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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatttttttaacatattttgtaatgtactacctccattttttttatttgacgctagctagttcaagtttacactaaccaacgtcaaatataaaaaactggagggagtaatttatattgacctgcttttaattattgatatgctattctgcagATTGCCGTAGGAGAAGAACTCGCCTATGATTACCGACAAAAGCTTGTAGCAGGCGATGGCTGCCCATGCCATTGTGGAACTACCAATTGCCGAGGCCGTG

Basic information

species Zea mays
transcript GRMZM2G172427_T01
intron # 10
splice site 3'
intron type U2

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|67021860|gb|CO450609.1|CO450609
EST:     AGAGCAAAGATTGCCAGCTTGCTCACATTGGATTGTTTGCTAATCAAGAT                         ATTGCCGTAGGAGAAGAACTCGCCTATGATTACCGACAAAAGCTTGTAGCA
genomic: AGAGCAAAGATTGCCAGCTTGCTCACATTGGATTGTTTGCTAATCAAGATgtaagatttt ... tattctgcagATTGCCGTAGGAGAAGAACTCGCCTATGATTACCGACAAAAGCTTGTAGCA
EST: gi|10191692|gb|BE761768.1|BE761768
EST:     AGAGCAAAGATTGCCAGCTTGCTCACATTGGATTGTTTGCTAATCAAGAT                         ATTGCCGTAGGAGAAGAACTCGCCTATGATTACCGACAAAAGCTTGTAGCA
genomic: AGAGCAAAGATTGCCAGCTTGCTCACATTGGATTGTTTGCTAATCAAGATgtaagatttt ... tattctgcagATTGCCGTAGGAGAAGAACTCGCCTATGATTACCGACAAAAGCTTGTAGCA
EST: gi|16377285|gb|BI991856.1|BI991856
EST:     AGAGCAAAGATTGCCAGCTTGCTCACATTGGATTGTTTGCTAATCAAGAT                         ATTGCCGTAGGAGAAGAACTCGCCTATGATTACCGACAAAAGCTTGTAGCA
genomic: AGAGCAAAGATTGCCAGCTTGCTCACATTGGATTGTTTGCTAATCAAGATgtaagatttt ... tattctgcagATTGCCGTAGGAGAAGAACTCGCCTATGATTACCGACAAAAGCTTGTAGCA
EST: gi|69351242|gb|DR452068.1|DR452068
EST:     AGAGCAAAGATTGCCAGCTTGCTCACATTGGATTGTTTGCTAATCAAGAT                         ATTGCCGTAGGAGAAGAACTCGCCTATGATTACCGACAAAAGCTTGTAGCA
genomic: AGAGCAAAGATTGCCAGCTTGCTCACATTGGATTGTTTGCTAATCAAGATgtaagatttt ... tattctgcagATTGCCGTAGGAGAAGAACTCGCCTATGATTACCGACAAAAGCTTGTAGCA
EST: gi|32935470|gb|CF040282.1|CF040282
EST:     GGATTGTTTGCTAATCAAGAT                         ATTGCCGTAGGAGAAGAACTCGCCTATGATTACCGACAAAAGCTTGTAGCA
genomic: GGATTGTTTGCTAATCAAGATgtaagatttt ... tattctgcagATTGCCGTAGGAGAAGAACTCGCCTATGATTACCGACAAAAGCTTGTAGCA
EST: gi|83278797|gb|DV942805.1|DV942805
EST:     AGAGCAAAGATTGCCAGCTTGCTCACATTGGATTGTTTGCTAATCAAGAT                         ATTGCCGTAGGAGAAGAACTCGCCTATGATTACCGACAAAAGCTTGTAGCA
genomic: AGAGCAAAGATTGCCAGCTTGCTCACATTGGATTGTTTGCTAATCAAGATgtaagatttt ... tattctgcagATTGCCGTAGGAGAAGAACTCGCCTATGATTACCGACAAAAGCTTGTAGCA
EST: gi|4646774|gb|AI621849.1|AI621849
EST:     GATTGTTTGCTAATCAAGAT                         ATTGCCGTAGGAGAAGAACTCGCCTATGATTACCGACAAAAGCTTGTAGCA
genomic: GATTGTTTGCTAATCAAGATgtaagatttt ... tattctgcagATTGCCGTAGGAGAAGAACTCGCCTATGATTACCGACAAAAGCTTGTAGCA

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: 47 (upstream exon), 49 (downstream exon)
Score: 210

TTGTTCCCCGAATCTCAGTACCCGGTTGGTTTTGGTAGAGAGCAAAGATTGCCAGCTTGCTCACATTGGATTGTTTGCTAATCAAGATgtaagatttt ... tattctgcagATTGCCGTAGGAGAAGAACTCGCCTATGATTACCGACAAAAGCTTGTAGCAGGCGATGGCTGCCCATGCCATTGTGGAACTACCAATTGCCGAGGCCGTG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 76

TTGTTCCCCGAATCTCAGTACCCGGTTGGTTTTGGTAGAGAGCAAAGATTGCCAGCTTGCTCACATTGGATTGTTTGCTAATCAAGATgtaagatttt ... tattctgcagATTGCCGTAGGAGAAGAACTCGCCTATGATTACCGACAAAAGCTTGTAGCAGGCGATGGCTGCCCATGCCATTGTGGAACTACCAATTGCCGAGGCCGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 108

TTGTTCCCCGAATCTCAGTACCCGGTTGGTTTTGGTAGAGAGCAAAGATTGCCAGCTTGCTCACATTGGATTGTTTGCTAATCAAGATgtaagatttt ... tattctgcagATTGCCGTAGGAGAAGAACTCGCCTATGATTACCGACAAAAGCTTGTAGCAGGCGATGGCTGCCCATGCCATTGTGGAACTACCAATTGCCGAGGCCGTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 93

TTGTTCCCCGAATCTCAGTACCCGGTTGGTTTTGGTAGAGAGCAAAGATTGCCAGCTTGCTCACATTGGATTGTTTGCTAATCAAGATgtaagatttt ... tattctgcagATTGCCGTAGGAGAAGAACTCGCCTATGATTACCGACAAAAGCTTGTAGCAGGCGATGGCTGCCCATGCCATTGTGGAACTACCAATTGCCGAGGCCGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggagggagtaatttatattgacctgcttttaattattgatatgctattctgcagATTGCCGTAGGAGAAGAACTCGCCTATGATTACCGACAAAAGCTTGTAGCAGGCGATGGCTGCCCATGCCATTGTGGAACTACCAATTGCCGAGGCCGTG
                                            ctattct  CT-rich tract
                           ttttaattattgatat  TA-rich tract