Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATGATATTCACATCGACATCATGGATTACATCTCACCTGCTACGTGTGCAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaatatgcttctctgtacattgcagttgtgaagtatccttaaactgtagtctcctttatgatcagtgttattctagcatgtaaggtttaaataacgggt...

Basic information

species Zea mays
transcript GRMZM2G378906_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G378906_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g17430.1 (Oryza sativa), 5'ss of exon 2
AAATGATATTCACATCGACATCATGGATTACATCTCACCTGCTACGTGTGCAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaatatgcttctctgtacattgcagttgtg---aagtatccttaaactgtagtctcctttatgatcagtgttattctagcatgtaaggtttaaataacgggt--
||||||||||||||| |||||||||||||| |||||||| || || || || |||||||||||||| |||||||||||||||||||| |||||||| ||||||  || ||| |   | | |||   || ||    | |    |||   ||| || |  | |  | ||   ||| || |||  | ||   |||    | | | |  
AAATGATATTCACATTGACATCATGGATTATATCTCACCAGCAACTTGCGCTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgta-catacttattcctgctttgatattttgttagaatgagtttactttgtcgtatgttatccgctccaagtt-ttgtagtctata---tttgttcatctgttta

upper sequence: GRMZM2G378906_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT4G31480.2 (Arabidopsis thaliana), 5'ss of exon 4
AAATGATATTCACATCGACATCATGGATTACATCTCACCTGCTACGTGTGCAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaatatgcttctctgtacattgcagttgtgaagtatccttaaactgtagtctcctttatgatcagtgttattctagcatgtaaggtttaaataacgggt
 ||||| || ||||| || |||||||| || ||||| ||||||  |||| |||| ||| ||||| | |  ||||||||||| || ||||||||||| |||||||| |  |      |   ||  ||||||    | |  |   |   | ||     || || |       ||||  |  ||||   ||||  | |     
TAATGACATACACATTGATATCATGGACTATATCTCCCCTGCTGTGTGTTCAGAGGTTGCTTTCAGAACTATGTGGGCAGAGTTCGAATGGGAAAACAAGgtaatttattgaaacctt--ttatagttgtaccttcttttcgtatgtttgttggagtt-tggtataaccaattcctgt-tgtattctttatgtcag----

upper sequence: GRMZM2G378906_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT4G31490.1 (Arabidopsis thaliana), 5'ss of exon 3
AAATGATATTCACATCGACATCATGGATTACATCTCACCTGCTACGTGTGCAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaatatgcttctctgtacattgcagttgtgaagtatccttaaactgtagtctcctttatgatcagtgttattctagcatgtaaggtt-taaataacgggt
 || || || ||||| || |||||||| || ||||| ||||||  |||  |||| ||| ||||| | |  ||||||||||| |||||||||||||| ||||||||    ||  |   || ||  |   ||      | |||    |||    |  ||     |  || | |   | || |||    || |  ||  | |  
TAACGACATACACATTGATATCATGGACTATATCTCCCCTGCTGTGTGCTCAGAGGTTGCTTTCAGAACTATGTGGGCAGAGTTTGAATGGGAAAACAAGgtaat----ttaccgaaaccttttaaaagtattaccttctttgtttgtttgtttgttagattttggtataaccattgcctgttgtattattcatgtcag--

upper sequence: GRMZM2G378906_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv04s0008g02320.t01 (Vitis vinifera), 5'ss of exon 2
AAATGATATTCACATCGACATCATGGATTACATCTCACCTGCTACGTGTGCAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaatatgcttctctgtacattgcagttgtgaagtatccttaaactgtagtctcctttatgatcagtgtt---attctagcatgtaaggtttaaataacgggt----
 ||||| |||||||| ||||||||||| ||||| || ||||||   ||| | |||||  | ||| | |  ||||||||||| |||||||||||||| |||||||      |  |||| |       ||      | | |  |||  |||   ||   | | ||  ||  |   ||  |    | ||    ||| |||     |    
CAATGACATTCACATTGACATCATGGACTACATATCTCCTGCTGTTTGTACTGATGTGGCCTTCAGAACTATGTGGGCAGAGTTTGAATGGGAAAACAAGgtaaatcatctagctgtcc-------ttccatgattttcccaaatggtaacatctgatctaatgggtacttgaatctttttgtttataccttacatagttatttttg

upper sequence: GRMZM2G378906_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S168_28V6.1 (Physcomitrella patens), 5'ss of exon 3
AAATGATATTCACATCGACATCATGGATTACATCTCACCTGCTACGTGTGCAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgta---atatgcttctctgtac-attgcagttgtgaagtatccttaaactgtagtctcctttatgatcagtgttattctagcatgtaaggtttaaataacgggt
 ||||| |||||||| ||||||||||| |||||||| |||||| | ||||| |||||| | || || ||||||||||| || ||||| |||||||| ||||||   ||    |  | |||     | ||  | | |      |||      || |   |    | |||  ||  ||     | |||     |  || ||     
GAATGACATTCACATTGACATCATGGACTACATCTCTCCTGCTTCATGTGCTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatctatcgattcttttgttttgcttcaagtttcattctctcttgtttcatacttatccccgt-atctttgacatcgc--cttgttgaaatcgaacaattat-

