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'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcataatcgatttcttttcttctccacattttcgagaaagtatttcttttttgaatttttctaatagtagttgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAGTTAGCTATGTCAAGTGGAAAG

Basic information

species Zea mays
transcript GRMZM2G141587_T05
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 9
gcataatcgatttcttttcttctccacattttcgagaaagtattt--cttttttgaatttttctaatagtagttgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAGTTAGCTATGTCAAGTGGAAAG
||| |   ||||  |||  || || |||||| | |||| || |||  |||| || || | || | | | || ||| | | ||||| ||||| |  ||||  ||||||||||||||||||| |   ||||| ||||||||||||||||  ||||||
gcacagatgattaatttatttatc-acatttccaagaatgtttttgtctttgttcaaatgttgtta-actatttgcttttcagGCAATTGCCATTGAGGCACAAAGTGAGTCCAAGTGGAGGCAGTTAGGAGAGTTAGCTATGTCAACCGGAAAG

upper sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 18
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 18
-----------------------------------------------------------------gcataatcgatttcttttcttctccacattttcgagaaagtatttcttttt--tgaatttttctaa----tagta-gttgttctg------cagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAGTTAGCTATGTCAAGTGGAAAG
                                                                 | | | |  |   | | | |  |      |   ||   | || | || | |    | ||| ||| |    ||| | | | ||||       ||||  |||||||| || |||||||||||||| || ||||||  ||| || || ||||||||||| | |||||||
gtaaattatgttgattttatgtcagtatagggatataaactagttctttgacagtttgttgacttgaacatttaagcacatctttattttcttctgaggaatgattagtcctctgtgacaattttatctgaaatatagcatgatcttctttgctttcagGACATTGCTACAGAAGTGCAAAGTGAGTCAAAATGGAAGCAATTGGGAGAATTAGCTATGTCCACTGGAAAG
















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|22489660|gb|BU049570.1|BU049570
EST:     ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAG                         GCGATTGCTACCGAGGTGCAAAGTGAGTCCA-GTGGAAGATA
genomic: ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAGgcataatcga ... tgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATA
EST: gi|67013287|gb|CO442036.1|CO442036
EST:     ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAG                         GCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG
genomic: ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAGgcataatcga ... tgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG
EST: gi|18384433|gb|BM417632.1|BM417632
EST:     ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAG                         GCGATTGC-ACC-AGGTGCAA-GTGAGTCCA-GTGGAAGATATTAGGGGAG
genomic: ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAGgcataatcga ... tgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG
EST: gi|18649807|gb|BM498626.1|BM498626
EST:     ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAG                         GCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG
genomic: ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAGgcataatcga ... tgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG
EST: gi|211291668|gb|FL235608.1|FL235608
EST:     ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCAAAG                         GCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG
genomic: ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAGgcataatcga ... tgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG
EST: gi|89106141|gb|DY576358.1|DY576358
EST:     ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAG                         GCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG
genomic: ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAGgcataatcga ... tgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG
EST: gi|60337474|gb|DN204447.1|DN204447
EST:     ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAG                         GCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG
genomic: ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAGgcataatcga ... tgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG
EST: gi|18649808|gb|BM498627.1|BM498627
EST:     ATTACAGATTTGACCTGGCTGTGCACCTTGGTCGACTTGAAATTGCGAAG                         GCGATTGCT-CCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG
genomic: ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAGgcataatcga ... tgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG
EST: gi|18384334|gb|BM417533.1|BM417533
EST:     ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAG                         GCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG
genomic: ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAGgcataatcga ... tgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG

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), 49 (downstream exon)
Score: 282

GGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGATAGCAACTGACACTAATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAGgcataatcga ... tgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAGTTAGCTATGTCAAGTGGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 331

GGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGATAGCAACTGACACTAATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAGgcataatcga ... tgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAGTTAGCTATGTCAAGTGGAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 345

GGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGATAGCAACTGACACTAATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAGgcataatcga ... tgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAGTTAGCTATGTCAAGTGGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 461

GGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGATAGCAACTGACACTAATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAGgcataatcga ... tgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAGTTAGCTATGTCAAGTGGAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattttcgagaaagtatttcttttttgaatttttctaatagtagttgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAGTTAGCTATGTCAAGTGGAAAG
                                ttctaat  putative branch site (score: 461)
                                            ttgttct  putative PPT
          aaagtatttctttttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcataatcgatttcttttcttctccacattttcgagaaagtatttcttttttgaatttttctaatagtagttgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAGTTAGCTATGTCAAGTGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA