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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttgaggcctttgaaccgatcaaatctttgtttcggcattcctctaatggaaaaggcgataaaaaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGCATGCCATGCAGATCGAAG

Basic information

species Zea mays
transcript GRMZM2G129513_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G129513_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os08g44810.1 (Oryza sativa), 3'ss of exon 10
gtaagttttgaggcctttga--accgatcaaatctttg-tttcggcattcctctaatggaaaaggcgataaaaaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGCATGCCATGCAGATCGAAG
||||  || ||| | ||||    |  ||    |||||  | |    ||  |||| |   ||||| | ||   ||||  | |||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| || |||
gtaaaattcgagacttttggttgctaattgtttctttaatattattatggctctcaaccaaaag-caatggtaaaa-catagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGACATCGTGTTCAGTATGCCATGCAGGTCAAAG

upper sequence: GRMZM2G129513_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv13s0019g05250.t01 (Vitis vinifera), 3'ss of exon 10
--------------------------------------------------------------------------------------------------gtaagttttgaggcctttgaac---cgatcaaatctttgtttcggcatt--cctctaatggaaa-aggcgataaaaaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGCATGCCATGCAGATCGAAG
                                                                                                   ||   |   |||    || |    |  |    | | || || |   ||   ||| | |   |  |    | |    ||||| |||||||||| || ||||||||||||||  ||||||||| ||| || ||||||||||||||| |||| || 
gtaagttttcatctgccgtatatggttgctgttctatttggttagtcttatgtaagaaatgaactagatctttccacaaacgtattgtttaagatcatatataatagtaggttgctgcagttgcatttttgtttatgattagttgttagtctccagtctcaccatttcaaacctcaaatatagGTTTATACCACCGGAAATCCTTATGGTGTAGCAGAGGGTATTGTTTTCAGCATGCCATGCCGATCAAAA
















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|15554238|gb|BI644236.1|BI644236
EST:     TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
genomic: TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|32802875|gb|CD955111.1|CD955111
EST:     GATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
genomic: GATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|16377496|gb|BI991968.1|BI991968
EST:     TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
genomic: TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|110219294|gb|EC901192.1|EC901192
EST:     TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTTTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
genomic: TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|13562222|gb|BG550442.1|BG550442
EST:     TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
genomic: TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|211178868|gb|FL449311.1|FL449311
EST:     TTTTCTACAGGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAG
genomic: TTTTCTACA-GGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAG
EST: gi|13558503|gb|BG549859.1|BG549859
EST:     ACCCCAGAAGGTGACTGGTTTTCTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
genomic: ACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|78089786|gb|DV518160.1|DV518160
EST:     TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
genomic: TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|32916975|gb|CF021787.1|CF021787
EST:     TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
genomic: TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|211195515|gb|FL441324.1|FL441324
EST:     TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCATGTTCAGC
genomic: TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|13198702|gb|BG354504.1|BG354504
EST:     TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
genomic: TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|148971653|gb|EE022376.2|EE022376
EST:     TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
genomic: TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|211178869|gb|FL449312.1|FL449312
EST:     TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
genomic: TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|15590379|gb|BI674995.1|BI674995
EST:     TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
genomic: TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|148928691|gb|EC873304.2|EC873304
EST:     TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTTTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
genomic: TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|32803142|gb|CD955378.1|CD955378
EST:     CCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
genomic: CCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|16379916|gb|BI993216.1|BI993216
EST:     TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGG                         GTTTATACGTCTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
genomic: TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|211129427|gb|FL299354.1|FL299354
EST:     TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
genomic: TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|211195516|gb|FL441325.1|FL441325
EST:     TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCATGTTCAGC
genomic: TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|32790887|gb|CD943123.1|CD943123
EST:     GATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
genomic: GATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|30706123|gb|CD059034.1|CD059034
EST:     TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
genomic: TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|74239371|gb|DT647285.1|DT647285
EST:     TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
genomic: TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|13490961|gb|BG517725.1|BG517725
EST:     TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
genomic: TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|15208823|gb|BI430707.1|BI430707
EST:     TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
genomic: TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|13558839|gb|BG550194.1|BG550194
EST:     TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
genomic: TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|13558038|gb|BG549394.1|BG549394
EST:     TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
genomic: TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|32825321|gb|CD965043.1|CD965043
EST:     ACCCCAGAAGGTGACTGGTTTTCTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
genomic: ACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|32790178|gb|CD942414.1|CD942414
EST:     GATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
genomic: GATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|12968102|gb|BG265049.1|BG265049
EST:     TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
genomic: TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|32825209|gb|CD964931.1|CD964931
EST:     GATCTCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
genomic: GATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
EST: gi|15079902|gb|BI388873.1|BI388873
EST:     TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGG                         GTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC
genomic: TTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGC

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: 45 (upstream exon), 48 (downstream exon)
Score: 19

ATGGGGCAGATCATCAGCTGCATCGACCGCTGTTTCGATAGTGGATGCTATTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGCATGCCATGCAGATCGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 368

ATGGGGCAGATCATCAGCTGCATCGACCGCTGTTTCGATAGTGGATGCTATTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGCATGCCATGCAGATCGAAG


Block sizes: 42 (upstream exon), 22 (downstream exon)
Score: 2

ATGGGGCAGATCATCAGCTGCATCGACCGCTGTTTCGATAGTGGATGCTATTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGCATGCCATGCAGATCGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 357

ATGGGGCAGATCATCAGCTGCATCGACCGCTGTTTCGATAGTGGATGCTATTAGATCCCTCGTAACTCCTACCCCAGAAGGTGACTGGTTTTCTACAGGGgtaagttttg ... aaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGCATGCCATGCAGATCGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcaaatctttgtttcggcattcctctaatggaaaaggcgataaaaaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGCATGCCATGCAGATCGAAG
                       ctctaat  putative branch site (score: 357)
                                        ataaaaaaaataca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttttgaggcctttgaaccgatcaaatctttgtttcggcattcctctaatggaaaaggcgataaaaaaaatacagGTTTATACGACTGGAAATCCTTATGGCATAGCAGAGGATATCGTGTTCAGCATGCCATGCAGATCGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT