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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAGgtaatatggttgactgtgcatgctgctaaagcttggcactcacaaatctgttgctcaatttgtttgctgctttcttgttgttcaacttaatatttgacct...

Basic information

species Zea mays
transcript GRMZM2G108829_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108829_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os02g47220.3 (Oryza sativa), 5'ss of exon 6
ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAGgta--atatg-----gttgactgtgcatgc--tgcta--aagcttggcactcacaaatctgt---tgctcaatttgtttgctgctttcttgttgttcaa-----cttaatatttgacct----------------------------------------------------
|||||||||| ||||||||||||||||| ||| |||||||||| |||||||| |||||||| || |||||  |||||      |    |||  ||||  || |   | | || | | ||||  |||| |   || |     ||| |  ||      |||| |||       |||| ||| |  | |                                                    
ATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAGgtataatatgcatatatcatatgtatatgcattgttgttatgatttgtagtcacgtatctctctgtgtttgccatgtattttgggcatctgttattctgtctctcttattatatttcttctttgtggtggtcatatttgctcattgctgttctctttatccaactgtttag

upper sequence: GRMZM2G108829_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA16G08080.1 (Glycine max), 5'ss of exon 8
ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAGgtaatatggttgactgtgcatgctgctaaagcttggcactcacaaatctgttgctcaatttgtttgctgctttcttgttgttcaacttaatat---ttgacct----
||||||||||||||||||| ||||||||||||||||| || |||| |||||| || || ||  | ||||| ||   ||  || |  | |   | |   ||   ||||     | ||      | || ||  || |  |||    | | | ||   ||||    ||||       
ATATGTGGGCAATGGGTGCTATAATGGCTGAGTTGTTCACTCTCCGTCCTCTATTCCCCGGTTCCAGgtatta-acttccctctcta-gtctccatttctctccacttctgcaact----tcccatatgactg-tatttttagttggataaaaccaataaatattgattaagga

upper sequence: GRMZM2G108829_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA01G35190.1 (Glycine max), 5'ss of exon 8
ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAGgtaatatggttg--actg--tgcatgctgctaaagcttggcactca-caaatctgttgctcaatttgtttgctgctttcttgttgttcaacttaatatttgacct
| ||||||||||||||||| |||||||||||| | ||  | || | |||||| || || ||  | ||||| |  | ||   |||   | |   |  | |||   |||   | | |  |      ||  || | | ||       |          || |||  |  |     
ACATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAGgtatttagcttctcacttactccccccctccaaatgatggtttttaactgagaaagagcaaaaatagattttcatcatggaaaacaaaaatttagcagct-----

upper sequence: GRMZM2G108829_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA09G34610.1 (Glycine max), 5'ss of exon 8
ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAGgtaatatggttgactgtgcatgctgctaaagcttggcactcacaaatct--gttgctcaatttgtttgc-tgctttcttgttgttcaacttaatatttgacct
||||||||||||||||||| |||||||||||| | ||  | || | |||||| || || ||  | ||||| |  | ||  |  | |      ||    | |   | | |    | |    ||   ||   |      |   || |  |     ||   || | ||     
ATATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAGgtatttagcttctcactccccctccctcccccatcctaatgatggtttttaactgagaaaagagcaaaaatagattttcatcagggaaaaaaaaaattag---

upper sequence: GRMZM2G108829_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA16G17580.1 (Glycine max), 5'ss of exon 8
ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAGgtaatatggttgactgtgcatgctgctaaagcttggcactcacaaatctgttgctcaatttgtttgctgctttcttgttgttcaacttaatatttgacct-----
||||||||||||||||||| ||||||||||||||||| || || | |||||| || |||||  | ||||||||   |   || | ||     ||    |       |   |  |  |||    ||      |    |||  ||   |        ||| |||||        
ATATGTGGGCAATGGGTGCTATAATGGCTGAGTTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAGgtaataactt---ctctccacttaacttc--ccatatgattgtattttagttagataaaaccaataaatcttgattaaggaattcacaaatctttgattcctggg

upper sequence: GRMZM2G108829_T01 (Zea mays), 5'ss of exon 11
lower sequence: AT5G45430.2 (Arabidopsis thaliana), 5'ss of exon 10
ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAGgtaat-----atggttgactgtgcatgctgctaaagcttggcactcacaaatctgttgctcaatttgtttgctgctttcttgttgttcaacttaatatttgacct
|||||||||| |||||||| || ||||| ||| ||||| | || |  ||||||||||||||| ||||||| |     |||||||| ||     | |   |           |    | |  | |||| ||       |    | ||   || || | | |   |        
ATATGTGGGCGATGGGTGCTATTATGGCGGAGCTGTTGTCTCTTCGCCCTCTCTTTCCTGGAGCTAGgtatttgtcaatggttgattgaattagttctaattagacaatgtttcagatttagatgctaaaccataaggtcaatgtcaccttattaatccttgcag-------

upper sequence: GRMZM2G108829_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv02s0033g01110.t01 (Vitis vinifera), 5'ss of exon 8
ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAGgtaatatggttgactgtgcatgc-tgctaaagcttggcactcacaaatctgttgctcaatttgtt-tgctgctttcttgttgttcaactta-atatttgacct
||||||||||||||||||| || |||||||| ||||| || |||| |||||||||||| ||| | |||||| ||| ||   |   | | | | |||    ||||   |  |   |   ||   | | || |  ||    || |  || ||| |  ||| ||| ||||   
ATATGTGGGCAATGGGTGCTATCATGGCTGAATTGTTTACTCTCCGTCCTCTCTTTCCAGGATCGAGgtaa-atgtttttttcccctttccttctaggtattggtttttcccttttgcttttactagttatggtgtatgttgcacgtggttaattttacataattgaa--

upper sequence: GRMZM2G108829_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv09s0070g00320.t01 (Vitis vinifera), 5'ss of exon 3
--ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAGgtaa-----tatggttgactgtgcatgc--tgctaaagcttggcactc--ac---aaatctgttgctcaatttgtttgctgctttcttgttgttcaacttaatatttgacct--
  ||||||||||||||||| | || |||||||| ||||| || |||| |||||||||||| ||| | ||  ||     |    || ||     ||||  || || |  | |||| ||  ||   ||||   | |  | |     ||    ||| ||  |  |   |  ||  | ||  |    
CGATATGTGGGCAATGGGTACTATCATGGCTGAATTGTTTACTCTCCTTCCTCTCTTTCCAGGATCGAGTGAAGCAGATGAAATTTACAAAATATGCAATgttatatatgggcagtccaacttaaaattcatgggccgagggacttaa-acttgctaatgctatcaactaccaattcccacag

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|60349468|gb|DN216441.1|DN216441
EST:     GCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAG                         TGAAGCTGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGA
genomic: GCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAGgtaatatggt ... tactatttagTGAAGCTGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGA
EST: gi|211496286|gb|FL041698.1|FL041698
EST:     GCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACCAG                         TGAAGCTGATGAGATTCACAAGATAT
genomic: GCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAGgtaatatggt ... tactatttagTGAAGCTGATGAGATTCACAAGATAT
EST: gi|32871065|gb|CF010747.1|CF010747
EST:     GCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAG                         TGAAGCTGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGA
genomic: GCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAGgtaatatggt ... tactatttagTGAAGCTGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGA
EST: gi|32932540|gb|CF037352.1|CF037352
EST:     GCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAG                         TGAAGCTGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGA
genomic: GCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAGgtaatatggt ... tactatttagTGAAGCTGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGA
EST: gi|71304777|gb|DR788504.1|DR788504
EST:     GCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAG                         TGAAGCTGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGA
genomic: GCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAGgtaatatggt ... tactatttagTGAAGCTGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGA
EST: gi|31350422|gb|CD434779.1|CD434779
EST:     GCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACCAG                         TGAAGCTGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGA
genomic: GCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAGgtaatatggt ... tactatttagTGAAGCTGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGA
EST: gi|32870331|gb|CF010013.1|CF010013
EST:     GCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAG                         TGAAGCTGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGA
genomic: GCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAGgtaatatggt ... tactatttagTGAAGCTGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGA
EST: gi|32869779|gb|CF009461.1|CF009461
EST:     GCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAG                         TGAAGCTGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGA
genomic: GCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAGgtaatatggt ... tactatttagTGAAGCTGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGA
EST: gi|67011156|gb|CO439905.1|CO439905
EST:     GCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACCAG                         TGAAGCTGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGA
genomic: GCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAGgtaatatggt ... tactatttagTGAAGCTGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGA
EST: gi|211496285|gb|FL041697.1|FL041697
EST:     GCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACCAG                         TGAAGCTGATGAGATTCACAAGATATGCAATGTC
genomic: GCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAGgtaatatggt ... tactatttagTGAAGCTGATGAGATTCACAAGATATGCAATGTC
EST: gi|5932684|gb|AW057045.1|AW057045
EST:     GCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACCAG                         TGAAGCTGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGA
genomic: GCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAGgtaatatggt ... tactatttagTGAAGCTGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGA

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: 340

ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAGgtaatatggt ... tactatttagTGAAGCTGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGAGCAATCTTGGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 208

ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAGgtaatatggt ... tactatttagTGAAGCTGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGAGCAATCTTGGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 173

ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAGgtaatatggt ... tactatttagTGAAGCTGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGAGCAATCTTGGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 198

ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAGgtaatatggt ... tactatttagTGAAGCTGATGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGAGCAATCTTGGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAG