Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCGGCGCGCTCGCCTGCGGCAGGAGCAGCTTCTCCTACCGCCGCCTCCCGGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCGgtaccctccggattgatccttgcgccatttacttttccccgaaagggatcgtggattttttatagggtaattgtggatttctccacgttttgcccgcgcacaaacag

Basic information

species Zea mays
transcript GRMZM2G377553_T01
intron # 1
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|93284366|gb|EB676630.1|EB676630
EST:     GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCG                         ACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
genomic: GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCGgtaccctccg ... gcacaaacagACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
EST: gi|76928498|gb|DV171644.1|DV171644
EST:     GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCG                         ACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
genomic: GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCGgtaccctccg ... gcacaaacagACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
EST: gi|71326344|gb|DR799859.1|DR799859
EST:     GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCG                         ACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
genomic: GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCGgtaccctccg ... gcacaaacagACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
EST: gi|78117224|gb|DV535611.1|DV535611
EST:     GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCG                         ACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
genomic: GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCGgtaccctccg ... gcacaaacagACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
EST: gi|71314124|gb|DR793678.1|DR793678
EST:     GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCG                         ACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
genomic: GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCGgtaccctccg ... gcacaaacagACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
EST: gi|211206648|gb|FL034811.1|FL034811
EST:     GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCG                         ACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
genomic: GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCGgtaccctccg ... gcacaaacagACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
EST: gi|93014288|gb|EB639808.1|EB639808
EST:     GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCG                         ACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
genomic: GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCGgtaccctccg ... gcacaaacagACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
EST: gi|78104956|gb|DV523374.1|DV523374
EST:     GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCG                         ACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
genomic: GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCGgtaccctccg ... gcacaaacagACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
EST: gi|76936196|gb|DV174629.1|DV174629
EST:     GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCG                         ACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
genomic: GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCGgtaccctccg ... gcacaaacagACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
EST: gi|93011929|gb|EB637449.1|EB637449
EST:     GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCG                         ACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
genomic: GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCGgtaccctccg ... gcacaaacagACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
EST: gi|50325977|gb|CO521103.1|CO521103
EST:     GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCG                         ACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
genomic: GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCGgtaccctccg ... gcacaaacagACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
EST: gi|76017697|gb|DT944867.1|DT944867
EST:     GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCG                         ACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
genomic: GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCGgtaccctccg ... gcacaaacagACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
EST: gi|50332317|gb|CO527443.1|CO527443
EST:     GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCG                         ACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
genomic: GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCGgtaccctccg ... gcacaaacagACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
EST: gi|71426506|gb|DR807556.1|DR807556
EST:     GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCG                         ACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
genomic: GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCGgtaccctccg ... gcacaaacagACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
EST: gi|71330675|gb|DR802122.1|DR802122
EST:     GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCG                         ACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
genomic: GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCGgtaccctccg ... gcacaaacagACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
EST: gi|71773330|gb|DR971234.1|DR971234
EST:     GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCG                         ACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
genomic: GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCGgtaccctccg ... gcacaaacagACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
EST: gi|91051217|gb|EB161635.1|EB161635
EST:     GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCG                         ACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
genomic: GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCGgtaccctccg ... gcacaaacagACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAG
EST: gi|21481504|gb|BQ578187.1|BQ578187
EST:     GGAGCCCCGCCTCCGCCTCACCGNTCAGAAGCTTGACGACTCCTTCTTCG                         ACATTGAAATCGCGCG
genomic: GGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCGgtaccctccg ... gcacaaacagACATTGAAATCGCGCG

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 2 RNA-Seq libraries.


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 34

ATCGGCGCGCTCGCCTGCGGCAGGAGCAGCTTCTCCTACCGCCGCCTCCCGGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCGgtaccctccg ... gcacaaacagACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAGAGAACTTGTTCTCCGCCCTCTATGACGACACCCAGAAGACCATCTCTTG


Block sizes: 28 (upstream exon), 47 (downstream exon)
Score: 12

ATCGGCGCGCTCGCCTGCGGCAGGAGCAGCTTCTCCTACCGCCGCCTCCCGGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCGgtaccctccg ... gcacaaacagACATTGAAATCGCGCGGTCGGCCACGGTGTGGGAGCTCAAGGTGACCATAGAGAACTTGTTCTCCGCCCTCTATGACGACACCCAGAAGACCATCTCTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCGGCGCGCTCGCCTGCGGCAGGAGCAGCTTCTCCTACCGCCGCCTCCCGGAGCCCCGCCTCCGCCTCACCGTTCAGAAGCTTGACGACTCCTTCTTCGgtaccctccggattgatccttgcgccatttacttttccccgaaagggatcgtggattttttatagggtaattgtggatttctccacgttttgcccgcgcacaaacag

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