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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgttcatgtttttcattgaacttggagcttttttttgctgccgccattgtgttattatcatattatgctttttcaatcactgccattttccccttctctgatttagttttgtaagatatcttttgatttacattttttgtttgtgaagTTGGGAACTGGAATGAGCATACTAATCTCAAAGAGCAATCCATCACTGGTAACTTCATTTGCCTTCTTGTCGTGTGGATATCTTCTCAGTTCATATCATG

Basic information

species Zea mays
transcript GRMZM5G833124_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G833124_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g34650.1 (Oryza sativa), 3'ss of exon 6
----------------------gtatgtgttcatgtttt--tcattgaacttggagcttttttttgctgccgccattgtgttattatcatattatgct--ttttcaatcactgccattttc-------cccttctctga---tttagttttgtaagatatcttttgatttacattttttgtttgtgaagTTGGGAACTGGAATGAGCATACTAATCTCAAAGAGCAATCCATCACTGGTAACTTCATTTGCCTTCTTGTCGTGTGGATATCTTCTCAGTTCATATCATG
                       | | | ||  || | |  | |    || || ||||| | | | |||| | |||  | ||||  | ||| ||||||   |   ||    || | | |||       | ||| | |||   |||   ||    || |  ||  |  ||     ||||| | ||||||||||||||||||  |||||||  |||| || ||||| ||||||||| |||| |||||||||||||||||||| ||||| ||||| || |||||||| ||||
gtaatcattcatcttttgcattttgtttcttgttggtctggttaccatacatgtagcttatatattctgctggcatcat-ttatgttaatagtatgctggctactaaaatttgtcttattcagtactgcacttatatgaaaatttgcattcaatagttcactgatatttctgtctttttatgtgtgaagTTGGGAACTGGTTTGAGCATTTTAATTTCTAAGAGGAATCCATCATTGGTGACTTCATTTGCCTTCTTGTCTTGTGGCTATCTCCTTAGTTCATACCATG
















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|32931635|gb|CF036447.1|CF036447
EST:     TCGGTGATGTTACTG-TAAAGGAGAAAGTGTTGGAAACATTGCTGATCTG                         TTGGGAACTGGAATGAGCATACTAATCTCAAAGAGCAATCCATCACTGGTA
genomic: TCGGTGATGTTACTGCTAAAGGAGAAAGTGTTGGAAACATTGCTGATCTGgtatgtgttc ... gtttgtgaagTTGGGAACTGGAATGAGCATACTAATCTCAAAGAGCAATCCATCACTGGTA
EST: gi|91874041|gb|EB403998.1|EB403998
EST:     TCGGTGATGTTACTGCTAAAGGAGAAAGTGTTGGAAACATTGCTGATCTG                         TTGGGAACTGGAATGAGCATACTAATCTCAAAGAGCAATCCATCGCTGGTA
genomic: TCGGTGATGTTACTGCTAAAGGAGAAAGTGTTGGAAACATTGCTGATCTGgtatgtgttc ... gtttgtgaagTTGGGAACTGGAATGAGCATACTAATCTCAAAGAGCAATCCATCACTGGTA
EST: gi|60356183|gb|DN223156.1|DN223156
EST:     TCGGTGATGTTACTGCTAAAGGAGAAAGTGTTGGAAACATTGCTGATCTG                         TTGGGAACTGGAATGAGCATACTAATCTCAAAGAGCAATCCATCACTGGTA
genomic: TCGGTGATGTTACTGCTAAAGGAGAAAGTGTTGGAAACATTGCTGATCTGgtatgtgttc ... gtttgtgaagTTGGGAACTGGAATGAGCATACTAATCTCAAAGAGCAATCCATCACTGGTA
EST: gi|32932638|gb|CF037450.1|CF037450
EST:     TCGGTGATGTTACTGCTAAAGGAGAAAGTGTTGGAAACATTGCTGATCTG                         TTGGGAACTGGAATGAGCATACTAATCTCAAAGAGCAATCCATCACTGGTA
genomic: TCGGTGATGTTACTGCTAAAGGAGAAAGTGTTGGAAACATTGCTGATCTGgtatgtgttc ... gtttgtgaagTTGGGAACTGGAATGAGCATACTAATCTCAAAGAGCAATCCATCACTGGTA

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), 49 (downstream exon)
Score: 199

CACCTCTACTCGAACACCAATTTACAAGGCGTATGCAAAAGGAGAAAACATCGGTGATGTTACTGCTAAAGGAGAAAGTGTTGGAAACATTGCTGATCTGgtatgtgttc ... gtttgtgaagTTGGGAACTGGAATGAGCATACTAATCTCAAAGAGCAATCCATCACTGGTAACTTCATTTGCCTTCTTGTCGTGTGGATATCTTCTCAGTTCATATCATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 378

CACCTCTACTCGAACACCAATTTACAAGGCGTATGCAAAAGGAGAAAACATCGGTGATGTTACTGCTAAAGGAGAAAGTGTTGGAAACATTGCTGATCTGgtatgtgttc ... gtttgtgaagTTGGGAACTGGAATGAGCATACTAATCTCAAAGAGCAATCCATCACTGGTAACTTCATTTGCCTTCTTGTCGTGTGGATATCTTCTCAGTTCATATCATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 363

CACCTCTACTCGAACACCAATTTACAAGGCGTATGCAAAAGGAGAAAACATCGGTGATGTTACTGCTAAAGGAGAAAGTGTTGGAAACATTGCTGATCTGgtatgtgttc ... gtttgtgaagTTGGGAACTGGAATGAGCATACTAATCTCAAAGAGCAATCCATCACTGGTAACTTCATTTGCCTTCTTGTCGTGTGGATATCTTCTCAGTTCATATCATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 475

CACCTCTACTCGAACACCAATTTACAAGGCGTATGCAAAAGGAGAAAACATCGGTGATGTTACTGCTAAAGGAGAAAGTGTTGGAAACATTGCTGATCTGgtatgtgttc ... gtttgtgaagTTGGGAACTGGAATGAGCATACTAATCTCAAAGAGCAATCCATCACTGGTAACTTCATTTGCCTTCTTGTCGTGTGGATATCTTCTCAGTTCATATCATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctctgatttagttttgtaagatatcttttgatttacattttttgtttgtgaagTTGGGAACTGGAATGAGCATACTAATCTCAAAGAGCAATCCATCACTGGTAACTTCATTTGCCTTCTTGTCGTGTGGATATCTTCTCAGTTCATATCATG
                           ttttgat  putative branch site (score: 475)
                                       ttttttgttt  putative PPT
                  taagatatcttttgat  TA-rich tract