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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctaattatatgcatcactctcatccatctggaggcttactaattgaaatacttcaacttattgttatatcacaaatttctacagAGGGTTCTAGAGCATTGTGATGATCCTAAAACACAGCAAATAATGATGGATGAGATTCTCCAGTCTGTTTGCTTGCTGGCTCAGGACCAGTATGGCAACT

Basic information

species Zea mays
transcript GRMZM2G042623_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042623_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g01910.1 (Oryza sativa), 3'ss of exon 5
gtatgctaattatatgcatcactctcatccatctggaggcttactaattgaaatacttcaactta-ttgttatatcaca---aatttctacagAGGGTTCTAGAGCATTGTGATGATCCTAAAACACAGCAAATAATGATGGATGAGATTCTCCAGTCTGTTTGCTTGCTGGCTCAGGACCAGTATGGCAACT
||||||  || |||||| |        |  || | |||| ||||  ||   ||||    |||| | |||| ||    ||    |      |||||||| || ||||||||||||||||||| |||||||||||||||||||||||||||||||||||| ||||||||||||||||| || || || |||||||
gtatgcatataatatgcgtgtaatcagtttatgttgaggtttacagatgttaatatgcaaactcacttgtcatccttcatgtgaaactcccagAGGGTGCTGGAGCATTGTGATGATCCTACAACACAGCAAATAATGATGGATGAGATTCTCCAGTCCGTTTGCTTGCTGGCTCAAGATCAATACGGCAACT

upper sequence: GRMZM2G042623_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g74030.1 (Oryza sativa), 3'ss of exon 5
-------------------gtatgcta---attatatgcatcactctcatccatctggaggcttactaattgaaatacttcaacttattgttatatca--caaatttctacagAGGGTTCTAGAGCATTGTGATGATCCTAAAACACAGCAAATAATGATGGATGAGATTCTCCAGTCTGTTTGCTTGCTGGCTCAGGACCAGTATGGCAACT
                   | ||||||    ||   ||| ||| | ||     | |  | |||   | || |  | |||  ||| | |||| ||   |    | |     |||||||| || ||||||||||||||||||||||| |||||||| |||||||||||||| || || ||||||||||||||||||   ||||||||||| ||||
gtacacttgtagtgccacagcatgctatccgttgattgcttcaatatccagtctattcatgctacttcatagctacact--aacct-ttgtcatgcaaattcactggacgcagAGGGTGCTGGAGCATTGTGATGATCCTAAAACCCAGCAAATCATGATGGATGAGATCCTACAATCTGTTTGCTTGCTGGCTACAGACCAGTATGGTAACT

upper sequence: GRMZM2G042623_T02 (Zea mays), 3'ss of exon 6
lower sequence: PP1S35_216V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------gtatgc-taattatatgcatcactctcatccatctg-gaggcttac----taattgaaatact--tcaacttattgttatatcacaaatttcta-----cagAGGGTTCTAGAGCATTGTGATGATCCTAAAACACAGCAAATAATGATGGATGAGATTCTCCAGTCTGTTTGCTTGCTGGCTCAGGACCAGTATGGCAACT
              |  || ||||||| | |  |    |   || | || || ||  ||    ||  |||||| ||    |||    ||   || |   | ||  |      ||||| ||||| ||||| ||    ||     | |  ||| |    || ||||| |||||| | |  ||    ||   ||||||||||||||||||||||||||
gtaagttcttgggattggcataattatgttctgctacattgcccttgtgagaagcacacgtgatacgtgaaatcctagctaacgaggtggggtaacgggatttggttgggttcagAGAGTTCTGGAGCACTGCACGGACGAGCAGAAGCAGAAGGGGATCATGGAAGAGATTTTACGTTCCACATGTACGCTGGCTCAGGACCAGTATGGCAACT

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|32935053|gb|CF039865.1|CF039865
EST:     GCCAAGTTGTAATGCTATCCACTCATCCATATGGTTGTCGAGTTATTCAG                         AGGGTTCTAGAGCATTGTGATGATCCTAAAACACAGCAAATAATGATGGAT
genomic: GCCAAGTTGTAATGCTATCCACTCATCCATATGGTTGTCGAGTTATTCAGgtatgctaat ... atttctacagAGGGTTCTAGAGCATTGTGATGATCCTAAAACACAGCAAATAATGATGGAT
EST: gi|32935072|gb|CF039884.1|CF039884
EST:     GCCAAGTTGTAATGCTATCCACTCATCCATATGGTTGTCGAGTTATTCAG                         AGGGTTCTAGAGCATTGTGATGATCCTAAAACACAGCAAATAATGATGGAT
genomic: GCCAAGTTGTAATGCTATCCACTCATCCATATGGTTGTCGAGTTATTCAGgtatgctaat ... atttctacagAGGGTTCTAGAGCATTGTGATGATCCTAAAACACAGCAAATAATGATGGAT

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), 48 (downstream exon)
Score: 202

AGAGTGCATTCCTCAGCATGCTATTGAGTTTATTATCTCGACATTCTATGGCCAAGTTGTAATGCTATCCACTCATCCATATGGTTGTCGAGTTATTCAGgtatgctaat ... atttctacagAGGGTTCTAGAGCATTGTGATGATCCTAAAACACAGCAAATAATGATGGATGAGATTCTCCAGTCTGTTTGCTTGCTGGCTCAGGACCAGTATGGCAACT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 85

AGAGTGCATTCCTCAGCATGCTATTGAGTTTATTATCTCGACATTCTATGGCCAAGTTGTAATGCTATCCACTCATCCATATGGTTGTCGAGTTATTCAGgtatgctaat ... atttctacagAGGGTTCTAGAGCATTGTGATGATCCTAAAACACAGCAAATAATGATGGATGAGATTCTCCAGTCTGTTTGCTTGCTGGCTCAGGACCAGTATGGCAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 83

AGAGTGCATTCCTCAGCATGCTATTGAGTTTATTATCTCGACATTCTATGGCCAAGTTGTAATGCTATCCACTCATCCATATGGTTGTCGAGTTATTCAGgtatgctaat ... atttctacagAGGGTTCTAGAGCATTGTGATGATCCTAAAACACAGCAAATAATGATGGATGAGATTCTCCAGTCTGTTTGCTTGCTGGCTCAGGACCAGTATGGCAACT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 92

AGAGTGCATTCCTCAGCATGCTATTGAGTTTATTATCTCGACATTCTATGGCCAAGTTGTAATGCTATCCACTCATCCATATGGTTGTCGAGTTATTCAGgtatgctaat ... atttctacagAGGGTTCTAGAGCATTGTGATGATCCTAAAACACAGCAAATAATGATGGATGAGATTCTCCAGTCTGTTTGCTTGCTGGCTCAGGACCAGTATGGCAACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaggcttactaattgaaatacttcaacttattgttatatcacaaatttctacagAGGGTTCTAGAGCATTGTGATGATCCTAAAACACAGCAAATAATGATGGATGAGATTCTCCAGTCTGTTTGCTTGCTGGCTCAGGACCAGTATGGCAACT
       tactaat  putative branch site (score: 92)
                                              tttctac  putative PPT
                            ttattgttatatcaca  TA-rich tract