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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAGgtaatatggttgactgtttgctggtaaagcttgtcactcacaaatcttttgctgctttcttgttggtcaccttaaagtttgacttatctcaaatttaatg...

Basic information

species Zea mays
transcript GRMZM2G178822_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178822_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os02g47220.3 (Oryza sativa), 5'ss of exon 6
ATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAGgta--atatg-----gttgactgt-------ttgctggtaaagcttgtcactcacaaatcttttgctgctttct-----tgttggtcaccttaaagtttgacttatct--caaatttaatg---------------------------------------------------
|||||||||| ||||||||||||||||| |||||||||||||| |||||||| |||||||| || |||||  |||||      |    |||       ||| || ||    |||| | ||||  |||| |   || || |      | |||| || ||   | | || ||    |   | ||||  |                                                    
ATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAGgtataatatgcatatatcatatgtatatgcattgttgttatgatttgt-agtcacgtatctctctgtgtttgccatgtattttgggcatctgttattctgtctctcttattatatttcttctttgtggtggtcatatttgctcattgctgttctctttatccaactgtttag

upper sequence: GRMZM2G178822_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA16G08080.1 (Glycine max), 5'ss of exon 8
ATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAGgtaatatggttgactgtttgctggtaaagcttgtcactcacaaatcttt---tgctgctttcttgttggtcaccttaaagtttgacttatctcaaatttaatg-
||||||||||||||||||| |||||||||||| |||| || |||| |||||| || || ||  ||||||| ||   |       | |     |   ||   ||||     | |||    |    || | || || ||    | |||     |   || |  |  |||| | 
ATATGTGGGCAATGGGTGCTATAATGGCTGAGTTGTTCACTCTCCGTCCTCTATTCCCCGGTTCCAGgtattaacttccctctctagtctccatttctctccacttctgcaacttcccatatgactgtatttttagttggataaaa--ccaataaatattga--ttaagga

upper sequence: GRMZM2G178822_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA01G35190.1 (Glycine max), 5'ss of exon 8
ATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAGgtaatatggttgactgtttgctggtaaagcttgtcactcacaaatcttttgctgctttcttgttggt-caccttaaagtttgacttatctcaaatttaatg---
| ||||||||||||||||| |||||||||||||| ||  | || | |||||| || || ||  ||||||| | | | |      || ||       |    ||        | |||  |||       |       |  ||    |       | |  |||||||      
ACATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAGgtatt-tagcttctcacttactcccc---ccctccaaatgatggtttttaactgagaaagagcaaaaatagattttcatcatggaaaacaaaaatttagcagct

upper sequence: GRMZM2G178822_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA09G34610.1 (Glycine max), 5'ss of exon 8
ATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAGgtaatatggttgactgtttgctggtaaagcttgtcactcacaaatcttt-tgctgctttcttgttggtcacct--taaagtttgacttatctcaaatttaatg--------
||||||||||||||||||| |||||||||||||| ||  | || | |||||| || || ||  ||||||| |     |  ||  |  ||       |   || ||| |  ||| |  || || ||| |   ||   |      |||  | || ||   |||     ||          
ATATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAGgtatt-----tagcttctcactc------cccctccctcccccatcctaatgatggtttttaactgagaaaagagcaaaaatagattttcatcagggaaaaaaaaaattag

upper sequence: GRMZM2G178822_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA16G17580.1 (Glycine max), 5'ss of exon 8
ATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAGgtaatatggttgactgtttgctggtaaagcttgtcactcacaaatcttttgctgctttcttgttggtca-ccttaaagtttgacttatctcaaatttaatg------
||||||||||||||||||| |||||||||||| |||| || || | |||||| || |||||  ||||||||||      |||  |  |   | || |||  ||        | ||||  |    |        | |  ||| |     || ||  |  |  ||| ||       
ATATGTGGGCAATGGGTGCTATAATGGCTGAGTTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAGgtaata------acttctctccacttaa-cttcccatatgattgtattttagttagataaaaccaataaatcttgattaaggaattcacaaatctttgattcctggg

upper sequence: GRMZM2G178822_T01 (Zea mays), 5'ss of exon 12
lower sequence: AT5G45430.2 (Arabidopsis thaliana), 5'ss of exon 10
ATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAGgtaatatggttgactgtttgctggtaaagcttgtcactcacaaatcttttgctgctttcttgttggtcaccttaaagtttgacttatctcaa-atttaatg---
|||||||||| |||||||| || ||||| ||||||||| | || |  ||||||||||||||| | ||||| |   ||  |  |||   ||    || |    | | | | |   |||     ||   || |    ||| ||| ||     | | || |  | |   ||   
ATATGTGGGCGATGGGTGCTATTATGGCGGAGCTGTTGTCTCTTCGCCCTCTCTTTCCTGGAGCTAGgtatt--tgtcaatggttgattgaattagttc--taattagacaatgtttcagatttagatgctaa--accataaggtcaatgtcaccttattaatccttgcag

upper sequence: GRMZM2G178822_T01 (Zea mays), 5'ss of exon 12
lower sequence: Vv02s0033g01110.t01 (Vitis vinifera), 5'ss of exon 8
ATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAGgtaata--tggttgactgtttgctggtaaagcttgtcactcacaaatcttttgctgctttcttgtt--ggtcaccttaaagtttgacttatctca---aatttaatg
||||||||||||||||||| || ||||||||  |||| || |||| |||||||||||| ||| | ||||||    |  ||  |  ||| ||  ||    |||    |  |    ||||||||  || || |||  |||     |      ||  | || | |   |||| ||  
ATATGTGGGCAATGGGTGCTATCATGGCTGAATTGTTTACTCTCCGTCCTCTCTTTCCAGGATCGAGgtaaatgtttttttcccctttccttctaggtattggtttttcc----cttttgct-tttactagttatggtgtatgttgcacgtggttaattttacataattgaa--

upper sequence: GRMZM2G178822_T01 (Zea mays), 5'ss of exon 12
lower sequence: Vv09s0070g00320.t01 (Vitis vinifera), 5'ss of exon 3
--ATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAGgtaatatggttgactgtttgctggtaaagcttgtcactcaca---aatct--tttgctgctttcttgttggtcaccttaaagtt-tgacttatctcaaat-ttaatg-------
  ||||||||||||||||| | || ||||||||  |||| || |||| |||||||||||| |||  |  || |    | |||   ||      ||     ||| |   |     | ||    ||     |     |  |     |||||| ||   | |  | |||| |   |||        
CGATATGTGGGCAATGGGTACTATCATGGCTGAATTGTTTACTCTCCTTCCTCTCTTTCCAGGA-TCGAGTGAAGCAGATGAAATTTACAAAATATGCAATgttatatatgggcagtccaacttaaaattcatgggccgagggacttaaacttgctaatgctatcaactaccaattcccacag

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|60345317|gb|DN212290.1|DN212290
EST:     GCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAG                         TGAAGCAGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGA
genomic: GCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAGgtaatatggt ... cactatttagTGAACCAGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGA
EST: gi|31361016|gb|CD445373.1|CD445373
EST:     GCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAG                         TGAAGCAGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGA
genomic: GCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAGgtaatatggt ... cactatttagTGAACCAGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGA
EST: gi|67015254|gb|CO444003.1|CO444003
EST:     GCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAG                         TGAAGCAGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGA
genomic: GCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAGgtaatatggt ... cactatttagTGAACCAGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGA
EST: gi|60352824|gb|DN219797.1|DN219797
EST:     GCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAG                         TGAACCAGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGA
genomic: GCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAGgtaatatggt ... cactatttagTGAACCAGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGA
EST: gi|211493408|gb|FL041695.1|FL041695
EST:     GCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAG                         TGAACCAGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGA
genomic: GCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAGgtaatatggt ... cactatttagTGAACCAGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGA

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: 186

ATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAGgtaatatggt ... cactatttagTGAACCAGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGAGCAATCTTGGCCTCAAGGATTGTCTCTTGCAGAAGCAATGAAGTATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 167

ATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAGgtaatatggt ... cactatttagTGAACCAGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGAGCAATCTTGGCCTCAAGGATTGTCTCTTGCAGAAGCAATGAAGTATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 122

ATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAGgtaatatggt ... cactatttagTGAACCAGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGAGCAATCTTGGCCTCAAGGATTGTCTCTTGCAGAAGCAATGAAGTATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 164

ATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAGgtaatatggt ... cactatttagTGAACCAGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGAGCAATCTTGGCCTCAAGGATTGTCTCTTGCAGAAGCAATGAAGTATCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAGgtaatatggttgactgtttgctggtaaagcttgtcactcacaaatcttttgctgctttcttgttggtcaccttaaagtttgacttatctcaaatttaatg

- - - - - - - - - - - - - - -  GCTGTT