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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctcttttgtaacattataataattctgttcaatgaagaaaaaaatatatcttacctggtgaacacttatgatttctctcccgcctacacagAGGCTCATAAGTACTTTGTTGAATATATATCCAAGGCATATCAAGCATTAACTGATCCTATATCTCGAGAGAATTATGAAAAATATGGTCACCCTGATGG

Basic information

species Zea mays
transcript GRMZM2G167868_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G167868_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g24180.1 (Oryza sativa), 3'ss of exon 4
gtacctcttttgtaacattataataattctgttcaatgaagaaaaaaatatatcttacctggtgaacact-tatgatttctctcccgcctacacagAGGCTCATAAGTACTTTGTTGAATATATATCCAAGGCATATCAAGCATTAACTGATCCTATATCTCGAGAGAATTATGAAAAATATGGTCACCCTGATGG
|||    || | | ||||| |    | ||  |      ||  || |||| || ||   ||  | |  | | | |  ||  | |    | | | ||||||| || |||||||||||||||| |||||||||||||||||| || |||||||||||| ||||||| || || ||||| || ||||||||||| |||||
gtaaagtttgtctcacatttttgataatcaatggtgctaaataagaaatgtagctgggcttattattattatttttttgttttgaaactttcccagAGGCCCACAAGTACTTTGTTGAATTTATATCCAAGGCATATCAGGCTTTAACTGATCCTGTATCTCGTGAAAACTATGAGAAGTATGGTCACCCAGATGG

upper sequence: GRMZM2G167868_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G20400.1 (Glycine max), 3'ss of exon 4
------------------gtacctcttttgtaacattataat---aattctgttcaatgaagaaaaaaatatatcttac------ctggtgaacacttatgatttctctcccgcctacacagAGGCTCATAAGTACTTTGTTGAATATATATCCAAGGCATATCAAGCATTAACTGATCCTATATCTCGAGAGAATTATGAAAAATATGGTCACCCTGATGG
                  ||     |||  ||   ||  |||   |||| || |   || || ||        || |||      ||    |||   |||  ||||  |||         |||||| || |||||||| ||||| || ||  |||| || ||||||||  | || ||||| ||| |||| || ||||||||||||||||| || ||||||||
gttgaaggtgtttcagttgtttagttttcttattgttgcaatgcaaattttgatgtttgcaggaatgtcggcttcctacaattgcctatgtaactgatatattttcattccttttattttagAGGCACACAAGTACTTCGTTGAGTACATTGCCAAAGCTTATCAAGCTCTTACAGATCCAATAGCTCGTGAAAATTATGAAAAATATGGCCATCCTGATGG

upper sequence: GRMZM2G167868_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S241_31V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------------------------------------------------------------------------------------------gtacctcttttgtaacattataataattctgttcaatgaagaaaaaaatatatcttacctggtgaacacttatgattt----ctctcccgcctacacagAGGCTCATAAGTACTTTGTTGAATATATATCCAAGGCATATCAAGCATTAACTGATCCTATATCTCGAGAGAATTATGAAAAATATGGTCACCCTGATGG
                                                                                                        |  |  || ||    |      || | |  |   |   |  | |   |    ||| |  | |  |||||   || |     | ||   | |   |||||||  | |||||||| || ||  | ||  | ||||||||||||||| |||| |||||| ||||  |||||||||| || || ||||||||||| |||||
gtgcgctcttattctgctttgtgatgtgtgtatgtgtgtgtgagtttttccctccccgtactgttagtgccattaggatctgtcgaagtcttattcacctttcgagtttattggtggtgtgggcggaactttagtatttcccgctacactaactctttagc--gcgtccacttgcaatctgacgttttcttccatgtgcagAGGCAAACAAGTACTTCGTGGAGCACATCACGAAGGCATATCAAGCACTAACGGATCCTGTATCAAGAGAGAATTACGAGAAGTATGGTCACCCCGATGG

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|211075046|gb|FL431334.1|FL431334
EST:     ATATAGGAGGCTTTCTATTCAGTACCATCCTGATAAAAATCCTGATCCAG                         AGGCTCATAAGTACTTTGTTGAATATATATCCAAGGCATATCAAGCATTAA
genomic: ATATAGGAGGCTTTCTATTCAGTACCATCCTGATAAAAATCCTGATCCAGgtacctcttt ... gcctacacagAGGCTCATAAGTACTTTGTTGAATATATATCCAAGGCATATCAAGCATTAA




















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: 49 (upstream exon), 49 (downstream exon)
Score: 81

AGTATTCTTGGACTGGAATCTGGGGCATCTGAATCTGATATCAAGAAATCATATAGGAGGCTTTCTATTCAGTACCATCCTGATAAAAATCCTGATCCAGgtacctcttt ... gcctacacagAGGCTCATAAGTACTTTGTTGAATATATATCCAAGGCATATCAAGCATTAACTGATCCTATATCTCGAGAGAATTATGAAAAATATGGTCACCCTGATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 41

AGTATTCTTGGACTGGAATCTGGGGCATCTGAATCTGATATCAAGAAATCATATAGGAGGCTTTCTATTCAGTACCATCCTGATAAAAATCCTGATCCAGgtacctcttt ... gcctacacagAGGCTCATAAGTACTTTGTTGAATATATATCCAAGGCATATCAAGCATTAACTGATCCTATATCTCGAGAGAATTATGAAAAATATGGTCACCCTGATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 47

AGTATTCTTGGACTGGAATCTGGGGCATCTGAATCTGATATCAAGAAATCATATAGGAGGCTTTCTATTCAGTACCATCCTGATAAAAATCCTGATCCAGgtacctcttt ... gcctacacagAGGCTCATAAGTACTTTGTTGAATATATATCCAAGGCATATCAAGCATTAACTGATCCTATATCTCGAGAGAATTATGAAAAATATGGTCACCCTGATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 72

AGTATTCTTGGACTGGAATCTGGGGCATCTGAATCTGATATCAAGAAATCATATAGGAGGCTTTCTATTCAGTACCATCCTGATAAAAATCCTGATCCAGgtacctcttt ... gcctacacagAGGCTCATAAGTACTTTGTTGAATATATATCCAAGGCATATCAAGCATTAACTGATCCTATATCTCGAGAGAATTATGAAAAATATGGTCACCCTGATGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaaaaatatatcttacctggtgaacacttatgatttctctcccgcctacacagAGGCTCATAAGTACTTTGTTGAATATATATCCAAGGCATATCAAGCATTAACTGATCCTATATCTCGAGAGAATTATGAAAAATATGGTCACCCTGATGG
           atcttac  putative branch site (score: 72)
                                   tttctctcccgcctac  putative PPT
     aaatatatctta  TA-rich tract