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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCGGCTGGGTCCGTACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAGgtgatgacgccatagcttcctcatcgtctgttattcgaccccatcattatgttcatcttatcacctcgtgatccaaaatgccagtcgtccattgcttggg...

Basic information

species Zea mays
transcript GRMZM2G064695_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064695_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g40830.1 (Oryza sativa), 5'ss of exon 2
GATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCGGCTGGGTCCGTACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAGgtgatgacgccatagcttcctcatcgtctgttattcgaccccatcattatgttcatcttatcacctcgtgatccaaaatgccagtcgtccattgcttggg-
|||||| || |||||||||||||||||||||||||||||||| || || ||  | ||||||||  || ||||||||||| | ||||| || |||||||||||||||   || |  |||  || |  |   || | || ||   |    |  ||  |  |  ||  |  |       | |   |    |  |  |  ||   
GATGGGGAAGTACGGGATCAACGTGCCCAGGGGCGCGGCGGCGGGATCGGTGGAGGAGGTCAAAAACACCTTGAAGAACGTCTTCCCTAGTGAGAAAGAGgtgatgtttccgttccttattctttattgcttgtgcggccaatttgagac-ttggttgtggcagttatttgatggtattaggatgtatatagagaatgtag
















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|211374289|gb|FL290759.1|FL290759
EST:     TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAG                         ATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTC
genomic: TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAGgtgatgacgc ... ctcattgcagATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTC
EST: gi|71760334|gb|DR958271.1|DR958271
EST:     TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAG                         ATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTC
genomic: TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAGgtgatgacgc ... ctcattgcagATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTC
EST: gi|149076126|gb|EE164711.2|EE164711
EST:     TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAG                         ATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTC
genomic: TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAGgtgatgacgc ... ctcattgcagATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTC
EST: gi|211376944|gb|FL290772.1|FL290772
EST:     TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAG                         ATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGAGGGCTNGGAACTTTC
genomic: TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAGgtgatgacgc ... ctcattgcagATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTC
EST: gi|211374290|gb|FL290760.1|FL290760
EST:     TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAG                         ATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTC
genomic: TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAGgtgatgacgc ... ctcattgcagATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTC
EST: gi|211374286|gb|FL290756.1|FL290756
EST:     TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAKAAAGAG                         ATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGAGGGCTGGG
genomic: TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAGgtgatgacgc ... ctcattgcagATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGAGGGCTGGG
EST: gi|211003343|gb|FL290782.1|FL290782
EST:     ACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCCAGCGAGAAAGAG                         ATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTC
genomic: ACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCC-AGCGAGAAAGAGgtgatgacgc ... ctcattgcagATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTC
EST: gi|211376939|gb|FL290767.1|FL290767
EST:     TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAG                         ATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCC
genomic: TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAGgtgatgacgc ... ctcattgcagATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCC
EST: gi|148935326|gb|EC879367.2|EC879367
EST:     TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAG                         ATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTC
genomic: TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAGgtgatgacgc ... ctcattgcagATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTC
EST: gi|211374280|gb|FL290750.1|FL290750
EST:     TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAG                         ATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGAGGGCTGGG
genomic: TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAGgtgatgacgc ... ctcattgcagATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGAGGGCTGGG
EST: gi|211374285|gb|FL290755.1|FL290755
EST:     TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAG                         ATAGTTGTTAAAAGTCAAATCCTTGCTGGTG
genomic: TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAGgtgatgacgc ... ctcattgcagATAGTTGTTAAAAGTCAAATCCTTGCTGGTG
EST: gi|211374291|gb|FL290761.1|FL290761
EST:     TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAG                         ATAGTTGTTAAAAGTCAAATCC
genomic: TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAGgtgatgacgc ... ctcattgcagATAGTTGTTAAAAGTCAAATCC
EST: gi|211374292|gb|FL290762.1|FL290762
EST:     TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAG                         ATAGTTGTTAAAAGTCAAATCCTNGCTGGTGGCCGAGGGCTGGGAACTTTC
genomic: TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAGgtgatgacgc ... ctcattgcagATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTC
EST: gi|211376937|gb|FL290765.1|FL290765
EST:     TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAG                         ATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTC
genomic: TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAGgtgatgacgc ... ctcattgcagATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTC
EST: gi|148951069|gb|EC896728.2|EC896728
EST:     TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAG                         ATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTC
genomic: TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAGgtgatgacgc ... ctcattgcagATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTC
EST: gi|211376949|gb|FL290777.1|FL290777
EST:     TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAG                         ATAGTTGTTAA
genomic: TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAGgtgatgacgc ... ctcattgcagATAGTTGTTAA
EST: gi|211376948|gb|FL290776.1|FL290776
EST:     TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAG                         ATAGTTGTAAAAAGTC
genomic: TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAGgtgatgacgc ... ctcattgcagATAGTTGTTAAAAGTC
EST: gi|211376940|gb|FL290768.1|FL290768
EST:     TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAG                         ATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGANGGCTGGGAACTTTC
genomic: TACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAGgtgatgacgc ... ctcattgcagATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 632

GATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCGGCTGGGTCCGTACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAGgtgatgacgc ... ctcattgcagATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTCAAAAGCGGACTGCAAGGTGGTGTCCATATTGTTAAGGCTGAGGAAGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 566

GATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCGGCTGGGTCCGTACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAGgtgatgacgc ... ctcattgcagATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTCAAAAGCGGACTGCAAGGTGGTGTCCATATTGTTAAGGCTGAGGAAGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 377

GATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCGGCTGGGTCCGTACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAGgtgatgacgc ... ctcattgcagATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTCAAAAGCGGACTGCAAGGTGGTGTCCATATTGTTAAGGCTGAGGAAGCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 719

GATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCGGCTGGGTCCGTACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAGgtgatgacgc ... ctcattgcagATAGTTGTTAAAAGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTCAAAAGCGGACTGCAAGGTGGTGTCCATATTGTTAAGGCTGAGGAAGCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCGGCTGGGTCCGTACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCAGCGAGAAAGAGgtgatgacgccatagcttcctcatcgtctgttattcgaccccatcattatgttcatcttatcacctcgtgatccaaaatgccagtcgtccattgcttggg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttcctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgacccc