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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCAgtgagttttacagccattcctccaagtgcttgaatctgttatctgtatggcaatatcacattgtgcttgggcattggcgttttctcatgttatggagaaa...

Basic information

species Zea mays
transcript GRMZM2G080652_T01
intron # 2
splice site 5'
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|89248438|gb|DY620224.1|DY620224
EST:     ACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCA                         TTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATC
genomic: ACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCAgtgagtttta ... gtatttccagTTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATC
EST: gi|101391113|gb|EB817490.1|EB817490
EST:     ACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCA                         TTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATC
genomic: ACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCAgtgagtttta ... gtatttccagTTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATC
EST: gi|32837961|gb|CD977639.1|CD977639
EST:     TCCACT-GAAGCNGATGTGCACGACACCNGACATGCTAATCCACAAATCA                         TTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATC
genomic: TCCACTGGAAGC-GATGTGCACGACACC-GACATGCTAATCCACAAATCAgtgagtttta ... gtatttccagTTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATC
EST: gi|31360794|gb|CD445151.1|CD445151
EST:     ACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCA                         TTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATC
genomic: ACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCAgtgagtttta ... gtatttccagTTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATC
EST: gi|78117501|gb|DV535888.1|DV535888
EST:     ACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCA                         TTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATC
genomic: ACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCAgtgagtttta ... gtatttccagTTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATC
EST: gi|50325208|gb|CO520334.1|CO520334
EST:     ACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCA                         TTGATGGATATTAACGAAAGCCCTGGTTATCTCCTATTAAATCCTACAATC
genomic: ACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCAgtgagtttta ... gtatttccagTTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATC
EST: gi|71330852|gb|DR802224.1|DR802224
EST:     ACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCA                         TTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATC
genomic: ACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCAgtgagtttta ... gtatttccagTTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATC
EST: gi|89248430|gb|DY620216.1|DY620216
EST:     ACTCCACTGGAAGCGATGCGCACGACACCGACATGCTAATCCACAAATCA                         TTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAAAT
genomic: ACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCAgtgagtttta ... gtatttccagTTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAA-T
EST: gi|71447371|gb|DR828421.1|DR828421
EST:     ACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCA                         TTGATGGATATTAACGAAAGCCCTGTTTATCTCCTTATTAAATCCTACAAT
genomic: ACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCAgtgagtttta ... gtatttccagTTGATGGATATTAACGAAAGCCCTGTTTATCTCCT-ATTAAATCCTACAAT
EST: gi|76294373|gb|DV033941.1|DV033941
EST:     ACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCA                         TTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATC
genomic: ACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCAgtgagtttta ... gtatttccagTTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATC
EST: gi|61119643|gb|DN560604.1|DN560604
EST:     ACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCA                         TTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATC
genomic: ACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCAgtgagtttta ... gtatttccagTTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATC
EST: gi|101386958|gb|EB815496.1|EB815496
EST:     ACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCA                         TTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATC
genomic: ACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCAgtgagtttta ... gtatttccagTTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATC
EST: gi|71309454|gb|DR791014.1|DR791014
EST:     ACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCA                         TTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATC
genomic: ACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCAgtgagtttta ... gtatttccagTTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATC

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: 47 (upstream exon), 49 (downstream exon)
Score: 62

ATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCAgtgagtttta ... gtatttccagTTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 31

ATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCAgtgagtttta ... gtatttccagTTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 44

ATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCAgtgagtttta ... gtatttccagTTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 28

ATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCAgtgagtttta ... gtatttccagTTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAAGAAGGTGTTCCCCGACTTCTACGTGCTCGGTTGGTACTCCACTGGAAGCGATGTGCACGACACCGACATGCTAATCCACAAATCAgtgagttttacagccattcctccaagtgcttgaatctgttatctgtatggcaatatcacattgtgcttgggcattggcgttttctcatgttatggagaaa

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