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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgccaactccagaatatacgtatatatatagttctctagggaatggctgacaaagccacaaggattcgtggttcaacacttcatctctggtgatctggaaagggtatttgacagatcgggattctgactgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAAGGTGGTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGCTTTTCGAT

Basic information

species Zea mays
transcript GRMZM2G391936_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G391936_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g52460.1 (Oryza sativa), 3'ss of exon 3
gtgccaactccagaatatacgtatatatatagttctctagggaatggctgacaaagccacaaggattcgtggttcaacacttcatctctggtgatctg--gaaagggtatttgacagatcgggattctgactgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAAGGTGGTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGCTTTTCGAT
|||| || ||||||   ||       || |  |||| || || || |        || ||             | ||         | ||||||||||  |||| || ||   | | || || | |    || |   |||||| ||||||||||| |||| ||||||| ||||||| || ||||||||||||||||| |||||||| |||||||| || ||||||||||| |||
gtgctaaatccagacagtata-----atgttcttctttacgggattgt-------gctactg-----------ttaa---------tttggtgatctgatgaaaagggataacaaaaat-ggaacttgctctctaactcagGTCCTAGCAGCAACTCAGACGCCTGGATCGGAGGGAAAGAGGTGGTTTCAGGGTACAGCTGATGCTGTTCGGCAATTTGACTGGCTTTTTGAT

upper sequence: GRMZM2G391936_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G01900.1 (Glycine max), 3'ss of exon 3
---------------------gtgccaactccag--aatatacgtatatatatagttctctagggaatggctgacaaagccacaaggattcgtggttcaacacttcatctctggtgatctggaaagggtattt------gacagatcgggattctgactgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAAGGTGGTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGCTTTTCGAT
                      |   |  |  ||  |   || |  | | ||| | |    |   | |    |   |   |  ||  ||     |   |     |  |   | || |      ||   || |       |  | |   |  | |   || | ||||||||||| ||||||||||| |  || ||   ||  || |||| ||||||||| |||||||||||||||||  |||||||  ||||||| || || 
gtatctcccatcttttacttgcttgtatttttagtcagcttatgcgtgtgtatggcttataaacaattatgcgtttagttcttaataatcttcagaaaataggctactaagtagtaaaagaagaactatactcctctaggttataaaagagtgcatgctctatttcagGTTCTTGCAGCAACCCAAACTCCAGGGGAGGCAGGTAAAAAGTGGTTTCAAGGTACTGCTGATGCAGTGAGGCAGTTTCACTGGCTCTTTGAG

upper sequence: GRMZM2G391936_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G38820.1 (Glycine max), 3'ss of exon 3
gtgccaactccagaatatacgtatatatatagttctctagggaatggctgacaaagccacaaggattcgtggttcaacacttcatctctggtgatctggaaagggtattt------gacagatcgggattctgactgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAAGGTGGTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGCTTTTCGAT
                                          |   || ||| ||   | ||  ||     |  ||     |  | | | || | |    ||   || |       |  | |   |  | |    | | ||||||||||| ||||||||||| |  || ||   ||  || |||| ||||||||| |||||||||||||| ||  |||||||| ||||||| || || 
------------------------------------------ataagccgaccaa---aaaaaaatcttcagaacatagactagtatgtagtaaacaaagaactatactcctctaggttataaaagagtgcatgttctatttcagGTTCTTGCAGCAACCCAAACTCCAGGGGAGGCAGGTAAAAAGTGGTTTCAAGGTACTGCTGATGCTGTGAGGCAGTTCCACTGGCTCTTTGAG

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|211117031|gb|FL303251.1|FL303251
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GTTCTAGCAGCAACCCAGAGGCCTGGAACGGA
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAACGGA
EST: gi|211118614|gb|FL303275.1|FL303275
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GGTCTAGCAGCAACCCAGAG
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGAG
EST: gi|211115439|gb|FL303219.1|FL303219
EST:     AGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTTCGTCGAG                         GTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAAGGTGGGTTTT
genomic: AGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATT-CGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAAGGTGG-TTT-
EST: gi|149101455|gb|EE187574.2|EE187574
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAAGGTGGTTTCAG
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAAGGTGGTTTCAG
EST: gi|211115452|gb|FL303232.1|FL303232
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GTTCTAGCAGCAACCCAGAGGCCTG
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGAGGCCTG
EST: gi|211117818|gb|FL303262.1|FL303262
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GTTCTAGCAGCAAC
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAAC
EST: gi|211115451|gb|FL303231.1|FL303231
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGG
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGG
EST: gi|211115441|gb|FL303221.1|FL303221
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAAGGT
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAAGGT
EST: gi|211114656|gb|FL303218.1|FL303218
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAA
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAA
EST: gi|71429963|gb|DR811013.1|DR811013
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAAGGTGGTTTCAG
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAAGGTGGTTTCAG
EST: gi|71435811|gb|DR816861.1|DR816861
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAAGGTGGTTTCAG
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAAGGTGGTTTCAG
EST: gi|211114649|gb|FL303211.1|FL303211
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGGAAAGGTGGTTTCAG
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAAGGTGGTTTCAG
EST: gi|211118620|gb|FL303281.1|FL303281
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGGAAAAG-TGGTTTTC
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGG-AAAAGGTGGTTT-C
EST: gi|211116232|gb|FL303236.1|FL303236
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GTTCTAGCAGCAACCCAGAAGCCCTGGA-CGGAGGGGGAAAAG-TGGTTTC
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGAGGCC-TGGAACGGAGGGG-AAAAGGTGGTTTC
EST: gi|211118617|gb|FL303278.1|FL303278
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GTTCTAGCAGCAACCCAGAAGCCTGGAACGGAGGGGAAAAGGTGTTTTCAG
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAAGGTGGTTTCAG
EST: gi|93281648|gb|EB673912.1|EB673912
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAAGGTGGTTTCAG
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAAGGTGGTTTCAG
EST: gi|211118626|gb|FL303287.1|FL303287
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACCGATTCGTCGAG                         GGTCTAGCACCAACCCAGAGGCCCGGAACGG
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAACGG
EST: gi|211117028|gb|FL303248.1|FL303248
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GTTCTAGCAGCAACC-AGAAGCCTGGAACGGAGGGGGAAAAGG-GGTTTCA
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGG-AAAAGGTGGTTTCA
EST: gi|91874078|gb|EB404035.1|EB404035
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GTTCTAGCCGCCACCCCAGAGGC
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCC-AGAGGC
EST: gi|211117038|gb|FL303258.1|FL303258
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAA
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAA
EST: gi|211114653|gb|FL303215.1|FL303215
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAA                         GTTCTAGCAGCAACCCAGAGGCCTGGA
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGA
EST: gi|211117825|gb|FL303269.1|FL303269
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAAGGTGGTTTCAG
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAAGGTGGTTTCAG
EST: gi|211114650|gb|FL303212.1|FL303212
EST:     GCCTACGATTTCAAGCAATGGCGTGGCCATCGGAGACGGATTNCGTCGAG                         GTTCTAGCAGCAACCCAGAAGCCTGGAAACGGAGGGGAA
genomic: GCCTACGATTTCA-GCAATGGCGTGGCCATCGGAGACGGATT-CGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAA-CGGAGGGGAA
EST: gi|211115446|gb|FL303226.1|FL303226
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAAAGGTGGTTTCA
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAA-GGTGGTTTCA
EST: gi|76291271|gb|DV030839.1|DV030839
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAAGGTGGTTTCAG
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAAGGTGGTTTCAG
EST: gi|211117033|gb|FL303253.1|FL303253
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GTTCTAGCAGCAACC
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACC
EST: gi|211117819|gb|FL303263.1|FL303263
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GTTCTAGCAGCAACCCA
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCA
EST: gi|211118623|gb|FL303284.1|FL303284
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GTTCTAGCAGCAACCCAGAAGCCTGGAACGGAGGGGGAAAAAGTGGTTTCA
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGG-AAAAGGTGGTTTCA
EST: gi|50335822|gb|CO530948.1|CO530948
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAAGGTGGTTTCAG
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAAGGTGGTTTCAG
EST: gi|78103576|gb|DV522004.1|DV522004
EST:     GAGCCTACGATTTCAGCTATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAA
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAA
EST: gi|211116235|gb|FL303239.1|FL303239
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GTTCTAGCAGCAACCCAGAAGCCTGGGAACGGAGGGGAAAA
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGG-AACGGAGGGGAAAA
EST: gi|211116234|gb|FL303238.1|FL303238
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGGAAAAGGTGGTTTCA
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGG-AAAAGGTGGTTTCA
EST: gi|211114648|gb|FL303210.1|FL303210
EST:     GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAG                         GTTCTAGCAGCAACCCAGA
genomic: GAGCCTACGATTTCAGCAATGGCGTGGCCATCGGAGACGGATTCGTCGAGgtgccaactc ... tgtttttcagGTTCTAGCAGCAACCCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctggtgatctggaaagggtatttgacagatcgggattctgactgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAAGGTGGTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGCTTTTCGAT
                                      ttctgac  putative branch site (score: 2)
                                            ctgtttttc  CT-rich tract
                     tatttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgccaactccagaatatacgtatatatatagttctctagggaatggctgacaaagccacaaggattcgtggttcaacacttcatctctggtgatctggaaagggtatttgacagatcgggattctgactgtttttcagGTTCTAGCAGCAACCCAGAGGCCTGGAACGGAGGGGAAAAGGTGGTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGCTTTTCGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT