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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtagcgcgatatatcatgatgttattcgatccgtgttataacgccgtggcatacatctttatcagtttagtggtcttgcttcctcttgcagAGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCTGCTTCCTCAGAGGAGATGCCAAAGATGGCGCCTGAGATGTAACCAGCGA

Basic information

species Zea mays
transcript GRMZM2G171354_T04
intron # 8
splice site 3'
intron type U2

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|40303122|gb|CK347509.1|CK347509
EST:     AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAG                         AGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
genomic: AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAGgttagtagcg ... cctcttgcagAGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
EST: gi|113702635|gb|EE680139.1|EE680139
EST:     AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAG                         AGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
genomic: AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAGgttagtagcg ... cctcttgcagAGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
EST: gi|71762206|gb|DR960143.1|DR960143
EST:     AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAG                         AGAAAGAAGAAAGCAATGCTTTGTTATTAGGACAAGGAGGGAGATATTTTT
genomic: AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAGgttagtagcg ... cctcttgcagAGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
EST: gi|211399534|gb|FL455814.1|FL455814
EST:     AAGAGGAACTGCTTGCGTACATCGACCGCAAARAGATTGCCAAGGCTCAG                         AGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTYT
genomic: AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAGgttagtagcg ... cctcttgcagAGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
EST: gi|113702380|gb|EE679884.1|EE679884
EST:     AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAG                         AGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
genomic: AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAGgttagtagcg ... cctcttgcagAGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
EST: gi|28983565|gb|BQ538689.2|BQ538689
EST:     AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAG                         AGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
genomic: AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAGgttagtagcg ... cctcttgcagAGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
EST: gi|211130597|gb|FL448938.1|FL448938
EST:     AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAG                         AGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
genomic: AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAGgttagtagcg ... cctcttgcagAGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
EST: gi|16920005|gb|BM074460.1|BM074460
EST:     AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAG                         AGAAAGAAGAAAGCAATGCTAATGCTACTAGGACAAGGAGGGAGATACTTC
genomic: AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAGgttagtagcg ... cctcttgcagAGAAAGAAGAAAGCAATGCTT-TGCTACTAGGACAAGGAGGGAGATACTTC
EST: gi|40337029|gb|CK371099.1|CK371099
EST:     AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAG                         AGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
genomic: AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAGgttagtagcg ... cctcttgcagAGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
EST: gi|211361627|gb|FL314636.1|FL314636
EST:     AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAG                         AGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
genomic: AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAGgttagtagcg ... cctcttgcagAGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
EST: gi|32936966|gb|CF041785.1|CF041785
EST:     AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAG                         AGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
genomic: AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAGgttagtagcg ... cctcttgcagAGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
EST: gi|5124115|gb|AI745739.1|AI745739
EST:     AAGAGGAACTGCTTGCGTACATCGGCCGCAAAGAGATTGCCAAGGCTCAG                         AGAAAGAAGAAAGCAATGCTTTGCTACTAGGGCAAGGAGGGAGATACTTCT
genomic: AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAGgttagtagcg ... cctcttgcagAGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
EST: gi|211399535|gb|FL455815.1|FL455815
EST:     AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAG                         AGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
genomic: AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAGgttagtagcg ... cctcttgcagAGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
EST: gi|6563798|gb|AW231330.1|AW231330
EST:     AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAG                         AGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
genomic: AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAGgttagtagcg ... cctcttgcagAGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
EST: gi|37397469|gb|CF636033.1|CF636033
EST:     AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAG                         AGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
genomic: AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAGgttagtagcg ... cctcttgcagAGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
EST: gi|45568449|gb|CK986069.1|CK986069
EST:     AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAG                         AGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
genomic: AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAGgttagtagcg ... cctcttgcagAGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
EST: gi|37379233|gb|CF626352.1|CF626352
EST:     AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAG                         AGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
genomic: AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAGgttagtagcg ... cctcttgcagAGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
EST: gi|44900735|gb|CK827280.1|CK827280
EST:     AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAG                         AGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
genomic: AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAGgttagtagcg ... cctcttgcagAGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
EST: gi|6539003|gb|AW225142.1|AW225142
EST:     AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAG                         AGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT
genomic: AAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAGgttagtagcg ... cctcttgcagAGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataacgccgtggcatacatctttatcagtttagtggtcttgcttcctcttgcagAGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCTGCTTCCTCAGAGGAGATGCCAAAGATGGCGCCTGAGATGTAACCAGCGA
 ttataac  putative branch site (score: 2)
                                     tcttgcttcctcttgc  putative PPT
                  atctttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtagcgcgatatatcatgatgttattcgatccgtgttataacgccgtggcatacatctttatcagtttagtggtcttgcttcctcttgcagAGAAAGAAGAAAGCAATGCTTTGCTACTAGGACAAGGAGGGAGATACTTCTGCTTCCTCAGAGGAGATGCCAAAGATGGCGCCTGAGATGTAACCAGCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG