Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAGgtaagagtttgttacctatttaattgcatcatttgtcgaagtcaaaccttctacacacctaaggccttgttcggttattcccaatacacatggattggat...

Basic information

species Zea mays
transcript GRMZM2G051004_T01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051004_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os02g07490.1 (Oryza sativa), 5'ss of exon 13
GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAGgtaagagtttgt-tacctatttaattgcatcatttgtcgaagt------caaaccttctacacacctaa-ggccttgttcggttattcccaatacacatggattggat
|||||||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||| |||||||||||||||||||||||||||| || || | | |  | ||| |   || | | |  ||    |      |||   |||||    ||||| |    |||||  || ||      |              
GTCAAGCATCTTTGATGCCAAGGCTGGTATTGGACTGAGCTCTTCCTTCATGAAGCTTGTGTCATGGTATGACAACGAGTGGGGCTACAGgtgagtgtctatatttccattaaggggcttaactcttcatctttttttccaattgttctattgtcctaatgattctgttccattctttgtttcag-------------

upper sequence: GRMZM2G051004_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA03G22790.1 (Glycine max), 5'ss of exon 13
GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAGgtaagagtttgttacctatttaattgcatcatttgtcgaagtcaaaccttctacacacctaaggccttgttcggttattcccaatacacatggattggat
|||||| |||||||||||||||||||| || | ||| ||  |||| ||  | ||||| || || ||||||||||| |||||||| |||||||| | ||   ||      ||   |   |    ||  ||| |      ||||   ||       | ||  | | |  ||   |||     |   ||| | 
GTCAAGTATCTTTGATGCCAAGGCTGGCATTGCACTAAGTGCTTCCTTTGTTAAGCTGGTTTCGTGGTATGACAATGAGTGGGGTTACAGgtatgtgtgcatt------ttgtgtatgtagagtgcagaaat------ttctgttcatgcggacctttaattgatatttttgaatg-gtttttgttgcag

upper sequence: GRMZM2G051004_T01 (Zea mays), 5'ss of exon 13
lower sequence: AT1G16300.1 (Arabidopsis thaliana), 5'ss of exon 13
GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAGgtaagagtttgttacctatttaattgcatcatttgtcgaagtcaaaccttctacacacctaaggccttgttcggttattcccaatacacatggattggat
|||||| ||||||||||| || ||||| || ||| | |||   || |||||||| ||||| || |||||||||||||| ||||| ||||||||| |||| ||   || | | ||| | | |    ||  | | |    ||    | ||| || | ||          |      |  | |||     |  
GTCAAGTATCTTTGATGCTAATGCTGGGATTGGATTAAGCAAGTCCTTCATGAAACTTGTCTCCTGGTATGACAACGAATGGGGTTACAGgtaacagttagt---ctctctcatttctttacc-atcacatttaccatttgacaatacccaaagactaaaatatgcgtgggtcttgta-atgttacag--

upper sequence: GRMZM2G051004_T01 (Zea mays), 5'ss of exon 13
lower sequence: Vv19s0085g00600.t01 (Vitis vinifera), 5'ss of exon 13
GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAGgtaagagtttgttacctatttaattgcatcatttgtcgaagtcaaaccttctacacacctaaggc--cttgttcggttattcccaatacacatggattggat----------
|||||| || |||||||| ||||| || || || |||||  |||| ||||||||||| ||  | |||||||||||||| ||||| ||||||||  |    | |  || | |  ||    ||      | |  ||| |||   |    ||    |   ||  |  | | || |  |||    ||   | || |          
GTCAAGTATATTTGATGCAAAGGCCGGGATAGGGCTGAGTGCTTCCTTCATGAAGCTCGTTGCATGGTATGACAACGAATGGGGATACAGgtacaacacggctctctctctctttctcacacacacagcatgcaagcctcagagcttccaggtggtgctaatgtgatgatacataatggttattt-tcggtttttcttacag

upper sequence: GRMZM2G051004_T01 (Zea mays), 5'ss of exon 13
lower sequence: PP1S309_73V6.2 (Physcomitrella patens), 5'ss of exon 11
GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAGgtaag---agtttgttacctatttaattgcatcatttgtcgaagtcaaaccttctacacacctaaggccttgttcggttattcccaatacac--atggattggat
||| |||||||| ||||||||||| || || |   ||||       ||  | ||||| ||||| ||||||||||||||||||||||||||||||     || |  |  ||  |    || ||| | |      |       |     ||   ||||   | |||  ||  |  |   |      |||  ||| | 
GTCGAGCATCTTCGATGCCAAGGCAGGAATTGCCTTGAGTGACAAGTTTGTCAAGCTGGTGTCGTGGTATGACAACGAGTGGGGCTACAGgtaattttggtgtaatctctggtgttgtggatcgtgtacttttgggcggtgtcggttacgggtaagatgtggttttgtcttgactgttgtgtgaatgttttgcag

upper sequence: GRMZM2G051004_T01 (Zea mays), 5'ss of exon 13
lower sequence: PP1S309_84V6.1 (Physcomitrella patens), 5'ss of exon 11
GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAGgtaa---gagtttgttacctatttaattgcatcatttgtcgaagtcaa-accttctacacacctaaggccttgttcggttattcccaatacac-atggattggat---------
||| |||||||| ||||| ||||| || || |   |||||      ||| ||||| | ||||| ||||||||||||||||||||||||||||||   | |||   |   |   |  ||  ||  |   ||   ||    | | |      ||         | |  |||  || |      || || |  || ||         
GTCGAGCATCTTCGATGCTAAGGCAGGAATTGCCTTGAGCGACAAGTTCGTGAAGTTGGTGTCGTGGTATGACAACGAGTGGGGCTACAGgtaatttgggttatgtgtttggctttttcgattgtgcatcttggtgggcatcgtggtggaactcggtaggatatatggtagtttcgttctgactatcgtgtgaatgtcttgcag

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|211015683|gb|FL453044.1|FL453044
EST:     TCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG                         CAACCGGGTTCTGGATCTGATCGCCCACATGGCTCTCGTCAGTGCCGCCGC
genomic: TCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAGgtaagagttt ... gctttgacagCAACCGGGTTCTGGATCTGATCGCCCACATGGCTCTCGTCAGTGCCGCCGC
EST: gi|211407297|gb|FL458695.1|FL458695
EST:     TCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG                         CAACCGGGTTCTGGATCTGATCGCCCACATGGCTCTCGTCAGTGCCGCCGC
genomic: TCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAGgtaagagttt ... gctttgacagCAACCGGGTTCTGGATCTGATCGCCCACATGGCTCTCGTCAGTGCCGCCGC
EST: gi|148928089|gb|EC872534.2|EC872534
EST:     TCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG                         CAACCGGGTTCTGGATCTGATCGCCCACATGGCTCTCGTCAGTGCCGCCGC
genomic: TCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAGgtaagagttt ... gctttgacagCAACCGGGTTCTGGATCTGATCGCCCACATGGCTCTCGTCAGTGCCGCCGC
EST: gi|37397668|gb|CF636141.1|CF636141
EST:     TCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG                         CAACCGGGTTCTGGATCTGATCGCCCACATGGCTCTCGTCAGTGCCGCCGC
genomic: TCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAGgtaagagttt ... gctttgacagCAACCGGGTTCTGGATCTGATCGCCCACATGGCTCTCGTCAGTGCCGCCGC
EST: gi|166452788|gb|EG181214.1|EG181214
EST:     TCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG                         CAACCGGGTTCTGGATCTGAT-GCCCACATGGCTC
genomic: TCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAGgtaagagttt ... gctttgacagCAACCGGGTTCTGGATCTGATCGCCCACATGGCTC
EST: gi|67025324|gb|CO454073.1|CO454073
EST:     TCTTCTTTCATGAAGCTCGTGTCTTGGTATGACAACGAGTGGGGCTACAG                         CAACCGGGTTCTGGATCTGATCGCCCACATGGCCCTCGTCAGCGCCGCCGC
genomic: TCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAGgtaagagttt ... gctttgacagCAACCGGGTTCTGGATCTGATCGCCCACATGGCTCTCGTCAGTGCCGCCGC
EST: gi|40337147|gb|CK371217.1|CK371217
EST:     TCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG                         CAACCGGGTTCTGGATCTGATCGCCCACATGGCTCTCGTCAGTGCCGCCGC
genomic: TCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAGgtaagagttt ... gctttgacagCAACCGGGTTCTGGATCTGATCGCCCACATGGCTCTCGTCAGTGCCGCCGC
EST: gi|84977532|gb|DW475954.1|DW475954
EST:     TCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG                         CAACCGGGTTCTGGATCTGATCGCCCACATGGCTCTCGTCAGTGCCGCCGC
genomic: TCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAGgtaagagttt ... gctttgacagCAACCGGGTTCTGGATCTGATCGCCCACATGGCTCTCGTCAGTGCCGCCGC
EST: gi|30306629|gb|CD001302.1|CD001302
EST:     TCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG                         CAACCGGGTTCTGGATCTGATCGCCCACATGGCTCTCGTCAGTGCCGCCGC
genomic: TCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAGgtaagagttt ... gctttgacagCAACCGGGTTCTGGATCTGATCGCCCACATGGCTCTCGTCAGTGCCGCCGC
EST: gi|31997624|gb|CD661686.1|CD661686
EST:     TCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG                         CAACCGGGTTCTGGATCTGATCGCCCACATGGCTCTCGTCAGTGCCGCCGC
genomic: TCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAGgtaagagttt ... gctttgacagCAACCGGGTTCTGGATCTGATCGCCCACATGGCTCTCGTCAGTGCCGCCGC
EST: gi|148944446|gb|EC889561.2|EC889561
EST:     TCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG                         CAACCGGGTTCTGGATCTGATCGCCCACATGGCTCTCGTCAGTGCCGCCGC
genomic: TCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAGgtaagagttt ... gctttgacagCAACCGGGTTCTGGATCTGATCGCCCACATGGCTCTCGTCAGTGCCGCCGC
EST: gi|6021812|gb|AW066740.1|AW066740
EST:     TCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG                         CAACCGGGTTCTGGATCTGATCGCCCACATGGCTCTCGTCAGTGCCGCCGC
genomic: TCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAGgtaagagttt ... gctttgacagCAACCGGGTTCTGGATCTGATCGCCCACATGGCTCTCGTCAGTGCCGCCGC

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: 48 (upstream exon), 48 (downstream exon)
Score: 91

GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAGgtaagagttt ... gctttgacagCAACCGGGTTCTGGATCTGATCGCCCACATGGCTCTCGTCAGTGCCGCCGCCAAGCTCTGATGTCCGTACTCGTTTCTCCAGTAGTAGCTTAGAAAAAAA


Block sizes: 46 (upstream exon), 38 (downstream exon)
Score: 37

GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAGgtaagagttt ... gctttgacagCAACCGGGTTCTGGATCTGATCGCCCACATGGCTCTCGTCAGTGCCGCCGCCAAGCTCTGATGTCCGTACTCGTTTCTCCAGTAGTAGCTTAGAAAAAAA


Block sizes: 46 (upstream exon), 43 (downstream exon)
Score: 20

GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAGgtaagagttt ... gctttgacagCAACCGGGTTCTGGATCTGATCGCCCACATGGCTCTCGTCAGTGCCGCCGCCAAGCTCTGATGTCCGTACTCGTTTCTCCAGTAGTAGCTTAGAAAAAAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 114

GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAGgtaagagttt ... gctttgacagCAACCGGGTTCTGGATCTGATCGCCCACATGGCTCTCGTCAGTGCCGCCGCCAAGCTCTGATGTCCGTACTCGTTTCTCCAGTAGTAGCTTAGAAAAAAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAGgtaagagtttgttacctatttaattgcatcatttgtcgaagtcaaaccttctacacacctaaggccttgttcggttattcccaatacacatggattggat

- - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC