Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaacgccctccgcatttcaccatttgtgacatttttctctgtggatcgtatatttctctttgttcatttgcaaatcatcctagttatgttttgtttctgtacag

Basic information

species Zea mays
transcript GRMZM2G034848_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G034848_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os09g20820.1 (Oryza sativa), 5'ss of exon 6
ATTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaacgccctccgcatttca---ccatttgtgacatttttctctgtggatcgtatatttctctttgttcatttgcaaatcatcctagttatgttttgtttctgtacag-----------------------------------
|| |||||||| ||||||||||| |||||||| ||||| || |||||||||||||  |  |    |   || ||   |||||| | ||     | |     |||  | || |||    |||   ||    | ||  |||     |  |   |  || |                                       
ATCAAAACTGGTGCTCCATGCCGTAGCGAGAGACTGGCAAAGTACAATCAGgtaaatattcttatcctgttccatatccatttttcaccaacctatactgagattatgtacttccacatgtcatttcctgattctacctcaagtttctccctcgctattttccccattacaccatactatgttttgttcctgtacag
















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|32867724|gb|CF007406.1|CF007406
EST:     TTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG                         CTTCTGCGGATTGAAGAGGAGCTTGGCAACGTGCGCTATGCAGGGGAGGCA
genomic: TTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaacgc ... ttctgtacagCTTCTGCGGATTGAAGAGGGGCTTGGCAACGTGCGCTATGCAGGGGAGGCA
EST: gi|91869806|gb|EB400550.1|EB400550
EST:     TTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG                         CTTTTGCGGATTGAAGAGGGGCTTGGCAACGTGCGCTATGCAGGGGAGGCA
genomic: TTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaacgc ... ttctgtacagCTTCTGCGGATTGAAGAGGGGCTTGGCAACGTGCGCTATGCAGGGGAGGCA
EST: gi|149086059|gb|EE175588.2|EE175588
EST:     TTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATCCAATCAG                         CTTTTGCGGATTGAAGAGGGGCTTGGCAACGTGCGCTATCCAGGGGAGGCA
genomic: TTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaacgc ... ttctgtacagCTTCTGCGGATTGAAGAGGGGCTTGGCAACGTGCGCTATGCAGGGGAGGCA
EST: gi|71446085|gb|DR827135.1|DR827135
EST:     TTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG                         CTTCTGCGGATTGAAGAGGGGCTTGGCAACGTGCGCTATGCAGGGGAGGCA
genomic: TTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaacgc ... ttctgtacagCTTCTGCGGATTGAAGAGGGGCTTGGCAACGTGCGCTATGCAGGGGAGGCA
EST: gi|71445334|gb|DR826384.1|DR826384
EST:     TTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG                         CTTTTGCGGATTGAAGAGGGGCTTGGCAACGTGCGCTATGCAGGGGAGGCA
genomic: TTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaacgc ... ttctgtacagCTTCTGCGGATTGAAGAGGGGCTTGGCAACGTGCGCTATGCAGGGGAGGCA
EST: gi|211293097|gb|FL433992.1|FL433992
EST:     TTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG                         CTTCTGCGGATTGAAGAGGGGCTTGGCAACGTGCGCTATGCAGGGGAGGCA
genomic: TTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaacgc ... ttctgtacagCTTCTGCGGATTGAAGAGGGGCTTGGCAACGTGCGCTATGCAGGGGAGGCA
EST: gi|7304518|gb|AW600457.1|AW600457
EST:     TTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG                         CTTCTGCGGATTGAAGAGGAGCTTGGCAACGTGCGCTATGCAGGGGAGGCA
genomic: TTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaacgc ... ttctgtacagCTTCTGCGGATTGAAGAGGGGCTTGGCAACGTGCGCTATGCAGGGGAGGCA
EST: gi|148965075|gb|EE015894.2|EE015894
EST:     TTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG                         CTTTTGCGGATTGAAGAGGGGCTTGGCAACGTGCGCTATGCAGGGGAGGCA
genomic: TTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaacgc ... ttctgtacagCTTCTGCGGATTGAAGAGGGGCTTGGCAACGTGCGCTATGCAGGGGAGGCA
EST: gi|101401519|gb|EB822439.1|EB822439
EST:     TTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG                         CTTTTGCGGATTGAAGAGGGGCTTGGCAACGTGCGCTATGCAGGGGAGGCA
genomic: TTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaacgc ... ttctgtacagCTTCTGCGGATTGAAGAGGGGCTTGGCAACGTGCGCTATGCAGGGGAGGCA
EST: gi|89250270|gb|DY622056.1|DY622056
EST:     TTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG                         CTTTTGCGGATTGAAGAGGGGCTTGGCAACGTGCGCTATCCAGGGGAGGCA
genomic: TTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaacgc ... ttctgtacagCTTCTGCGGATTGAAGAGGGGCTTGGCAACGTGCGCTATGCAGGGGAGGCA
EST: gi|60348134|gb|DN215107.1|DN215107
EST:     TTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG                         CTTCTGCGGATTGAAGAGGGGCTTGGCAACGTGCGCTATGCAGGGGAGGCA
genomic: TTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaacgc ... ttctgtacagCTTCTGCGGATTGAAGAGGGGCTTGGCAACGTGCGCTATGCAGGGGAGGCA
EST: gi|211133333|gb|FL444548.1|FL444548
EST:     TTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG                         CTTCTGCGGATTGAAGAGGGGCTTGGCAACGTGCGCTATGCAGGGGAGGCA
genomic: TTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaacgc ... ttctgtacagCTTCTGCGGATTGAAGAGGGGCTTGGCAACGTGCGCTATGCAGGGGAGGCA
EST: gi|211242539|gb|FL481663.1|FL481663
EST:     TTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG                         CTTCTGCGGATTGAAGAGGGGCTTGGCAACGTGCGCTATGCAGGGGAGGCA
genomic: TTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaacgc ... ttctgtacagCTTCTGCGGATTGAAGAGGGGCTTGGCAACGTGCGCTATGCAGGGGAGGCA

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 7

ATTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaacgc ... ttctgtacagCTTCTGCGGATTGAAGAGGGGCTTGGCAACGTGCGCTATGCAGGGGAGGCATTCAGGTCTCCATAAGAAATAGACTTTAAATCACCGCGCGTGTGTGAGA


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 2

ATTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaacgc ... ttctgtacagCTTCTGCGGATTGAAGAGGGGCTTGGCAACGTGCGCTATGCAGGGGAGGCATTCAGGTCTCCATAAGAAATAGACTTTAAATCACCGCGCGTGTGTGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 7

ATTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaacgc ... ttctgtacagCTTCTGCGGATTGAAGAGGGGCTTGGCAACGTGCGCTATGCAGGGGAGGCATTCAGGTCTCCATAAGAAATAGACTTTAAATCACCGCGCGTGTGTGAGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTAAAACTGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAGgtaagaacgccctccgcatttcaccatttgtgacatttttctctgtggatcgtatatttctctttgttcatttgcaaatcatcctagttatgttttgtttctgtacag

- - - - - - - - - - - - -  GAGAGG