Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatatttatttatgttcaatcttggacttctttgataatacctagctaccatacatattatatcattgtttatccttattgtcttctctaccaactcttcagGTGAGATATGTTATGAGATGCATATTTGGAGACCCAAAGAATGCTCCTCCTCCTCTTGTAAGGTTGTCTGGGAAAAGTCTGGTATCTGCCATCTGGAAAG

Basic information

species Zea mays
transcript GRMZM5G812144_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G812144_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g08210.1 (Oryza sativa), 3'ss of exon 12
gtgaatatttatttatgttcaatcttggacttctttgata---atacctagctaccatacatattatatcatt------------gtttatccttattgtcttctct--accaac----tcttcagGTGAGATATGTTATGAGATGCATATTTGGAGACCCAAAGAATGCTCCTCCTCCTCTTGTAAGGTTGTCTGGGAAAAGTCTGGTATCTGCCATCTGGAAAG
|||   |||| | |     | | |||| | || ||   ||    |    |   | ||| ||   |  |  |              || | | || ||    || | |  | ||      | ||||||| |||||||| ||||||||||||||||| || || ||||||||||||||||| || || ||| |  |||||| |||||| || ||||||||||||||||
gtgcgcattt-tatgccccctagcttgaagttattcagtataagtgaacaaaaaacatgcactatgcactaacaacccaaaagaagtctcttctgatgcatttttatggatcattgttatgttcagGTAAGATATGTCATGAGATGCATATTTGGGGATCCCAAGAATGCTCCTCCTCCACTGGTGAGGCTAACTGGGAGAAGTCTAGTTTCTGCCATCTGGAAAG
















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|60337036|gb|DN204009.1|DN204009
EST:     AGGGAGTATTAAATTCAAGATTACAACAAATAGTGCATACACTTGACAAG                         GTGAGATATGTTATGAGATGCATATTTGGAGACCCAAAGAATGCTCCTCCT
genomic: AGGGAGTATTAAATTCAAGATTACAACAAATAGTGCATACACTTGACAAGgtgaatattt ... aactcttcagGTGAGATATGTTATGAGATGCATATTTGGAGACCCAAAGAATGCTCCTCCT
EST: gi|76285995|gb|DV025563.1|DV025563
EST:     AGGGAGTATTAAATTCAAGATTACAACAAATAGTGCATACACTTGACAAG                         GTGAGATATGTTATGAGATGCATATTTGGAGACCCAAAGAATGCTCCTCCT
genomic: AGGGAGTATTAAATTCAAGATTACAACAAATAGTGCATACACTTGACAAGgtgaatattt ... aactcttcagGTGAGATATGTTATGAGATGCATATTTGGAGACCCAAAGAATGCTCCTCCT
EST: gi|60672647|gb|DN475345.1|DN475345
EST:     GATTACAACAAATAGTGCATACACTTGACAAG                         GTGAGATATGTTATGAGATGCATATTTGGAGACCCAAAGAATGCTCCTCCT
genomic: GATTACAACAAATAGTGCATACACTTGACAAGgtgaatattt ... aactcttcagGTGAGATATGTTATGAGATGCATATTTGGAGACCCAAAGAATGCTCCTCCT
EST: gi|6851505|gb|AW352515.1|AW352515
EST:     AGGGAGTATTAAATTCAAGATTACAGCAAATAGTGCATACACTTGACAAG                         GTGAGATATGTTATGAGATGCATATTTGGAGACCCAAAGAATGCTCCTCCT
genomic: AGGGAGTATTAAATTCAAGATTACAACAAATAGTGCATACACTTGACAAGgtgaatattt ... aactcttcagGTGAGATATGTTATGAGATGCATATTTGGAGACCCAAAGAATGCTCCTCCT

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), 46 (downstream exon)
Score: 272

GCAGAGGGAGTATTAAATTCAAGATTACAACAAATAGTGCATACACTTGACAAGgtgaatattt ... aactcttcagGTGAGATATGTTATGAGATGCATATTTGGAGACCCAAAGAATGCTCCTCCTCCTCTTGTAAGGTTGTCTGGGAAAAGTCTGGTATCTGCCATCTGGAAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 130

GCAGAGGGAGTATTAAATTCAAGATTACAACAAATAGTGCATACACTTGACAAGgtgaatattt ... aactcttcagGTGAGATATGTTATGAGATGCATATTTGGAGACCCAAAGAATGCTCCTCCTCCTCTTGTAAGGTTGTCTGGGAAAAGTCTGGTATCTGCCATCTGGAAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 199

GCAGAGGGAGTATTAAATTCAAGATTACAACAAATAGTGCATACACTTGACAAGgtgaatattt ... aactcttcagGTGAGATATGTTATGAGATGCATATTTGGAGACCCAAAGAATGCTCCTCCTCCTCTTGTAAGGTTGTCTGGGAAAAGTCTGGTATCTGCCATCTGGAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 172

GCAGAGGGAGTATTAAATTCAAGATTACAACAAATAGTGCATACACTTGACAAGgtgaatattt ... aactcttcagGTGAGATATGTTATGAGATGCATATTTGGAGACCCAAAGAATGCTCCTCCTCCTCTTGTAAGGTTGTCTGGGAAAAGTCTGGTATCTGCCATCTGGAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accatacatattatatcattgtttatccttattgtcttctctaccaactcttcagGTGAGATATGTTATGAGATGCATATTTGGAGACCCAAAGAATGCTCCTCCTCCTCTTGTAAGGTTGTCTGGGAAAAGTCTGGTATCTGCCATCTGGAAAG
                                               ctcttc  CT-rich tract
     acatattatatcattg  TA-rich tract