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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtatttattgtgttattcatgttctgttttcctgagtcttattttgattatggatcttgcagGTTCCGAAAACCTTCAATTTTAGCTTATCTGGTGCTTCTTCAAGGTCTTGCAAATATGTGTTAAACACACTCATGCAG

Basic information

species Zea mays
transcript GRMZM2G068755_T03
intron # 41
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 43
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 42
gttagtatttattgtgttattcatgttctgttttcctgagtcttattttgattatgg---atcttgcagGTTCCGAAAACCTTCAATTTTAGCTTATCTGGTGCTTCTTCAAGGTCTTGCAAATATGTGTTAAACACACTCATGCAG
|| || ||||  | | || || | |||    |||  | | | | | | ||||  |||   | ||| |||||||| ||||| || ||||||||| ||||||| ||||| ||||| |||||||||||||| ||||| || |||||||||
gtaagcatttgctattttctttaggtta-acttttgtcactataactctgatgttggcaaacctttcagGTTCCAAAAACTTTTAATTTTAGCCTATCTGGGGCTTCGTCAAGATCTTGCAAATATGTTTTAAATACTCTCATGCAG
















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|211199225|gb|FL044865.1|FL044865
EST:     AGATCTTATTAAGGAAGCTGACAGATTAGTGTCNTGCTTGGGCTGGTATG                         GTTCCGAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTC
genomic: AGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGG-CTGTTATGgttagtattt ... gatcttgcagGTTCCGAAAACCTTCAATTTTAGCTTATCTGGTGCTTCTTC
EST: gi|67021414|gb|CO450163.1|CO450163
EST:     AAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATG                         GTTCCGAAAACCTTCAATTTTAGCTTATCTGGTGCTTCTTCAAGGTCTTGC
genomic: AAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATGgttagtattt ... gatcttgcagGTTCCGAAAACCTTCAATTTTAGCTTATCTGGTGCTTCTTCAAGGTCTTGC
EST: gi|71317537|gb|DR795494.1|DR795494
EST:     GACAGATTAGTGTCATGCTTGGCTGTTATG                         GTTCCGAAAACCTTCAATTTTAGCTTATCTGGTGCTTCTTCAAGGTCTTGC
genomic: GACAGATTAGTGTCATGCTTGGCTGTTATGgttagtattt ... gatcttgcagGTTCCGAAAACCTTCAATTTTAGCTTATCTGGTGCTTCTTCAAGGTCTTGC

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), 48 (downstream exon)
Score: 144

TATATGCCATGAGCTAACACAGGCAGCTGACCCTGAAAGCACATTGCTTGAAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATGgttagtattt ... gatcttgcagGTTCCGAAAACCTTCAATTTTAGCTTATCTGGTGCTTCTTCAAGGTCTTGCAAATATGTGTTAAACACACTCATGCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 69

TATATGCCATGAGCTAACACAGGCAGCTGACCCTGAAAGCACATTGCTTGAAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATGgttagtattt ... gatcttgcagGTTCCGAAAACCTTCAATTTTAGCTTATCTGGTGCTTCTTCAAGGTCTTGCAAATATGTGTTAAACACACTCATGCAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 62

TATATGCCATGAGCTAACACAGGCAGCTGACCCTGAAAGCACATTGCTTGAAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATGgttagtattt ... gatcttgcagGTTCCGAAAACCTTCAATTTTAGCTTATCTGGTGCTTCTTCAAGGTCTTGCAAATATGTGTTAAACACACTCATGCAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 96

TATATGCCATGAGCTAACACAGGCAGCTGACCCTGAAAGCACATTGCTTGAAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATGgttagtattt ... gatcttgcagGTTCCGAAAACCTTCAATTTTAGCTTATCTGGTGCTTCTTCAAGGTCTTGCAAATATGTGTTAAACACACTCATGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgttattcatgttctgttttcctgagtcttattttgattatggatcttgcagGTTCCGAAAACCTTCAATTTTAGCTTATCTGGTGCTTCTTCAAGGTCTTGCAAATATGTGTTAAACACACTCATGCAG
                                  ttttgat  putative branch site (score: 96)
                             tcttattttgattat  TA-rich tract