upper sequence: GRMZM2G378906_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S42_100V6.1 (Physcomitrella patens), 5'ss of exon 3
AAATGATATTCACATCGACATCATGGATTACATCTCACCTGCTACGTGTGCAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaatatgcttctctgtacattgcagttgtgaagtatccttaaactgtagtctcctttatgatcagtgttattctagcatgtaaggtttaaataacgggt----
 ||||| || || |||||||||||||||||||||||||||||  | |||||||||||    ||| | ||||||||||| ||||||||||||||||| |||||||  |     ||| |   || || ||      | |  |||||   |  |    |||  | |   | | | | |    |  |     |  | ||    |    
GAATGACATACATATCGACATCATGGATTACATCTCACCTGCATCTTGTGCAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaacctcacaatctcttttttacatttcccct-tttttttaaa---tgattcgatttcgggtttttataaattttatcttcagaacctgtagaagaactatgt

upper sequence: GRMZM2G378906_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S309_15V6.2 (Physcomitrella patens), 5'ss of exon 3
AAATGATATTCACATCGACATCATGGATTACATCTCACCTGCTACGTGTGCAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaatatgcttctctgtacattgcagttgtgaagtatccttaaactgtagtctcctttatga--tcagtgtt---attctagcatgtaaggtttaaataacgggt
 |||||||| ||||| ||||||||||| |||||| | |||||  ||||| | ||| |  ||||||| |||||||||||||| ||||||||||| || ||||||  | |     || |  |||   |  || || |    |      |||  || | ||||    ||||  ||   ||     |||  | | | |  | ||     
GAATGATATCCACATTGACATCATGGACTACATCGCTCCTGCCTCGTGTACTGATATAGCTTTCCGCAACATGTGGGCAGAGTTTGAATGGGAGAACAAGgtaccaagtgctcctttttattttggccgtaaattcgtttcgtttcgtatcctacgttattgattcagcattttgatctcgacattgacgctatcgaaaa-----

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|32800512|gb|CD952748.1|CD952748
EST:     CAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAG                         GTGGCTGTGAATACTGTGTTTCAGGATGAGAAGGAATTC
genomic: CAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaatatgct ... tgtttatcagGTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC
EST: gi|32934625|gb|CF039437.1|CF039437
EST:     CAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAG                         GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC
genomic: CAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaatatgct ... tgtttatcagGTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC
EST: gi|32799977|gb|CD952213.1|CD952213
EST:     CAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAG                         GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC
genomic: CAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaatatgct ... tgtttatcagGTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC
EST: gi|13316152|gb|BG410599.1|BG410599
EST:     CAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAG                         GTGGCTGTGAATACTGTGTATTCAGGATGAGAAGGAATTC
genomic: CAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaatatgct ... tgtttatcagGTGGCTGTGAATACTGTG-ATTCAGGATGAGAAGGAATTC
EST: gi|6194839|gb|AW146943.1|AW146943
EST:     CAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAG                         GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC
genomic: CAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaatatgct ... tgtttatcagGTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC
EST: gi|6056701|gb|AW091106.1|AW091106
EST:     CCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAG                         GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC
genomic: CCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaatatgct ... tgtttatcagGTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC
EST: gi|149101059|gb|EE187158.2|EE187158
EST:     CAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAG                         GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC
genomic: CAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaatatgct ... tgtttatcagGTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC
EST: gi|32788938|gb|CD941174.1|CD941174
EST:     CAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAG                         GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC
genomic: CAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaatatgct ... tgtttatcagGTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC
EST: gi|60336783|gb|DN203756.1|DN203756
EST:     AGAATTTGAATGGGAAAATAAG                         GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC
genomic: AGAATTTGAATGGGAAAATAAGgtaatatgct ... tgtttatcagGTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC
EST: gi|32913449|gb|CF018261.1|CF018261
EST:     CAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAG                         GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC
genomic: CAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaatatgct ... tgtttatcagGTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC
EST: gi|148991091|gb|EE032539.2|EE032539
EST:     CAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAG                         GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC
genomic: CAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaatatgct ... tgtttatcagGTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC
EST: gi|78022282|gb|DV490669.1|DV490669
EST:     CAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAG                         GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC
genomic: CAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaatatgct ... tgtttatcagGTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC
EST: gi|211326076|gb|FL182495.1|FL182495
EST:     CAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAG                         GKGGCTGKGAATACTGKGATTCAGGATGAGAAGGAATTC
genomic: CAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaatatgct ... tgtttatcagGTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC
EST: gi|91054946|gb|EB165364.1|EB165364
EST:     CAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAG                         GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC
genomic: CAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaatatgct ... tgtttatcagGTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC

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), 39 (downstream exon)
Score: 361

AAATGATATTCACATCGACATCATGGATTACATCTCACCTGCTACGTGTGCAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaatatgct ... tgtttatcagGTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 345

AAATGATATTCACATCGACATCATGGATTACATCTCACCTGCTACGTGTGCAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaatatgct ... tgtttatcagGTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 464

AAATGATATTCACATCGACATCATGGATTACATCTCACCTGCTACGTGTGCAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaatatgct ... tgtttatcagGTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC


Block sizes: 48 (upstream exon), 39 (downstream exon)
Score: 405

AAATGATATTCACATCGACATCATGGATTACATCTCACCTGCTACGTGTGCAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaatatgct ... tgtttatcagGTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAATGATATTCACATCGACATCATGGATTACATCTCACCTGCTACGTGTGCAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaatatgcttctctgtacattgcagttgtgaagtatccttaaactgtagtctcctttatgatcagtgttattctagcatgtaaggtttaaataacgggt

- - - - - - - - - - - - - - - - - - - - - - - - - CAGATG