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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCCTGCGGAAGCTGACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtgtgatgtatttaaatcttttattgcttacatatttcagtttacagaatatgtatcatgcattaagtactgttggattaatgttcattgctataa...

Basic information

species Zea mays
transcript GRMZM2G387076_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G387076_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g64650.2 (Oryza sativa), 5'ss of exon 4
GATCCTGCGGAAGCTGACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtgtgatgtatttaaatcttttattgcttacatatttcagtttacagaatatgtatcatgcattaagtactgttggattaatgttcattgctataa--
|| ||||| || |||||||| ||||||||||| ||||||||||||||||||||||||||||||||||||||| | || || ||| | ||| || | || ||| || | | |||| | || ||| || |
GACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtatttcttaccagaaaaaaaaattataga-atagctctgccattcatattggtaaataccaacacttcttgttctaacaa-actcaatgacccgatc

upper sequence: GRMZM2G387076_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA09G13840.1 (Glycine max), 5'ss of exon 4
GATCCTGCGGAAGCTGACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtgtgatgtatttaaatcttttattgct-tacatatttcagtttacagaatatgtatcatgcattaagtactgttggattaatgttcattgctataa--
|||||||| || || ||||| || |||||||| ||||| || ||||||||||| ||||| ||||| ||||| || || | || | | || || | || || | ||| | | | | | | || || | | ||| ||| ||
GATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTTgtaagaacacaatacttcatatttgcaaaacagtatatgggttccctt-catcttttgtcttctaaagttacttctctttaa--gacattctgtgccatgtag

upper sequence: GRMZM2G387076_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA13G19950.1 (Glycine max), 5'ss of exon 4
GATCCTGCGGAAGCTGACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtgtgatgtatttaaatcttttattgct-tacatatttcagtttacagaatatgtatcatgcattaagtactgttggattaatgttcattgctataa--
|||||||| || |||||||| || |||||||||||||| || ||||||||||||||||| ||||| ||||| || || || | || | | || || | || || | | | | | | | | || || | | ||| | | ||
GATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTTgtaagcatgcaatactttatatttgcaaaacagtatatgggttccctt-catcttttaccttctaaagttacttctcttcaa--gacattctgtcatgtagtt

upper sequence: GRMZM2G387076_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv14s0060g00090.t01 (Vitis vinifera), 5'ss of exon 4
GATCCTGCGGAAGCTGACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtg-tgatgtatttaaatcttttattgcttacatatttcagtttacagaatatgtatcatgcattaagtactg--ttggattaatgttcattgctataa--
|| ||||| || ||||| || || |||||||||||||||| |||||||| || ||||||||||| || |||| ||| | | || ||||| | || | || | | | | | || | | | |||| | ||| | || | | || | |
GACCCTGCAGAGGCTGATAAGTTGCTGAAAATTCAGAGGGATTTGGATGAGACCAAAATTATCCTTgtgagtgctgaaattgtgcaagattttact-----tgtaatgcattctgcggcctccccattactcttctagtattcccttgtgcttttgccccctactttgatt

upper sequence: GRMZM2G387076_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv11s0206g00130.t01 (Vitis vinifera), 5'ss of exon 4
GATCCTGCGGAAGCTGACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtgtgatgtatttaaatcttttattgcttacatat---ttcagtttacagaatatgtatcatgcat-taagtactgttggattaatgttcattgctataa
||||||||||| ||||| || || ||||||||||||| || ||||||||||| |||||||| || || ||| | | | | || | ||||| | |||| | |||| || | || || || | | | | || | || | | || || |
GATCCTGCGGAGGCTGATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagtttta-atttacaattgcattattttatgtatatagatccagtatatataa-atagattgtctttctctttccttctttatcagttcatatacctgt--

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|74235349|gb|DT643263.1|DT643263
EST:     ACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTCCTTGCCAGAGGAGAGAGATTGGATAGCTTG
genomic: ACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtgtga ... attttaacagCATAAAACTATTGAGAGTGTCCTTGCCAGAGGAGAGAGATTGGATAGCTTG
EST: gi|211529456|gb|FL249093.1|FL249093
EST:     ACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTTGAGAGTGTCC
genomic: ACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtgtga ... attttaacagCATAAAACTATT-GAGAGTGTCC
EST: gi|211460687|gb|FL127589.1|FL127589
EST:     ACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAARACTATTGAGAGTGTCCTTGCCAGAGGAGAGAGATTGGATAGCTTG
genomic: ACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtgtga ... attttaacagCATAAAACTATTGAGAGTGTCCTTGCCAGAGGAGAGAGATTGGATAGCTTG
EST: gi|211529460|gb|FL249097.1|FL249097
EST:     ACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTCCTTGCCAGAGGAGAGAGATTGGATAGCTTG
genomic: ACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtgtga ... attttaacagCATAAAACTATTGAGAGTGTCCTTGCCAGAGGAGAGAGATTGGATAGCTTG
EST: gi|60354098|gb|DN221071.1|DN221071
EST:     ACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTCCTTGCCAGAGGAGAGAGATTGGATAGCTTG
genomic: ACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtgtga ... attttaacagCATAAAACTATTGAGAGTGTCCTTGCCAGAGGAGAGAGATTGGATAGCTTG
EST: gi|149057998|gb|EE156679.2|EE156679
EST:     ACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTCCTTGCCAGAGGAGAGAGATTGGATAGCTTG
genomic: ACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtgtga ... attttaacagCATAAAACTATTGAGAGTGTCCTTGCCAGAGGAGAGAGATTGGATAGCTTG
EST: gi|211529454|gb|FL249091.1|FL249091
EST:     ACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTCCTTGCCAGAGGAG
genomic: ACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtgtga ... attttaacagCATAAAACTATTGAGAGTGTCCTTGCCAGAGGAG
EST: gi|44681914|gb|CK786962.1|CK786962
EST:     ACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTCCTTGCCAGAGGAGAGAGATTGGATAGCTTG
genomic: ACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtgtga ... attttaacagCATAAAACTATTGAGAGTGTCCTTGCCAGAGGAGAGAGATTGGATAGCTTG

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: 42 (upstream exon), 43 (downstream exon)
Score: 53

GATCCTGCGGAAGCTGACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtgtga ... attttaacagCATAAAACTATTGAGAGTGTCCTTGCCAGAGGAGAGAGATTGGATAGCTTGGTTGAGAAAAGCTCTGATCTGAGTGCTGCTTCTCAG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 60

GATCCTGCGGAAGCTGACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtgtga ... attttaacagCATAAAACTATTGAGAGTGTCCTTGCCAGAGGAGAGAGATTGGATAGCTTGGTTGAGAAAAGCTCTGATCTGAGTGCTGCTTCTCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 60

GATCCTGCGGAAGCTGACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtgtga ... attttaacagCATAAAACTATTGAGAGTGTCCTTGCCAGAGGAGAGAGATTGGATAGCTTGGTTGAGAAAAGCTCTGATCTGAGTGCTGCTTCTCAG


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 65

GATCCTGCGGAAGCTGACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtgtga ... attttaacagCATAAAACTATTGAGAGTGTCCTTGCCAGAGGAGAGAGATTGGATAGCTTGGTTGAGAAAAGCTCTGATCTGAGTGCTGCTTCTCAG