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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGAgtatccccactaacattttgtaacgcgtctcttaaagctagtctactgatttggctaaactctcgatagcttctttctcgttttctttggtcccgcttgt...

Basic information

species Zea mays
transcript GRMZM2G052546_T01
intron # 6
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052546_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g01750.5 (Oryza sativa), 5'ss of exon 5
AGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGAgtatccccactaacattttgtaacgcgtctcttaaagctagtctactgatttggctaaactctcgatagcttctttctcgttttctttggtcccgcttgt---
|| ||||||||||||||||| ||| || | |||||||| ||||| ||||||||| ||||||||||| |||| |||||||||||| | ||    ||| |      |||| | | |||  |  |  ||   |   |  |     ||     ||   |       ||||  ||   |  |   
AGCCCACTTGATGTTGATAAACTTAGGGACATTGGTGTAAAAACAGTATTCTGCCTGCAGCAAGATCCAGACCTTGAgtatccctattattgatttttttt---tctcatcatgcttataaaaagaaaggagcatgccaattatgttgcctggtttagagaatttgagcctcttgattct

upper sequence: GRMZM2G052546_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA10G34370.1 (Glycine max), 5'ss of exon 6
AGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGAgtatccccactaacatttt--gtaa----cgcgtct----cttaaagctagtct--actgatttggctaaactctcgatagcttctttctcgttttctttggtcccgcttgt
| |||    ||||| || ||| | || |  ||||| || |||||| |||| ||||| || ||||||||||| |||||||||||  |  |   | ||   |||    | | |       || |  | | | |  | |   |    |  | ||| | |||        |   |||||||    |  |||  
ACTCCTGAAGATGTAGACAAGTTGCGTAGAATTGGAGTGAAAACTATATTTTGCTTACAACAAGATTCAGACCTTGAgtatcctaatcagtttctttaataagattcactttcagtatttgagacaaatatgaaatacctcatatttaatctagctagtgaaccattgtgtttctttacaactacttag

upper sequence: GRMZM2G052546_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv00s0250g00020.t01 (Vitis vinifera), 5'ss of exon 6
AGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGAgtatccccactaacatt-ttgtaacgcgtctcttaaagctagtctactgatttggctaaactctcgatagcttctttctcgttttctttggtcccgcttgt---------------------------------------------
||||||   |||||||| ||||||||||  ||||| || |||||  | || ||||| || |||||||||||||||||||||||  |  ||  || |||| | | || || |   |    |||| |   |    | | || | |||  |||   |   |    ||   | |    ||||                                             
AGTCCAGAAGATGTTGACAAGCTTCGGAGTATTGGGGTGAAAACCATTTTTTGCTTACAACAAGATTCAGATCTTGAgtatcctaaacaattttattgtta-gagtttcatttggactatctattatat--atttagcttttgatcacttgagttaagacaactactgacaaaattgtctgagtgaggaagtacactgttaattccttgacttgtatgtccag

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|148952817|gb|EC898809.2|EC898809
EST:     AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGA                         ATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
genomic: AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGAgtatccccac ... acttgttcagATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
EST: gi|148970824|gb|EE021591.2|EE021591
EST:     AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGA                         ATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
genomic: AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGAgtatccccac ... acttgttcagATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
EST: gi|15427195|gb|BI543017.1|BI543017
EST:     AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGA                         ATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
genomic: AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGAgtatccccac ... acttgttcagATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
EST: gi|21621474|gb|BQ619480.1|BQ619480
EST:     AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGA                         ATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
genomic: AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGAgtatccccac ... acttgttcagATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
EST: gi|67023551|gb|CO452300.1|CO452300
EST:     AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGA                         ATATTTTAGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
genomic: AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGAgtatccccac ... acttgttcagATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
EST: gi|211183157|gb|FL428740.1|FL428740
EST:     AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGA                         ATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
genomic: AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGAgtatccccac ... acttgttcagATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
EST: gi|71435430|gb|DR816480.1|DR816480
EST:     AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGA                         ATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
genomic: AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGAgtatccccac ... acttgttcagATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
EST: gi|76290045|gb|DV029613.1|DV029613
EST:     AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGA                         ATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
genomic: AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGAgtatccccac ... acttgttcagATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
EST: gi|211478786|gb|FL377818.1|FL377818
EST:     AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGA                         ATATTTTGGAGTCGACATCCGTGCCATTCACGATTATTCTCTACAATTCAC
genomic: AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGAgtatccccac ... acttgttcagATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
EST: gi|76914764|gb|DV165677.1|DV165677
EST:     AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGA                         ATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
genomic: AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGAgtatccccac ... acttgttcagATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
EST: gi|74234762|gb|DT642676.1|DT642676
EST:     AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGA                         ATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
genomic: AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGAgtatccccac ... acttgttcagATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
EST: gi|149081546|gb|EE170685.2|EE170685
EST:     AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGA                         ATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
genomic: AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGAgtatccccac ... acttgttcagATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
EST: gi|148967268|gb|EE018472.2|EE018472
EST:     AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGA                         ATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
genomic: AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGAgtatccccac ... acttgttcagATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
EST: gi|211266638|gb|FL405762.1|FL405762
EST:     AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGA                         ATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
genomic: AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGAgtatccccac ... acttgttcagATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
EST: gi|148934585|gb|EC878634.2|EC878634
EST:     AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGA                         ATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
genomic: AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGAgtatccccac ... acttgttcagATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
EST: gi|91876121|gb|EB406078.1|EB406078
EST:     AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGA                         ATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA
genomic: AAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGAgtatccccac ... acttgttcagATATTTTGGAGTCGACATCCGTGCCATTCAAGATTATTCTCTACAATTCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGAgtatccccactaacattttgtaacgcgtctcttaaagctagtctactgatttggctaaactctcgatagcttctttctcgttttctttggtcccgcttgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA