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

GTGCCGCCCAAGTTCTCCAAGGCAGCCAGGAGGTTTTACAATGAGAATATCAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttgtcctactgtttttctggacctcaggcattcaatcaagtagtaatagctggaggagtattctagatgagtttttttccatgcgttaacgtt...

Basic information

species Zea mays
transcript GRMZM2G315806_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G315806_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g05806.1 (Oryza sativa), 5'ss of exon 1
GTGCCGCCCAAGTTCTCCAAGGCAGCCAGGAGGTTTTACAATGAGAATATCAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttgtcctact----gtttttctggacctcaggcattcaatcaagtagtaatagctggaggagtatt--ctagatg-agtttttttcca--tgcgttaacgtt--------------------
| ||||||||||||||||||||| || ||||| || ||||||||||||||||||||||  || ||||| ||||||||||||||||||||||| ||||||||||||| |  |   ||      |||| ||| |   |  | |||  |   | |      |     ||   ||||   ||| |  ||        ||  ||  | || | |                    
GCGCCGCCCAAGTTCTCCAAGGCCGCGAGGAGATTCTACAATGAGAATATCAAGGAGCACGAACCGCAGCGGCTCGCCAAGGTCCTTGCCGCGGCAGGAGgtagtcttcctatcacgcatgattttactgaagtgcttgaattggacagaatcaattcaatcaaagttatattacttagttacagcaacacatcagttgtctgaatgctggcctgattgctccttccag
















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|148987677|gb|EE031557.2|EE031557
EST:     CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAG                         TGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
genomic: CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttg ... ctctttccagTGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
EST: gi|148957814|gb|EC903956.2|EC903956
EST:     CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAG                         TGGCATCAAGAAGGACCAGTGGAGGAGCTCATCTTCCAAGGGAAGGTGGAC
genomic: CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttg ... ctctttccagTGGCATCAAGAAGGACCAGTG-AGGAGCTCATCTTCCAAGGGAAGGTG-AC
EST: gi|78111429|gb|DV529826.1|DV529826
EST:     CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAG                         TGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
genomic: CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttg ... ctctttccagTGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
EST: gi|71310508|gb|DR791549.1|DR791549
EST:     CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAG                         TGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
genomic: CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttg ... ctctttccagTGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
EST: gi|50330874|gb|CO526000.1|CO526000
EST:     CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAG                         TGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
genomic: CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttg ... ctctttccagTGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
EST: gi|149079210|gb|EE168172.2|EE168172
EST:     CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAG                         TGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
genomic: CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttg ... ctctttccagTGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
EST: gi|149083253|gb|EE172532.2|EE172532
EST:     CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAG                         TGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
genomic: CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttg ... ctctttccagTGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
EST: gi|211522997|gb|FL114322.1|FL114322
EST:     CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAG                         TGGCATCAAGA
genomic: CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttg ... ctctttccagTGGCATCAAGA
EST: gi|211519990|gb|FL114312.1|FL114312
EST:     CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAG                         TGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
genomic: CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttg ... ctctttccagTGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
EST: gi|211519996|gb|FL114318.1|FL114318
EST:     CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAG                         TGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
genomic: CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttg ... ctctttccagTGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
EST: gi|74237372|gb|DT645286.1|DT645286
EST:     CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAG                         TGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
genomic: CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttg ... ctctttccagTGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
EST: gi|211519992|gb|FL114314.1|FL114314
EST:     AGGGAGCGG-AGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCNAG-AG                         TGGCATCAAGAAAGGAC-AGTGAGGAGCTCA
genomic: AAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGC-AGGAGgtagtccttg ... ctctttccagTGGCATCAAGAA-GGACCAGTGAGGAGCTCA
EST: gi|89761484|gb|DY689481.1|DY689481
EST:     CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAG                         TGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
genomic: CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttg ... ctctttccagTGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
EST: gi|71446099|gb|DR827149.1|DR827149
EST:     CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAG                         TGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
genomic: CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttg ... ctctttccagTGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
EST: gi|148946321|gb|EC891627.2|EC891627
EST:     CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAG                         TGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
genomic: CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttg ... ctctttccagTGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
EST: gi|50331088|gb|CO526214.1|CO526214
EST:     CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAG                         TGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
genomic: CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttg ... ctctttccagTGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
EST: gi|14191222|gb|BG833452.1|BG833452
EST:     AAGGAGCGGGCAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAG                         TGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
genomic: AAGGAGCGGG-AGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttg ... ctctttccagTGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
EST: gi|148938500|gb|EC882821.2|EC882821
EST:     CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAG                         TGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
genomic: CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttg ... ctctttccagTGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
EST: gi|211522998|gb|FL114323.1|FL114323
EST:     CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAG                         TGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
genomic: CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttg ... ctctttccagTGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
EST: gi|71436711|gb|DR817761.1|DR817761
EST:     CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAG                         TGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
genomic: CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttg ... ctctttccagTGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
EST: gi|101386864|gb|EB815449.1|EB815449
EST:     CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAG                         TGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
genomic: CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttg ... ctctttccagTGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
EST: gi|14191223|gb|BG833453.1|BG833453
EST:     CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAG                         TGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
genomic: CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttg ... ctctttccagTGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
EST: gi|71306649|gb|DR789484.1|DR789484
EST:     CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAG                         TGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG
genomic: CAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttg ... ctctttccagTGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTG

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: 36 (upstream exon), 43 (downstream exon)
Score: 26

GTGCCGCCCAAGTTCTCCAAGGCAGCCAGGAGGTTTTACAATGAGAATATCAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttg ... ctctttccagTGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAG


Block sizes: 31 (upstream exon), 45 (downstream exon)
Score: 18

GTGCCGCCCAAGTTCTCCAAGGCAGCCAGGAGGTTTTACAATGAGAATATCAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttg ... ctctttccagTGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAG


Block sizes: 17 (upstream exon), 44 (downstream exon)
Score: 4

GTGCCGCCCAAGTTCTCCAAGGCAGCCAGGAGGTTTTACAATGAGAATATCAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttg ... ctctttccagTGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAG


Block sizes: 38 (upstream exon), 41 (downstream exon)
Score: 12

GTGCCGCCCAAGTTCTCCAAGGCAGCCAGGAGGTTTTACAATGAGAATATCAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttg ... ctctttccagTGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCCGCCCAAGTTCTCCAAGGCAGCCAGGAGGTTTTACAATGAGAATATCAAGGAGCGGGAGCCGCAACGGCTCGCCAAGGTCCTTGCCGCCGCAGGAGgtagtccttgtcctactgtttttctggacctcaggcattcaatcaagtagtaatagctggaggagtattctagatgagtttttttccatgcgttaacgtt

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG