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

gttagacgtggagaacgatgcttgaagtttgccggtagttgaacagcacatttttctctgacgtgtttagtttccgtttcattcttacagGATCGAAGGGCTGACTATGTTTCTGCGATTCTGGAGAAGCTTGTGTCGTGGGAAACAGTCGAGTCCAGGCTCGCGAAAGCCGTTGCACGGGCGGTAGAAA

Basic information

species Zea mays
transcript GRMZM2G042080_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042080_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g02500.1 (Oryza sativa), 3'ss of exon 7
gttagacgtggagaacgatgcttgaagtttgccggtagttgaacagcacatttttctctgacgtgtttagtttccg-tttcattcttacagGATCGAAGGGCTGACTATGTTTCTGCGATTCTGGAGAAGCTTGTGTCGTGGGAAACAGTCGAGTCCAGGCTCGCGAAAGCCGTTGCACGGGCGGTAGAAA
||||||  ||   |  |||||||  | ||     ||| || || |  |||||||  | | || | ||| |||   |  |  ||  || |||||||| ||  |||||||||| ||  |  |||| |||||||||||||| |||||||| || |||||||||||   ||| |||||   |||||| |||||||
gttaga--tgacaagtgatgcttacattt----agtacttaaaaaaaacattttgtttt-acttattttgttcatggctatatctttgcagGATCGGAGATCTGACTATGTCTCCACATTTCTAGAGAAGCTTGTGTCATGGGAAACTGTTGAGTCCAGGCTTAAGAAGGCCGTACAACGGGCAGTAGAAA
















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|211285315|gb|FL458633.1|FL458633
EST:     GCATGCATACTATCTGGATTACGAG                         GATCGAAGGSCTGACTATGTTTCTSCGATTCTGGAGAAGCTTGTGTCSTGG
genomic: GCATGCATACTATCTGGATTACGAGgttagacgtg ... attcttacagGATCGAAGGGCTGACTATGTTTCTGCGATTCTGGAGAAGCTTGTGTCGTGG
EST: gi|60348098|gb|DN215071.1|DN215071
EST:     GCATGCATACTATCTGGATTACGAG                         GATCGAAGGGCTGACTATGTTTCTGCGATTCTGGAGAAGCTTGTGTCGTGG
genomic: GCATGCATACTATCTGGATTACGAGgttagacgtg ... attcttacagGATCGAAGGGCTGACTATGTTTCTGCGATTCTGGAGAAGCTTGTGTCGTGG
EST: gi|5439233|gb|AI820154.1|AI820154
EST:     GCATGCATCCTATNTGGATTCCNAG                         GATCGAAGGGCTGACTATGTTTNTGCGATTCTGGAGAAGCTTGTGTCGTGG
genomic: GCATGCATACTATCTGGATTACGAGgttagacgtg ... attcttacagGATCGAAGGGCTGACTATGTTTCTGCGATTCTGGAGAAGCTTGTGTCGTGG
EST: gi|148935524|gb|EC879565.2|EC879565
EST:     GCATGCATACTATCTGGATTACGAG                         GATCGAAGGGCTGACTATGTTTCTGCGATTCTGGAGAAGCTTGTGTCGTGG
genomic: GCATGCATACTATCTGGATTACGAGgttagacgtg ... attcttacagGATCGAAGGGCTGACTATGTTTCTGCGATTCTGGAGAAGCTTGTGTCGTGG
EST: gi|78026637|gb|DV495024.1|DV495024
EST:     GCATGCATACTATCTGGATTACGAG                         GATCGAAGGGCTGACTATGTTTCTGCGATTCTGGAGAAGCTTGTGTCGTGG
genomic: GCATGCATACTATCTGGATTACGAGgttagacgtg ... attcttacagGATCGAAGGGCTGACTATGTTTCTGCGATTCTGGAGAAGCTTGTGTCGTGG

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: 41 (upstream exon), 49 (downstream exon)
Score: 83

CATGCATACTATCTGGATTACGAGgttagacgtg ... attcttacagGATCGAAGGGCTGACTATGTTTCTGCGATTCTGGAGAAGCTTGTGTCGTGGGAAACAGTCGAGTCCAGGCTCGCGAAAGCCGTTGCACGGGCGGTAGAAA


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 125

CATGCATACTATCTGGATTACGAGgttagacgtg ... attcttacagGATCGAAGGGCTGACTATGTTTCTGCGATTCTGGAGAAGCTTGTGTCGTGGGAAACAGTCGAGTCCAGGCTCGCGAAAGCCGTTGCACGGGCGGTAGAAA


Block sizes: 37 (upstream exon), 49 (downstream exon)
Score: 43

CATGCATACTATCTGGATTACGAGgttagacgtg ... attcttacagGATCGAAGGGCTGACTATGTTTCTGCGATTCTGGAGAAGCTTGTGTCGTGGGAAACAGTCGAGTCCAGGCTCGCGAAAGCCGTTGCACGGGCGGTAGAAA


Block sizes: 30 (upstream exon), 49 (downstream exon)
Score: 34

CATGCATACTATCTGGATTACGAGgttagacgtg ... attcttacagGATCGAAGGGCTGACTATGTTTCTGCGATTCTGGAGAAGCTTGTGTCGTGGGAAACAGTCGAGTCCAGGCTCGCGAAAGCCGTTGCACGGGCGGTAGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttgaacagcacatttttctctgacgtgtttagtttccgtttcattcttacagGATCGAAGGGCTGACTATGTTTCTGCGATTCTGGAGAAGCTTGTGTCGTGGGAAACAGTCGAGTCCAGGCTCGCGAAAGCCGTTGCACGGGCGGTAGAAA
                    ctctgac  putative branch site (score: 34)
                                   tttccgtttcattctt  putative PPT
            acattttt  TA-rich tract