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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaataatgttcaggggctctcgacatttggatgatttgtttttcatttattttggagtacgaaatcaaggaaaacttcctcatgatacttttgttacagGTATGGAGATGGTGAGCCGACTGACAATGCTGCTAGGTTCTACAAATGGTTCACTGAGGGAAATGAGAGGGGTGTCTGGCTAAATGACTTTGAGTATGCT

Basic information

species Zea mays
transcript AC217947.4_FGT002
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC217947.4_FGT002 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g14570.1 (Oryza sativa), 3'ss of exon 3
tgaataatgttcaggggctctcgacatttggatgatttgtttttcatttattttggagtacgaaatcaaggaaaacttcctcatgatactt--ttg---ttacagGTATGGAGATGGTGAGCCGACTGACAATGCTGCTAGGTTCTACAAATGGTTCACTGAGGGAAATGAGAGGGGTGTCTGGCTAAATGACTTTGAGTATGCT
    |     |||   |   |  | |     || | |  | ||  |||||| ||||  |||    | | ||||| |||  | ||  |  ||  |||   || |||||| ||||||||||| |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||| ||| | ||||||||  ||||||||
---ctttcagtcaaaagaaataca-aggaacatcaatcttcttctatttatgttggtatactgtgtta-ggaaacctttgtaatattttttggttgacatttcagGTACGGAGATGGTGAACCGACTGACAATGCTGCTAGGTTCTATAAATGGTTCACTGAGGGAAATGAGAGGGGTGTTTGGTTGAATGACTTCCAGTATGCT

upper sequence: AC217947.4_FGT002 (Zea mays), 3'ss of exon 3
lower sequence: AT4G30210.1 (Arabidopsis thaliana), 3'ss of exon 3
-tgaataatgttcaggggctctcgacatttggatgattt--gtttttcatttattttggagtacgaaatcaaggaaaacttcctcatgatacttttgttacagGTATGGAGATGGTGAGCCGACTGACAATGCTGCTAGGTTCTACAAATGGTTCACTGAGGGAAATGAGAGGGGTGTCTGGCTAAATGACTTTGAGTATGCT
 | | |  | ||    |    |     |  |   | | |  || ||  ||||  ||||   |  |      |       || ||      | | | | |  || ||||||||||||||||| || |||||||| || || ||||||||||||||||| |||                                          
gttagttttcttagctgatcttttgtttgggatcggtataagtattaaatttgatttgttct-tgtggctgacttggttttactatctggaatctggatgtagATATGGAGATGGTGAGCCTACCGACAATGCAGCGAGATTCTACAAATGGTTCACCGAG------------------------------------------
















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|108953570|gb|EC364784.1|EC364784
EST:     AGGAGAAGCTAGCGTTGTTCTTCGTGGCAAC                         GTATGGAGATGGTGAGCCGACTGACAATGCTGCTAGGTTCTACAAATGGTT
genomic: AGGAGAAGCTAGCGTTGTTCTTCGTGGCAACgtgaggcatt ... tttgttacagGTATGGAGATGGTGAGCCGACTGACAATGCTGCTAGGTTCTACAAATGGTT
EST: gi|148961292|gb|EE012017.2|EE012017
EST:     GAATATGAGAAGTTGAAGAAGGAGAAGCTAGCGTTGTTCTTCGTGGCAAC                         GTATGGAGATGGTGAGCCGACTGACAATGCTGCTAGGTTCTACAAATGGTT
genomic: GAATATGAGAAGTTGAAGAAGGAGAAGCTAGCGTTGTTCTTCGTGGCAACgtgaggcatt ... tttgttacagGTATGGAGATGGTGAGCCGACTGACAATGCTGCTAGGTTCTACAAATGGTT
EST: gi|31441089|gb|CD510520.1|CD510520
EST:     GAATATGAGAAGTTGAAGAAGGAGAAGCTAGCGTTGTTCTTCGTGGCAAC                         GTATGGAGATGGTGAGCCGACTGACAATGCTGCTAGGTTCTACAAATGGTT
genomic: GAATATGAGAAGTTGAAGAAGGAGAAGCTAGCGTTGTTCTTCGTGGCAACgtgaggcatt ... tttgttacagGTATGGAGATGGTGAGCCGACTGACAATGCTGCTAGGTTCTACAAATGGTT
EST: gi|38502682|gb|CF972542.1|CF972542
EST:     TATGAGGAGAAGTTGAAGGAGGAGAAGCTAGCGTTGTTCTTCGTGGCAAC                         GTATGGAGATGGTGAGCCGACTGACAATGCTGCTAGGTTCTACAAATGGTT
genomic: TAT---GAGAAGTTGAAGAAGGAGAAGCTAGCGTTGTTCTTCGTGGCAACgtgaggcatt ... tttgttacagGTATGGAGATGGTGAGCCGACTGACAATGCTGCTAGGTTCTACAAATGGTT
EST: gi|28910222|gb|CB331332.1|CB331332
EST:     GAATATGAGAAGTTGAAGAAGGAGAAGCTAGCGTTGTTCTTCGTGGCAAC                         GTATGGAGATGGTGAGCCGACTGACAATGCTGCTAGGTTCTACAAATGGTT
genomic: GAATATGAGAAGTTGAAGAAGGAGAAGCTAGCGTTGTTCTTCGTGGCAACgtgaggcatt ... tttgttacagGTATGGAGATGGTGAGCCGACTGACAATGCTGCTAGGTTCTACAAATGGTT
EST: gi|74235808|gb|DT643722.1|DT643722
EST:     GAATATGAGAAGTTGAAGAAGGAGAAGCTAGCGTTGTTCTTCGTGGCAAC                         GTATGGAGATGGTGAGCCGACTGACAATGCTGCTAGGTTCTACAAATGGTT
genomic: GAATATGAGAAGTTGAAGAAGGAGAAGCTAGCGTTGTTCTTCGTGGCAACgtgaggcatt ... tttgttacagGTATGGAGATGGTGAGCCGACTGACAATGCTGCTAGGTTCTACAAATGGTT
EST: gi|13149591|gb|BG319913.1|BG319913
EST:     TATGAGGAGAAGTTGAAGGAGGAGAAGCTAGCGTTGTTCTTCGTGGCAAC                         GTATGGAGATGGTGAGCCGACTGACAATGCTGCTAGGTTCTACAAATGGTT
genomic: TAT---GAGAAGTTGAAGAAGGAGAAGCTAGCGTTGTTCTTCGTGGCAACgtgaggcatt ... tttgttacagGTATGGAGATGGTGAGCCGACTGACAATGCTGCTAGGTTCTACAAATGGTT
EST: gi|74235807|gb|DT643721.1|DT643721
EST:     GAATATGAGAAGTTGAAGAAGGAGAAGCTAGCGTTGTTCTTCGTGGCAAC                         GTATGGAGATGGTGAGCCGACTGACAATGCTGCTAGGTTCTACAAATGGTT
genomic: GAATATGAGAAGTTGAAGAAGGAGAAGCTAGCGTTGTTCTTCGTGGCAACgtgaggcatt ... tttgttacagGTATGGAGATGGTGAGCCGACTGACAATGCTGCTAGGTTCTACAAATGGTT

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: 44 (upstream exon), 49 (downstream exon)
Score: 51

GATGATTATGCAGCAGAGGACGAGGAATATGAGAAGTTGAAGAAGGAGAAGCTAGCGTTGTTCTTCGTGGCAACgtgaggcatt ... tttgttacagGTATGGAGATGGTGAGCCGACTGACAATGCTGCTAGGTTCTACAAATGGTTCACTGAGGGAAATGAGAGGGGTGTCTGGCTAAATGACTTTGAGTATGCT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 221

GATGATTATGCAGCAGAGGACGAGGAATATGAGAAGTTGAAGAAGGAGAAGCTAGCGTTGTTCTTCGTGGCAACgtgaggcatt ... tttgttacagGTATGGAGATGGTGAGCCGACTGACAATGCTGCTAGGTTCTACAAATGGTTCACTGAGGGAAATGAGAGGGGTGTCTGGCTAAATGACTTTGAGTATGCT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 188

GATGATTATGCAGCAGAGGACGAGGAATATGAGAAGTTGAAGAAGGAGAAGCTAGCGTTGTTCTTCGTGGCAACgtgaggcatt ... tttgttacagGTATGGAGATGGTGAGCCGACTGACAATGCTGCTAGGTTCTACAAATGGTTCACTGAGGGAAATGAGAGGGGTGTCTGGCTAAATGACTTTGAGTATGCT


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 323

GATGATTATGCAGCAGAGGACGAGGAATATGAGAAGTTGAAGAAGGAGAAGCTAGCGTTGTTCTTCGTGGCAACgtgaggcatt ... tttgttacagGTATGGAGATGGTGAGCCGACTGACAATGCTGCTAGGTTCTACAAATGGTTCACTGAGGGAAATGAGAGGGGTGTCTGGCTAAATGACTTTGAGTATGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttattttggagtacgaaatcaaggaaaacttcctcatgatacttttgttacagGTATGGAGATGGTGAGCCGACTGACAATGCTGCTAGGTTCTACAAATGGTTCACTGAGGGAAATGAGAGGGGTGTCTGGCTAAATGACTTTGAGTATGCT
                                           cttttgtt  CT-rich tract
                                        atactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaataatgttcaggggctctcgacatttggatgatttgtttttcatttattttggagtacgaaatcaaggaaaacttcctcatgatacttttgttacagGTATGGAGATGGTGAGCCGACTGACAATGCTGCTAGGTTCTACAAATGGTTCACTGAGGGAAATGAGAGGGGTGTCTGGCTAAATGACTTTGAGTATGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - -acatttg
- - - - - - - - - - - - - - - - tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaggaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatact