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

gtaatgaagctttttatctgccaaacagtccatatagatctcattcagctatactcacagattatattgtttcatcttcagCTGGACGTGAACACGTATCCCTCGATGTTCCTAGAGGAAGGTACAAGACGACTAGTTTGCCTGTTCCTGGTCTTGGTTCAAGCAGAGGTTATCAGTTGTT

Basic information

species Zea mays
transcript GRMZM5G830874_T04
intron # 1
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|78124910|gb|DV543294.1|DV543294
EST:     AAGTCCTACATCACCAGCATCATATGCCCAAAATGGTCTTGGAAACTATG                         CTGGACGTGAACACGTATCCCTCGATGTTCCTAGAGGAAGGTACAAGACGA
genomic: AAGTCCTACATCACCAGCATCATATGCCCAAAATGGTCTTGGAAACTATGgtaatgaagc ... tcatcttcagCTGGACGTGAACACGTATCCCTCGATGTTCCTAGAGGAAGGTACAAGACGA
EST: gi|78110728|gb|DV529126.1|DV529126
EST:     CAGCATCATATGCCCAAAATGGTCTTGGAAACTATG                         CTGGACGTGAACACGTATCCCTCGATGTTCCTAGAGGAAGGTACAAGACGA
genomic: CAGCATCATATGCCCAAAATGGTCTTGGAAACTATGgtaatgaagc ... tcatcttcagCTGGACGTGAACACGTATCCCTCGATGTTCCTAGAGGAAGGTACAAGACGA
EST: gi|78543868|gb|DV621366.1|DV621366
EST:     TCACCAGCATCATATGCCCAAAATGGTCTTGGAAACTATG                         CTGGACGTGAACACGTATCCCTCGATGTTCCTAGAGGAAGGTACAAGACGA
genomic: TCACCAGCATCATATGCCCAAAATGGTCTTGGAAACTATGgtaatgaagc ... tcatcttcagCTGGACGTGAACACGTATCCCTCGATGTTCCTAGAGGAAGGTACAAGACGA
EST: gi|60400536|gb|DN233343.1|DN233343
EST:     AAGTCCTACATCACCAGCATCATATGCCCAAAATGGTCTTGGAAACTATG                         CTGGACGTGAACACGTATCCCTCGATGTTCCTAGAGGAAGGTACAAGACGA
genomic: AAGTCCTACATCACCAGCATCATATGCCCAAAATGGTCTTGGAAACTATGgtaatgaagc ... tcatcttcagCTGGACGTGAACACGTATCCCTCGATGTTCCTAGAGGAAGGTACAAGACGA
EST: gi|211376348|gb|FL146641.1|FL146641
EST:     AAGTCCTACATCACCAGCATCATATGCCCAAAATGGTCTTGGAAACTATG                         CTGGACGTGAACACGTATCCCTCGATGTTCCTAGAGGAAGGTACAAGACGA
genomic: AAGTCCTACATCACCAGCATCATATGCCCAAAATGGTCTTGGAAACTATGgtaatgaagc ... tcatcttcagCTGGACGTGAACACGTATCCCTCGATGTTCCTAGAGGAAGGTACAAGACGA

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: 100

GTCGATGGACGACGCAGTCAGAACCTCAGGTCACTATCATTTGGAAATTCAAGTCCTACATCACCAGCATCATATGCCCAAAATGGTCTTGGAAACTATGgtaatgaagc ... tcatcttcagCTGGACGTGAACACGTATCCCTCGATGTTCCTAGAGGAAGGTACAAGACGACTAGTTTGCCTGTTCCTGGTCTTGGTTCAAGCAGAGGTTATCAGTTGTT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 115

GTCGATGGACGACGCAGTCAGAACCTCAGGTCACTATCATTTGGAAATTCAAGTCCTACATCACCAGCATCATATGCCCAAAATGGTCTTGGAAACTATGgtaatgaagc ... tcatcttcagCTGGACGTGAACACGTATCCCTCGATGTTCCTAGAGGAAGGTACAAGACGACTAGTTTGCCTGTTCCTGGTCTTGGTTCAAGCAGAGGTTATCAGTTGTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 194

GTCGATGGACGACGCAGTCAGAACCTCAGGTCACTATCATTTGGAAATTCAAGTCCTACATCACCAGCATCATATGCCCAAAATGGTCTTGGAAACTATGgtaatgaagc ... tcatcttcagCTGGACGTGAACACGTATCCCTCGATGTTCCTAGAGGAAGGTACAAGACGACTAGTTTGCCTGTTCCTGGTCTTGGTTCAAGCAGAGGTTATCAGTTGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 109

GTCGATGGACGACGCAGTCAGAACCTCAGGTCACTATCATTTGGAAATTCAAGTCCTACATCACCAGCATCATATGCCCAAAATGGTCTTGGAAACTATGgtaatgaagc ... tcatcttcagCTGGACGTGAACACGTATCCCTCGATGTTCCTAGAGGAAGGTACAAGACGACTAGTTTGCCTGTTCCTGGTCTTGGTTCAAGCAGAGGTTATCAGTTGTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtccatatagatctcattcagctatactcacagattatattgtttcatcttcagCTGGACGTGAACACGTATCCCTCGATGTTCCTAGAGGAAGGTACAAGACGACTAGTTTGCCTGTTCCTGGTCTTGGTTCAAGCAGAGGTTATCAGTTGTT
                         tactcac  putative branch site (score: 109)
                                           tttcatcttc  putative PPT
                                  attatattgtttcat  TA-rich tract