Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGAAGCCAACCGAGACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcctatatagggttgcattgcccaactccttgcacgaaatgggttttgattttttagaactttttttcctttggaattgtag

Basic information

species Zea mays
transcript GRMZM2G108829_T01
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108829_T01 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os02g47220.2 (Oryza sativa), 5'ss of exon 17
AAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGAAGCCAACCGAGACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcctatatagggttgcattgcccaactccttgcacgaaatgggttttgattttttagaactttttttcctttg---gaattgtag
|||||| |  ||||||||||| |  | || |||  ||  || || || |||| ||  ||||||||||| || ||||| ||||| ||  ||||||||||||||||||||||     |  ||||| ||     | | ||  ||  || | |   |||| |||  |||  |   || ||||||    |||| |||
AAACTTCAAATGGATCGTCAGGCGCCACAGAAGATTAAAAAACCTACTGAGAGTAATAATAAACTAACCACTAATCGAGTACCTGCAAGGAATAGCCCAGgcaagtttcc-----atagttgctttatttgaattct-acatcaatttgtggttgactttgaagatttacattccctttgtggcaattatag
















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|86469589|gb|DY235959.1|DY235959
EST:     GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
genomic: GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
EST: gi|78078782|gb|DV507194.1|DV507194
EST:     GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
genomic: GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
EST: gi|24764828|gb|CA399990.1|CA399990
EST:     GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
genomic: GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
EST: gi|211129651|gb|FL443400.1|FL443400
EST:     GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
genomic: GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
EST: gi|32864986|gb|CF004668.1|CF004668
EST:     GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
genomic: GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
EST: gi|84980182|gb|DW530531.1|DW530531
EST:     GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
genomic: GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
EST: gi|78022750|gb|DV491137.1|DV491137
EST:     GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGGAGCTTACCTGAAACTGGCCGAGGAG
genomic: GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
EST: gi|32864987|gb|CF004669.1|CF004669
EST:     GGCTAGCAATAAACTAACTACGAATCGGGTGCCAGCTCGGAATAGCCCAG                         GGAATCCTGTTCTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
genomic: GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
EST: gi|40334857|gb|CK368927.1|CK368927
EST:     GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
genomic: GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
EST: gi|37378370|gb|CF625872.1|CF625872
EST:     GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
genomic: GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
EST: gi|76285158|gb|DV024726.1|DV024726
EST:     AGCAATAAACTAATTACGAATCGGGTACCAGCTCGGAATAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
genomic: AGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
EST: gi|211129652|gb|FL443401.1|FL443401
EST:     AGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
genomic: AGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
EST: gi|5770191|gb|AI973365.1|AI973365
EST:     GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGGAGCTTACCTGAAACTGGCCGAGGAG
genomic: GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
EST: gi|211496287|gb|FL041699.1|FL041699
EST:     GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAA                         GGNAATCCTGTACTTAGGCATTCACGGAGCTTGCCT
genomic: GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcc ... ggaattgtagGG-AATCCTGTACTTAGGCATTCACGGAGCTTGCCT
EST: gi|31359660|gb|CD444017.1|CD444017
EST:     CGGGTACCAGCTCGGAATAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
genomic: CGGGTACCAGCTCGGAATAGCCCAGgcaagtttcc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
EST: gi|5919395|gb|AW054492.1|AW054492
EST:     GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
genomic: GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
EST: gi|60349834|gb|DN216807.1|DN216807
EST:     GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
genomic: GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
EST: gi|116824201|gb|EC867803.1|EC867803
EST:     GACTA-CAATAAACTAACTACG-ATCGGGT-CCAGCTCGGAATAGCCCA-                         GGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
genomic: GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
EST: gi|5325074|gb|AI783265.1|AI783265
EST:     GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGGAGCTTACCTGAAACTGGCCGAGGAG
genomic: GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
EST: gi|5846886|gb|AI999969.1|AI999969
EST:     GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGGAGCTTACCTGAAACTGGCCGAGG
genomic: GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGG
EST: gi|87155121|gb|DY399910.1|DY399910
EST:     GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
genomic: GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
EST: gi|15215165|gb|BI431185.1|BI431185
EST:     GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
genomic: GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
EST: gi|60358960|gb|DN225933.1|DN225933
EST:     GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
genomic: GACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAG
EST: gi|211386736|gb|FL133265.1|FL133265
EST:     TAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAG                         GGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAWRACTGGCCGAGGA
genomic: TAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGA-AACTGGCCGAGGA

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: 287

AAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGAAGCCAACCGAGACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAGCAATACAGAAGGTCTCATCAATTACAGAGAAACTATCCCAAATGTCTGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 172

AAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGAAGCCAACCGAGACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAGCAATACAGAAGGTCTCATCAATTACAGAGAAACTATCCCAAATGTCTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 224

AAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGAAGCCAACCGAGACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAGCAATACAGAAGGTCTCATCAATTACAGAGAAACTATCCCAAATGTCTGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 210

AAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGAAGCCAACCGAGACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcc ... ggaattgtagGGAATCCTGTACTTAGGCATTCACGGAGCTTGCCTGAAACTGGCCGAGGAGCAATACAGAAGGTCTCATCAATTACAGAGAAACTATCCCAAATGTCTGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGAAGCCAACCGAGACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcctatatagggttgcattgcccaactccttgcacgaaatgggttttgattttttagaactttttttcctttggaattgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC