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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTGGTCCATCAGGATCTTCCGGAAACGTCGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGTCAGgtaaactttctgatacttctaaccctgtcaaacatttagttttgctgtttctgttattgactgatagggatatcatgtcatttgattcgatacattttccccatttttaagaaatatgtatgtagctctgtctgaatacttctgttctatttgcctcag

Basic information

species Zea mays
transcript GRMZM2G174284_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174284_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g20310.4 (Oryza sativa), 5'ss of exon 8
CCTTGGTCCATCAGGATCTTCCGGAAACGTCGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGTCAGgtaaactttctgatacttctaaccctgtcaaacatttagttttgctgtttctgttattgactgatagggatatcatgtcatttgattcgatacattttccccatttttaagaaatatgtatgtagctctgtctgaatacttctgttctatttgcctcag
||||||||||||||||||||| || ||||| |||||||| |||||||||||||||||||||||||| |||||||| || || ||||||||||| |||||||||| | |  |     |   || | |||   | ||||       ||||||| |  |||  ||| ||    | ||   |  |   |  | || || | |    |||  |   | |                                             
CCTTGGTCCATCAGGATCTTCAGGGAACGTGGCAAACTACATGGGTCAAATGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAGgtaagcgtctt-----tcaaaatcatgtggcatatttcaa---actgtttc-gaaattttctgtta----tctctgattctggcaagc-atgcactcttgttattgctgtaaca---------------------------------------------

upper sequence: GRMZM2G174284_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA20G39050.1 (Glycine max), 5'ss of exon 11
CCTTGGTCCATCAGGATCTTCCGGAAACGTCGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGTCAGgtaaactttctgatacttctaaccctgtcaaacatttagttttgctgtttctgttattg-actgatagggatatcatgtcatttgattcgatacattttccccatttttaagaaatatgtatgtagctctgtctgaatacttctgttctatttgcctcag--
 |||||  | || || || || || || || ||||| || |||||||||||||||||||||||||| ||||| || ||||| |||   ||| ||   ||||||||||||    ||||   |     |  |    ||| |||    | | ||    |     ||  |    | | ||| ||||   |    ||  || |    |||   ||  ||| ||  |  |||||||||      | || |||  |  |    | |   
ACTTGGCTCCTCTGGTTCATCAGGCAATGTGGCAAATTACATGGGTCAAATGGCTATGGCCATGGGTAAACTAGGGACACTTGAGGGGTTCATTAAGCAGgtaaacttttct-tactcacatgtacgcgatcagtttggttcatttttctcaaagaaaatgctctttcatacagcatttcatggcagattattgatatcaaacatcactattaaa-ata-acttagctctgttc----atttttgtggtggtcatttgaaag

upper sequence: GRMZM2G174284_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA03G28400.1 (Glycine max), 5'ss of exon 5
CCTTGGTCCATCAGGATCTTCCGGAAACGTCGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGTCAGgtaaactttctgatacttctaaccctgtcaaacatttagttttgctgtttctgttattgactgatagggatatcatgtcatttgattcgatacattttccccatttttaagaaatatgtatgtagctctgtctgaatacttctgttctatttgcctcag
 |   |  ||||||| ||  | ||||| || |||||  | |||||||||||  |||||||||||||||| ||||| ||||| |||   || ||||  ||||||  ||   |      |||||  ||||       | |  ||   | ||| ||  ||  |  ||       |   | | | || | |   |  | |||                                                             
GCCCAGCTCATCAGGCTCCCCGGGAAATGTGGCAAATAACATGGGTCAAATAACTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCTCCAGgtacgctcattttccggtctaattctgtt---ttctcaacttccatctttttgaaataaagagaactcaggaagctttgaattaactgagtttaatttatttg--------------------------------------------------------

upper sequence: GRMZM2G174284_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA19G31050.2 (Glycine max), 5'ss of exon 9
CCTTGGTCCATCAGGATCTTCCGGAAACGTCGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGTCAGgtaaactttctgatacttctaaccctgtcaaacatttagttttgctgtttctgttattgactgatagggata--tcatgtcatttg--attcgatacattttccccatttttaagaaatatgtatgtagctctgtctgaatacttctgttctatttgcctcag
 |   |  ||||||| || || ||||| || ||||  || ||||| ||||||||||||||||||||||| ||||| || || ||    || ||||| ||||||  ||   |      |||||  ||||       | |  ||   | ||| ||  ||  |  ||||  || |  ||| |    ||   |||   |   ||                                                               
ACCCAGCACATCAGGCTCCTCGGGAAATGTGGCAAGTTACATGGGGCAAATGGCTATGGCCATGGGAAAGCTTGGTACTCTTGATGGGTTTCTTCGCCAGgtacgctcattttccggtctaattctgtt---ttctcaacttccatctttttgaaataaagagataaagagaactcaggaagcttagaattaagtgagttaaa------------------------------------------------------------

upper sequence: GRMZM2G174284_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA10G44270.1 (Glycine max), 5'ss of exon 9
CCTTGGTCCATCAGGATCTTCCGGAAACGTCGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGTCAGgtaaactttctgatacttctaaccctgtcaaacatttagttttgctgtttctgttattg-actgatagggatatcatgtcatttgattcgatacattttccccatttttaagaaatatgtatgtagctctgtctgaatacttctgttctatttgcctcag
 |||||  | || || || || || || || ||||| || |||||||||||||||||||||||||| ||||| || ||||| |||   ||| ||   ||||||  ||||    ||||   |    ||  |    ||| ||     | | ||    |     ||  |    | | ||| ||||   |    ||  ||      |||   ||  ||| ||  |  | ||||||| |  ||  || || || |||||      
ACTTGGCTCCTCTGGTTCATCAGGCAATGTGGCAAATTACATGGGTCAAATGGCTATGGCCATGGGTAAACTAGGGACACTTGAGGGATTCATTAAGCAGgtatgcttttct-tactcacatgtgtgcgatcagtttggtacatatttctcaaagaaaatgctctttcatacagcatttcatggcagattattgataacaaacatcactattaaa-ata-acttggctctgttt--atttttgtggtc-atttgaaag--

upper sequence: GRMZM2G174284_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA03G28320.1 (Glycine max), 5'ss of exon 11
CCTTGGTCCATCAGGATCTTCCGGAAACGTCGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGTCAGgtaaactttctgatacttctaaccctgtcaaacatttagttttgctgtttctgttattgactga--tagggatatcatg--tcatttga-ttcgatacattttccccatttttaagaaatatgtatgtagctctgtctgaatacttctgttctatttgcctcag
 |   |  ||||||| || || ||||| || ||||| || ||||| ||||||||||||||||||||||| ||||| ||||| |||   || ||||  ||||||  ||   |      |||||  ||||       | |  ||   | ||| ||  ||  |  ||  |  |||     ||  | || ||| ||  ||  || |                                                              
GCCCAGCTCATCAGGCTCCTCGGGAAATGTGGCAAATTACATGGGGCAAATGGCTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAGgtacgctcattttccggtctaattctgtt---ttctcaacttccatctttttgaaataaagagaactcaggaagctttgaattatctgagtttaatttatatg-------------------------------------------------------------

upper sequence: GRMZM2G174284_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv13s0084g00660.t01 (Vitis vinifera), 5'ss of exon 11
CCTTGGTCCATCAGGATCTTCCGGAAACGTCGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGTCAGgtaaactttctgatacttctaaccctgtcaaacatttagttttgctgtttctgttattgactgatagggatatcatgtcatttgattcgatacattttccccatttttaagaaatatgtatgtagctctgtctgaatacttctgttctatttgcctcag
 |||||  | || || || || ||||| || ||||||||||||||||||||||| |||||||||||||| || || || || |||   ||  |||||||||||  | |||| |   ||  |             |||  |||             ||  | |  |    |||| |||   | || ||  ||  ||   ||  |   ||| |||||                                            
TCTTGGCTCTTCTGGTTCATCTGGAAATGTGGCAAACTATATGGGTCAAATGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAGgtattccttctaaagttttga-------------ttttctttcctgacaataagaataaaatcttgatcatattatg--gtctgttt--atg-atcaaccagaaagttaggaaatgga-----------------------------------------

upper sequence: GRMZM2G174284_T01 (Zea mays), 5'ss of exon 9
lower sequence: PP1S126_196V6.1 (Physcomitrella patens), 5'ss of exon 7
CCTTGGTCCATCAGGATCTTCCGGAAACGTCGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGTCAGgtaaactttctgatacttctaaccctgtcaaacatttagttttgctgtttctgttattgactgatagggatat------catgtcatttgattcgat--acattttccccatttttaagaaatatgta-tgtagctctgtctgaatacttctgttctatttgcctcag-----------------------
  ||||| |    || || || | ||| || || |  |||||||| || ||||| ||||||||||| |||||||||||||| ||   |||| |  |||||||| |  ||   ||   | |  |   |       ||  || | | | ||| ||        || | || |         |||||   |||  ||      |||| |     || ||   |   ||| | |  ||  |  | | |    || | |||   |    | |                        
TGTTGGTTCTCTTGGCTCATCAGCAAATGTAGCTATTTATATGGGACAGATGGCCATGGCCATGGGGAAACTTGGCACACTTGAAGCTTTCATGTGTCAGgtatatatttatattgattttgcatagctgggtgtt--gtatggttttttatgcggcattttggttggaagtctcgaggcatgttgcttgtatcatctagcattatgtgggttgttctcagtaatgcagtacagtacgctattagccttttttttcaggtcagttaacgattgttttgatggttttgacag

upper sequence: GRMZM2G174284_T01 (Zea mays), 5'ss of exon 9
lower sequence: EFJ22847 (Selaginella moellendorffii), 5'ss of exon 5
CCTTGGTCCATCAGGATCTTCCGGAAACGTCGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGTCAGgtaaacttt--ctgatacttctaaccctgtcaaa--catttagttttgctgtttctgttattgactgatagggatatcatgtcatttgattcgatacattttccccatttttaagaaatatgtatgtagctctgtctgaatacttctgttctatttgcctcag
|   ||  |    ||  | ||    |||||||||||||| ||||| || ||||||||||||||||| || || ||||| || || || ||  |||||||||||||      ||  | |||||     | |||    ||     ||||  || |  || | |  | | ||     |      | | ||  ||| | |  ||||                                                             
CTCGGGATCGCTGGGGGCCTCGTCCAACGTCGCAAACTACATGGGACAGATGGCTATGGCCATGGGGAAGCTCGGCACTCTGGAAAACTTTGTTCGTCAGgtaaagccaaactctttcttcttcttttttcatttccagcagtttttcttggtcttgctctcca-taatgaaagttctgccttagtt--ttccacagcttttt------------------------------------------------------------

upper sequence: GRMZM2G174284_T01 (Zea mays), 5'ss of exon 9
lower sequence: EFJ28227 (Selaginella moellendorffii), 5'ss of exon 7
CCTTGGTCCATCAGGATCTTCCGGAAACGTCGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGTCAGgtaaactttctgatacttctaaccctgtcaaacatttagttttgctgtttctgttattgactgatagggatatcatgtcatttgattcgatacattttccccatttttaagaaatatgtatgtagctctgtctgaatacttctgttctatttgcctcag
   |||  | |  ||  || |    || ||||| ||||||||||| |||||||| ||||| |||||||| || || || |||||||| ||  |||| ||||| |    | ||||   |||     | |||    | | || |     || ||  ||                                                                                                       
GACTGGCTCCTTGGGCGCTGCGTCGAATGTCGCCAACTATATGGGACAAATGGCGATGGCGATGGGAAAGCTGGGAACGCTCGAGAACTTTGTTCGCCAGgtga----tgtgatgtatctg-tggtttcacgattgttgtctcaactttccttctaccag---------------------------------------------------------------------------------------------------

upper sequence: GRMZM2G174284_T01 (Zea mays), 5'ss of exon 9
lower sequence: EFJ30797 (Selaginella moellendorffii), 5'ss of exon 6
CCTTGGTCCATCAGGATCTTCCGGAAACGTCGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGTCAGgtaaa--------ctttctgatacttctaaccctgtcaaacatttagttttgctgtttctgttattgactgatagggatatcatgtcatttgattcgatacattttccccatttttaagaaatatgtatgtagctctgtctgaatacttctgttctatttgcctcag
|   ||  |    ||  | ||    |||||||||||||| ||||| || ||||||||||||||||| || || ||||| || || || ||  |||||||||||||        ||||||  | ||| |   | | || | || ||   |||  || |  || | |  | | ||     | |    | | ||  ||| | |  ||||                                                             
CTCGGGATCGCTGGGGGCCTCGTCCAACGTCGCAAACTACATGGGACAGATGGCTATGGCCATGGGGAAGCTCGGCACTCTGGAAAACTTTGTTCGTCAGgtaaagccaaactctttcttcttcttttc-tcttttccagcagtt---tttcttggtcttgctctcca-taatgaaagttttgccttagtt--ttccacagcttttt------------------------------------------------------------

upper sequence: GRMZM2G174284_T01 (Zea mays), 5'ss of exon 9
lower sequence: EFJ29724 (Selaginella moellendorffii), 5'ss of exon 7
CCTTGGTCCATCAGGATCTTCCGGAAACGTCGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGTCAGgtaaactttctgatacttctaaccctgtcaaacatttagttttgctgtttctgttattgactgatagggatatcatgtcatttgattcgatacattttccccatttttaagaaatatgtatgtagctctgtctgaatacttctgttctatttgcctcag
   |||  | |  ||  || |    || ||||| ||||||||||| |||||||| ||||| |||||||| || || || |||||||| ||  |||| ||||| |    | ||||   |||     | |||    | |  | |     || ||  ||                                                                                                       
GACTGGCTCCTTGGGCGCTGCGTCGAATGTCGCCAACTATATGGGACAAATGGCGATGGCGATGGGAAAGCTGGGAACGCTCGAGAACTTTGTTCGCCAGgtga----tgtgatgtatctg-tggtttcaccattgttatctcaactttccttctaccag---------------------------------------------------------------------------------------------------

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|78092101|gb|DV520475.1|DV520475
EST:     TGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGTCAG                         GCTGACAATCTACGACAGCAGACCTTGCATCAGATGCAACGCATCCTGACA
genomic: TGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGTCAGgtaaactttc ... tttgcctcagGCTGACAATCTACGACAGCAGACCTTGCATCAGATGCAACGCATCCTGACA
EST: gi|8665253|gb|BE186069.1|BE186069
EST:     TGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGTCAG                         GCTGACAATCTACGACAGCAGACCTTGCATCAGATGCAACGCATCCTGACA
genomic: TGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGTCAGgtaaactttc ... tttgcctcagGCTGACAATCTACGACAGCAGACCTTGCATCAGATGCAACGCATCCTGACA
EST: gi|8665558|gb|BE186374.1|BE186374
EST:     TGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGTCAG                         GCTGACAATCTACGACAGCAGACCTTGCATCAGATGCAACGCATCCTGACA
genomic: TGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGTCAGgtaaactttc ... tttgcctcagGCTGACAATCTACGACAGCAGACCTTGCATCAGATGCAACGCATCCTGACA
EST: gi|50325947|gb|CO521073.1|CO521073
EST:     TGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGTCAG                         GCTGACAATCTACGACAGCAGACCTTGCATCAGATGCAACGCATCCTGACA
genomic: TGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGTCAGgtaaactttc ... tttgcctcagGCTGACAATCTACGACAGCAGACCTTGCATCAGATGCAACGCATCCTGACA
EST: gi|32827062|gb|CD966740.1|CD966740
EST:     TGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGTCAG                         GCTGACAATCTACGACAGCAGACCTTGCATCAGATGCAACGCATCCTGACA
genomic: TGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGTCAGgtaaactttc ... tttgcctcagGCTGACAATCTACGACAGCAGACCTTGCATCAGATGCAACGCATCCTGACA

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), 49 (downstream exon)
Score: 60

CCTTGGTCCATCAGGATCTTCCGGAAACGTCGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGTCAGgtaaactttc ... tttgcctcagGCTGACAATCTACGACAGCAGACCTTGCATCAGATGCAACGCATCCTGACAATTCGACAAGCCGCTCGCGCGCTTCTTGCAATACACGACTACTTTTCAC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 228

CCTTGGTCCATCAGGATCTTCCGGAAACGTCGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGTCAGgtaaactttc ... tttgcctcagGCTGACAATCTACGACAGCAGACCTTGCATCAGATGCAACGCATCCTGACAATTCGACAAGCCGCTCGCGCGCTTCTTGCAATACACGACTACTTTTCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 260

CCTTGGTCCATCAGGATCTTCCGGAAACGTCGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGTCAGgtaaactttc ... tttgcctcagGCTGACAATCTACGACAGCAGACCTTGCATCAGATGCAACGCATCCTGACAATTCGACAAGCCGCTCGCGCGCTTCTTGCAATACACGACTACTTTTCAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 60

CCTTGGTCCATCAGGATCTTCCGGAAACGTCGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGTCAGgtaaactttc ... tttgcctcagGCTGACAATCTACGACAGCAGACCTTGCATCAGATGCAACGCATCCTGACAATTCGACAAGCCGCTCGCGCGCTTCTTGCAATACACGACTACTTTTCAC