gb|EE290376.2|EE290376
EST:     GTCTACGCCGTCTTCTGGCGCATCCTGCCCCGGAACTACCCGCCCCCCAA                         ATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAA
genomic: GTCTACGCCGTCTTCTGGCGCATCCTGCCCCGGAACTACCCGCCCCCCAAgtgcgtgagc ... gcttgatcagATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAA
EST: gi|78119598|gb|DV537982.1|DV537982
EST:     GTCTACGCCGTCTTCTGGCGCATCCTGCCCCGGAACTACCCGCCCCCCAA                         ATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAA
genomic: GTCTACGCCGTCTTCTGGCGCATCCTGCCCCGGAACTACCCGCCCCCCAAgtgcgtgagc ... gcttgatcagATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAA
EST: gi|94477121|gb|EB706079.1|EB706079
EST:     GTCTACGCCGTCTTCTGGCGCATCCTGCCCCGGAACTACCCGCCCCCCAA                         ATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAA
genomic: GTCTACGCCGTCTTCTGGCGCATCCTGCCCCGGAACTACCCGCCCCCCAAgtgcgtgagc ... gcttgatcagATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAA
EST: gi|78111427|gb|DV529824.1|DV529824
EST:     GTCTACGCCGTCTTCTGGCGCATCCTGCCCCGGAACTACCCGCCCCCCAA                         ATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAA
genomic: GTCTACGCCGTCTTCTGGCGCATCCTGCCCCGGAACTACCCGCCCCCCAAgtgcgtgagc ... gcttgatcagATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcattctaatcgcgaccgtgtttcttcgcttaataacaacctgtgcttgatcagATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTG
                               taataac  putative branch site (score: 1)
                              ttaataacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtgagctgatctcctctcagttctcactcagatccctatctgctaatgcgcattctaatcgcgaccgtgtttcttcgcttaataacaacctgtgcttgatcagATGGGATCTCCCTGGCGCCGCGTACGACAGGACCCGAGGGAACAGGAGGAACTG

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