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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATAAATTTGAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAGgttttatttcagatacctaatgctatttatgaaatctgtattggatgtttgtaattctttcaacctcttcaaggcaaattttaggcatccacgtgttctctgttgaatatattctttctatctttgcag

Basic information

species Zea mays
transcript GRMZM2G013890_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G013890_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os02g58020.3 (Oryza sativa), 5'ss of exon 11
CTATAAATTTGAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAGgttttatttcagata-----cctaatgctattta-tgaaatctgtattggatgtttgtaattctttcaacctcttcaaggcaaattttaggcatccacgtgttctctgttgaatatattctttctatctttgcag-------------------------------------------
||||||||| ||||||||||| ||||||||||||||||| |||||||||||||||||||||||| ||||| ||||      ||     | ||||  ||||| |||  |       |||    |  |       |          ||      ||    ||  |   |  |   | | || ||   ||||  ||||                                           
CTATAAATTCGAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCATCAGCTTCAGgtttcatttctgatatgttttctttcaatgtttaacgaaatttgttctcttcccatgtgcaaccatggtttcttgttctctggcttgctactatatttgtaattctttctagctttcttattaagatcta-gcagttagtacattctgaggtatttatgttacgatctgtttgtgcag
















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|60343993|gb|DN210966.1|DN210966
EST:     GAATTTCCGACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAG                         TGATGCCTCATTTGGTTACCCTGGAGGGCCTACCTTGTTTAAAAATTTGAA
genomic: GAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAGgttttatttc ... atctttgcagTGATGCCTCATTTGGTTACCCTGGAGGGCCTACCTTGTTTAAAAATTTGAA
EST: gi|32930219|gb|CF035031.1|CF035031
EST:     GAATTTCCGACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAG                         TGATGCCTCATTTGGTTACCCTGGAGGGCCTACCTTGTTTAAAAATTTGAA
genomic: GAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAGgttttatttc ... atctttgcagTGATGCCTCATTTGGTTACCCTGGAGGGCCTACCTTGTTTAAAAATTTGAA
EST: gi|211238345|gb|FL044423.1|FL044423
EST:     AATTTCCCGACCC-AGATGACCGCCCTGGGCCACCAATCATCAGCTTCAG                         TGATGCCTCAATTTG-TTACCCTGGGAGGGCCTACTTTGTT-AAAAATTTG
genomic: AATTTCCA-ACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAGgttttatttc ... atctttgcagTGATGCCTCA-TTTGGTTACCCTGG-AGGGCCTACCTTGTTTAAAAATTTG
EST: gi|211429008|gb|FL174617.1|FL174617
EST:     GAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAG                         TGATGCCTCATTTGGTTACCCTGGAGGGCCTACCTTGTTTAAAAATTTGAA
genomic: GAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAGgttttatttc ... atctttgcagTGATGCCTCATTTGGTTACCCTGGAGGGCCTACCTTGTTTAAAAATTTGAA
EST: gi|67015572|gb|CO444321.1|CO444321
EST:     GAATTTCTTACCCCANATGACCGCCCTGGGCCACCAATCATCAGCTTCAG                         TGATGCCTCATTTGGTTACCCTGGAGGGCCTACCTTGTTTAAAAATTTGAA
genomic: GAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAGgttttatttc ... atctttgcagTGATGCCTCATTTGGTTACCCTGGAGGGCCTACCTTGTTTAAAAATTTGAA
EST: gi|60349362|gb|DN216335.1|DN216335
EST:     GAATTTCCGACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAG                         TGATGCCTCATTTGGTTACCCTGGAGGGCCTACCTTGTTTAAAAATTTGAA
genomic: GAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAGgttttatttc ... atctttgcagTGATGCCTCATTTGGTTACCCTGGAGGGCCTACCTTGTTTAAAAATTTGAA
EST: gi|71307303|gb|DR789832.1|DR789832
EST:     GAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAG                         TGATGCCTCATTTGGTTACCCTGGAGGGCCTACCTTGTTTAAAAATTTGAA
genomic: GAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAGgttttatttc ... atctttgcagTGATGCCTCATTTGGTTACCCTGGAGGGCCTACCTTGTTTAAAAATTTGAA
EST: gi|32932155|gb|CF036967.1|CF036967
EST:     GAATTTCCGACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAG                         TGATGCCTCATTTGGTTACCCTGGAGGGCCTACCTTGTTTAAAAATTTGAA
genomic: GAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAGgttttatttc ... atctttgcagTGATGCCTCATTTGGTTACCCTGGAGGGCCTACCTTGTTTAAAAATTTGAA
EST: gi|32932545|gb|CF037357.1|CF037357
EST:     GAATTTCCGACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAG                         TGATGCCTCATTTGGTTACCCTGGAGGGCCTACCTTGTTTAAAAATTTGAA
genomic: GAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAGgttttatttc ... atctttgcagTGATGCCTCATTTGGTTACCCTGGAGGGCCTACCTTGTTTAAAAATTTGAA
EST: gi|86472924|gb|DY239294.1|DY239294
EST:     GGCCACCAATCATCAGCTTCAG                         TGATGCCTCATTTGGTTACCCTGGAGGGCCTACCTTGTTTAAAAATTTGAA
genomic: GGCCACCAATCATCAGCTTCAGgttttatttc ... atctttgcagTGATGCCTCATTTGGTTACCCTGGAGGGCCTACCTTGTTTAAAAATTTGAA

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: 210

CTATAAATTTGAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAGgttttatttc ... atctttgcagTGATGCCTCATTTGGTTACCCTGGAGGGCCTACCTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 276

CTATAAATTTGAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAGgttttatttc ... atctttgcagTGATGCCTCATTTGGTTACCCTGGAGGGCCTACCTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 287

CTATAAATTTGAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAGgttttatttc ... atctttgcagTGATGCCTCATTTGGTTACCCTGGAGGGCCTACCTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 173

CTATAAATTTGAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAGgttttatttc ... atctttgcagTGATGCCTCATTTGGTTACCCTGGAGGGCCTACCTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATAAATTTGAATTTCCAACCCCAGATGACCGCCCTGGGCCACCAATCATCAGCTTCAGgttttatttcagatacctaatgctatttatgaaatctgtattggatgtttgtaattctttcaacctcttcaaggcaaattttaggcatccacgtgttctctgttgaatatattctttctatctttgcag

- - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT