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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTCACTTTGCATGAAATGCTGCCTCTTGCATTTGACTATTGTGGCCAGAAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAGgtttgtcgattcttcaaattaagcaaagggattccttgagtaaacattttgtcttaatgaccagtatggatttgctttccctttccgcaaaagactcgta...

Basic information

species Zea mays
transcript GRMZM2G050484_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G050484_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os02g10230.1 (Oryza sativa), 5'ss of exon 11
TCCTCACTTTGCATGAAATGCTGCCTCTTGCATTTGACTATTGTGGCCAGAAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAGgtttgtcgattcttcaaattaagcaaagggattccttgagtaaacattttgtcttaatgaccagtatggatttgctttccct-----ttccgcaaaagactcgta
|||||||||||||||||||| | ||||| ||||||||||||  ||| || || || ||||||||||| |||||||| |||||||||| |||||||||||||||||| |||  ||||||| ||| |     | |   |     | |||     | |  |||| | | ||||||||| |||  |     ||   |   | | |  | 
TCCTCACTTTGCATGAAATGTTACCTCTAGCATTTGACTATGCTGGTCAAAAACAGGCTGTCAAAGCAGTCTTTGTTGGCATGGCCTTCATGTCTGCAAGgtttgttgatgtttcaaataaagtactcctaatatgtttcagatcatc----cattgtgactaatgtggatttgcattcagtaaagattttcctttatattttt-

upper sequence: GRMZM2G050484_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA15G03820.2 (Glycine max), 5'ss of exon 11
TCCTCACTTTGCATGAAATGCTGCCTCTTGCATTTGACTATTGTGGCCAGAAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAGgtttgtcgattcttcaaattaagcaaagggattcct------tgagtaaaca--ttttgtcttaatgaccagtatggatttgctttccctttccgcaaaagactcgta
| || ||  | ||||||||||||||  | || ||||| |||   || ||||||||| |||| || ||||||||| |||| ||||| | ||||||||||||||     || |||      ||| ||||  | ||         |||  | | |  || | |||| ||  | | | |||       ||   |       |  | |     
TTCTGACCCTTCATGAAATGCTGCCATTGGCTTTTGATTATGCGGGACAGAAGCAATCTGTTAAGGCTGTCTTTTTGGGGATGGCTTTCATGTCTGCAAGgta---agaatctcattgctaatcaaatagtttttcaagagctgatgatatagcttctttctttattgctactttggtaagatatttaatgcatttgagtgtc-----

upper sequence: GRMZM2G050484_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA13G41580.1 (Glycine max), 5'ss of exon 11
TCCTCACTTTGCATGAAATGCTGCCTCTTGCATTTGACTATTGTGGCCAGAAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAGgtttgtcgatt-cttcaaattaagcaaagggattccttgagtaaacattttgtcttaatgaccagtatggatttgctttccctttccgcaaaagactcgta----
| || ||  | ||||||||||| ||  | || ||||| |||   || ||||||||| |||| || ||||||||| |||| ||||| | ||||||||||||||  |    |   ||| ||| ||  |   |  || |  |||   |   | |  |||  | |    |||   |||  || |   ||  | || | | |        
TTCTGACCCTTCATGAAATGCTTCCATTGGCTTTTGATTATGCGGGACAGAAGCAATCTGTGAAGGCTGTCTTTTTGGGGATGGCTTTCATGTCTGCAAGgtcagaatctcatttctaatcaaata---gtttttcaagagctgatgatatagcttt-ttatttttattttttta-ttgctactttggtaagatatttaatgcat

upper sequence: GRMZM2G050484_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv06s0004g01860.t01 (Vitis vinifera), 5'ss of exon 11
TCCTCACTTTGCATGAAATGCTGCCTCTTGCATTTGACTATTGTGGCCAGAAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAGgtttg-tcgattcttcaaattaagcaaagggattccttgagtaaacattttg-----tcttaatgaccagtatggatttgctttccctttc-cgcaaaagactcgta-
| || || |||||||||||||||||  | ||||||||||||  ||| | ||||||||||||||| || |||||  | || ||||| | ||||||||||||||    || | || |       ||||  |  | || || || |  |||||       |  |  | |     |||  |||| |  ||||    |    ||||     | 
TTCTTACCTTGCATGAAATGCTGCCATTGGCATTTGACTATGCTGGGCCGAAGCAAGCTGTCAAGGCAGTCTTCTTTGGAATGGCTTTCATGTCTGCAAGgtaaaatcaactcct-------agcag-gacactctttcagaagccatttaaaaagtttctggtaatttcaatgattttggtagccctacaacctggaagaaaaaaaa

