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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatgcattcccaggcattgttggactcttcccttgtgcacattatacttttgtaccttgctggttgccacacgttgatattgattgactgacgcttgttatttctttcacagtgcagGCTTGATACTAGCTTCTTGGTTTCTTTCATTGGG

Basic information

species Zea mays
transcript GRMZM2G017365_T07
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017365_T08 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g58580.1 (Oryza sativa), 3'ss of exon 5
gtac-atgcattcccagg-cattgttggactcttcccttgtgcacattatacttttgtaccttgctggttgccacacgttgatattgattgactgacgcttgttatttctttcacagtgcagGCTTGATACTAGCTTCTTGGTTTCTTTCATTGGG
|||  |   | || || | || |||  | |||||||||| |  | ||| | || ||     |   | ||  | |   |||  |  |  ||   ||||   ||| | | ||    |||||||||||||||||||||||| |||||||||||||||||
gtatgagatactctcatgtcactgt--gcctcttcccttata-atatt-tgctctt-----tctgtagtcacgaa--gttagttatttttagttgacatgtgtaaatcctccatcagTGCAGGCTTGATACTAGCTTCCTGGTTTCTTTCATTGGG
















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|76014355|gb|DT941525.1|DT941525
EST:     ATGAATTACCACTCGGTCTGTTTGCATGTGTTGGCAGATTCAATACGGAG                         GCTTGATACTAGCTTCTTGGTTTCTTTCATTGGG
genomic: ATGAATTACCACTCGGTCTGTTTGCATGTGTTGGCAGATTCAATACGGAGgtacatgcat ... cacagtgcagGCTTGATACTAGCTTCTTGGTTTCTTTCATTGGG
EST: gi|211384669|gb|FL388814.1|FL388814
EST:     ATGAATTACCACTCGGTCTGTTTGCATGTGTTGGCAGATTCAATACGGAGTGCAG                     
genomic: ATGAATTACCACTCGGTCTGTTTGCATGTGTTGGCAGATTCAATAC---G-G-AGgtacatgcat ... cacagt
EST: gi|9953706|gb|BE640289.1|BE640289
EST:     TCGGTCTGTTTGCATGTGTTGGCAGATTCAATACGGAGTGCAG                     
genomic: TCGGTCTGTTTGCATGTGTTGGCAGATTCAATAC---G-G-AGgtacatgcat ... cacagt

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: 48 (upstream exon), 48 (downstream exon)
Score: 64

TTTACAGGAATGCAGAGGATATGAATTACCACTCGGTCTGTTTGCATGTGTTGGCAGATTCAATACGGAGgtacatgcat ... cacagtgcagGCTTGATACTAGCTTCTTGGTTTCTTTCATTGGG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 43

TTTACAGGAATGCAGAGGATATGAATTACCACTCGGTCTGTTTGCATGTGTTGGCAGATTCAATACGGAGgtacatgcat ... cacagtgcagGCTTGATACTAGCTTCTTGGTTTCTTTCATTGGG


Block sizes: 47 (upstream exon), 41 (downstream exon)
Score: 61

TTTACAGGAATGCAGAGGATATGAATTACCACTCGGTCTGTTTGCATGTGTTGGCAGATTCAATACGGAGgtacatgcat ... cacagtgcagGCTTGATACTAGCTTCTTGGTTTCTTTCATTGGG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 38

TTTACAGGAATGCAGAGGATATGAATTACCACTCGGTCTGTTTGCATGTGTTGGCAGATTCAATACGGAGgtacatgcat ... cacagtgcagGCTTGATACTAGCTTCTTGGTTTCTTTCATTGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgccacacgttgatattgattgactgacgcttgttatttctttcacagtgcagGCTTGATACTAGCTTCTTGGTTTCTTTCATTGGG
                       gactgac  putative branch site (score: 38)
                               cttgttatttctttc  CT-rich tract
                                   ttatttcttt  TA-rich tract