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|211041256|gb|FL123860.1|FL123860
EST:     AAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAG                         CTTGTACTTCTTGGAAGTCAGCTTAGCAAAGGAGATAAGCTTGTAGCATCG
genomic: AAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAGgtttgtcgat ... taattgacagCTTGTACTTCTTGGAAGTCAGCTTACCAAAGGAGATAAGCTTGTAGCATCG
EST: gi|88749903|gb|DY534044.1|DY534044
EST:     AAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAG                         CTTGTACTTCTTGGAAGTCAGCTTACCAAAGGAGATAAGCTTGTAGCATCG
genomic: AAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAGgtttgtcgat ... taattgacagCTTGTACTTCTTGGAAGTCAGCTTACCAAAGGAGATAAGCTTGTAGCATCG
EST: gi|78115522|gb|DV533910.1|DV533910
EST:     AAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAG                         CTTGTACTTCTTGGAAGTCAGCTTACCAAAGGAGATAAGCTTGTAGCATCG
genomic: AAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAGgtttgtcgat ... taattgacagCTTGTACTTCTTGGAAGTCAGCTTACCAAAGGAGATAAGCTTGTAGCATCG
EST: gi|18164662|gb|BM334501.1|BM334501
EST:     AAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAG                         CTTGTACTTCTTGGAAGTCAGCTTACCAAAGGAGATAAGCTTGTAGCATCG
genomic: AAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAGgtttgtcgat ... taattgacagCTTGTACTTCTTGGAAGTCAGCTTACCAAAGGAGATAAGCTTGTAGCATCG
EST: gi|211350243|gb|FL472543.1|FL472543
EST:     AAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAG                         CTTGTACTTCTTGGAAGTCAGCTTAGCAAAGGAGATAAGCTTGTAGCATCG
genomic: AAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAGgtttgtcgat ... taattgacagCTTGTACTTCTTGGAAGTCAGCTTACCAAAGGAGATAAGCTTGTAGCATCG
EST: gi|18178000|gb|BM379210.1|BM379210
EST:     AAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAG                         CTTGTACTTCTTGGAAGTCAGCTTACCAAAGGAGATAAGCTTGTAGCATCG
genomic: AAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAGgtttgtcgat ... taattgacagCTTGTACTTCTTGGAAGTCAGCTTACCAAAGGAGATAAGCTTGTAGCATCG
EST: gi|71308419|gb|DR790442.1|DR790442
EST:     AAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAG                         CTTGTACTTCTTGGAAGTCAGCTTACCAAAGGAGATAAGCTTGTAGCATCG
genomic: AAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAGgtttgtcgat ... taattgacagCTTGTACTTCTTGGAAGTCAGCTTACCAAAGGAGATAAGCTTGTAGCATCG
EST: gi|76288875|gb|DV028443.1|DV028443
EST:     AAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAG                         CTTGTACTTCTTGGAAGTCAGCTTACCAAAGGAGATAAGCTTGTAGCATCG
genomic: AAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAGgtttgtcgat ... taattgacagCTTGTACTTCTTGGAAGTCAGCTTACCAAAGGAGATAAGCTTGTAGCATCG
EST: gi|50324963|gb|CO520089.1|CO520089
EST:     AAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAG                         CTTGTACTTCTTGGAAGTCAGCTTACCAAAGGAGATAAGCTTGTAGCATCG
genomic: AAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAGgtttgtcgat ... taattgacagCTTGTACTTCTTGGAAGTCAGCTTACCAAAGGAGATAAGCTTGTAGCATCG
EST: gi|71300310|gb|DR786224.1|DR786224
EST:     AAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAG                         CTTGTACTTCTTGGAAGTCAGCTTACCAAAGGAGATAAGCTTGTAGCATCG
genomic: AAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAGgtttgtcgat ... taattgacagCTTGTACTTCTTGGAAGTCAGCTTACCAAAGGAGATAAGCTTGTAGCATCG
EST: gi|71446246|gb|DR827296.1|DR827296
EST:     AAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAG                         CTTGTACTTCTTGGAAGTCAGCTTACCAAAGGAGATAAGCTTGTAGCATCG
genomic: AAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAGgtttgtcgat ... taattgacagCTTGTACTTCTTGGAAGTCAGCTTACCAAAGGAGATAAGCTTGTAGCATCG
EST: gi|91052253|gb|EB162671.1|EB162671
EST:     AAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAG                         CTTGTACTTCTTGGAAGTCAGCTTACCAAAGGAGATAAGCTTGTAGCATCG
genomic: AAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAGgtttgtcgat ... taattgacagCTTGTACTTCTTGGAAGTCAGCTTACCAAAGGAGATAAGCTTGTAGCATCG

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: 47 (upstream exon), 47 (downstream exon)
Score: 63

TCCTCACTTTGCATGAAATGCTGCCTCTTGCATTTGACTATTGTGGCCAGAAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAGgtttgtcgat ... taattgacagCTTGTACTTCTTGGAAGTCAGCTTACCAAAGGAGATAAGCTTGTAGCATCGCGCTGCAGGTACTGGGAGGCCATAGCCTGTCAGTAGATCCTGAATTCTA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 118

TCCTCACTTTGCATGAAATGCTGCCTCTTGCATTTGACTATTGTGGCCAGAAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAGgtttgtcgat ... taattgacagCTTGTACTTCTTGGAAGTCAGCTTACCAAAGGAGATAAGCTTGTAGCATCGCGCTGCAGGTACTGGGAGGCCATAGCCTGTCAGTAGATCCTGAATTCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 157

TCCTCACTTTGCATGAAATGCTGCCTCTTGCATTTGACTATTGTGGCCAGAAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAGgtttgtcgat ... taattgacagCTTGTACTTCTTGGAAGTCAGCTTACCAAAGGAGATAAGCTTGTAGCATCGCGCTGCAGGTACTGGGAGGCCATAGCCTGTCAGTAGATCCTGAATTCTA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 181

TCCTCACTTTGCATGAAATGCTGCCTCTTGCATTTGACTATTGTGGCCAGAAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAGgtttgtcgat ... taattgacagCTTGTACTTCTTGGAAGTCAGCTTACCAAAGGAGATAAGCTTGTAGCATCGCGCTGCAGGTACTGGGAGGCCATAGCCTGTCAGTAGATCCTGAATTCTA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTCACTTTGCATGAAATGCTGCCTCTTGCATTTGACTATTGTGGCCAGAAGCAAGCTGTCAAAGCTGTCTTTGTGGGCATGGCCTGCATGTCTGCAAGgtttgtcgattcttcaaattaagcaaagggattccttgagtaaacattttgtcttaatgaccagtatggatttgctttccctttccgcaaaagactcgta

- - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagcaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcaaaaga