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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcttgtctaaaaaaatgtgatacctattttttggccaccaatatatctgattgcacatgatatgtcgtcttcatagtatttgtacttcaatgtttttagAACGAAGGCTTGGGAAAGCGCCTTGCTCATGGATACCCATTTTTGGAAGCTGAAGTAGCATACTGTGCTCGTTATGAGTACTGTGAATCTGCCGTGGATT

Basic information

species Zea mays
transcript GRMZM2G446108_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G446108_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g14790.1 (Oryza sativa), 3'ss of exon 5
tgcttgtctaaaaaaatgtgatacctattttttggccaccaatatatctgattgcaca---tgatatgtcgtcttcatagtatttgtacttcaatgtttttagAACGAAGGCTTGGGAAAGCGCCTTGCTCATGGATACCCATTTTTGGAAGCTGAAGTAGCATACTGTGCTCGTTATGAGTACTGTGAATCTGCCGTGGATT
   |     |   ||   | ||   | |     |    |   | | | |   || |||   | |||     |  |  || |  || | ||||| | | ||||||| ||||||||||| ||||| |||||||||||||||||||||||||| |||||||||||||||||||||||  | ||||||||||||||||| ||||| |
---tcagaaatccaagcttcattattctgcccggaaaccttttttttttccctgtacaacttaataatgttttgtggtaatcattatgcttcattttgtttagAATGAAGGCTTGGGGAAGCGACTTGCTCATGGATACCCATTTTTGGAGGCTGAAGTAGCATACTGTGCTCGCCACGAGTACTGTGAATCTGCTGTGGACT

upper sequence: GRMZM2G446108_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA02G28000.1 (Glycine max), 3'ss of exon 5
tgcttgtctaaaaaaatgtgatacctattttttggccaccaatat-atctgattgcacatgatatgtcgtcttcatagtatttgtacttcaat--gtttttagAACGAAGGCTTGGGAAAGCGCCTTGCTCATGGATACCCATTTTTGGAAGCTGAAGTAGCATACTGTGCTCGTTATGAGTACTGTGAATCTGCCGTGGATT
   || ||||    ||     | | | |    |    || | | | |     || ||   | |   ||     ||  || | | |  |  | |  || |  |||| |||   ||||| ||||| ||||| ||||| ||||| |||||||| ||||| || || |||||||| ||| |||| || |||||||||||  | || |
--tttttctatctgaacactgtgcttttgcaatttatacaagttttagtcagtttcatg-gtttcatcaatgccaaggtttatattatatattttgtatgcagAATGAAAATTTGGGCAAGCGACTTGCCCATGGTTACCCTTTTTTGGAGGCTGAGGTGGCCTACTGTGCCCGTCATGAATATTGTGAATCTGCGATTGACT

upper sequence: GRMZM2G446108_T03 (Zea mays), 3'ss of exon 5
lower sequence: Vv13s0019g04730.t01 (Vitis vinifera), 3'ss of exon 5
--tgcttgt-ctaaa---aaaatgtgatacctattttttggccaccaatatatctgattgcacatgatatgtcgtcttcatagtatttgtacttcaatgtttttagAACGAAGGCTTGGGAAAGCGCCTTGCTCATGGATACCCATTTTTGGAAGCTGAAGTAGCATACTGTGCTCGTTATGAGTACTGTGAATCTGCCGTGGATT
  ||||  | |||||   ||| ||||| |   | | | ||     |||   ||  ||| |  |    | |  | | || |    ||||   || ||      | || | |||    | || ||||| ||||| ||||||||||| ||| | || |||||||| ||||||||||| ||| ||||||||||||||||||| || ||||
cttgctcattctaaatacaaattgtgaaagtgaatatgtgaat-tcaactaattggatggttctgattgtaacatattgagttcattttctctaca-----ctcagGATGAACATCTAGGGAAGCGGCTTGCCCATGGATACCCTTTTCTAGAGGCTGAAGTGGCATACTGTGCCCGTAATGAGTACTGTGAATCTGCTGTAGATT

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|60352738|gb|DN219711.1|DN219711
EST:     TATCGCATGCATATGGATCTTTGGCTGAACAAGTGGCTACTATTGCCCAG                         AACGAAGGCTTGGGAAAGCGCCTTGCTCATGGATACCCATTTTTGGAAGCT
genomic: TATCGCATGCATATGGATCTTTGGCTGAACAAGTGGCTACTATTGCCCAGgtgtgttctc ... atgtttttagAACGAAGGCTTGGGAAAGCGCCTTGCTCATGGATACCCATTTTTGGAAGCT
EST: gi|148946266|gb|EC891566.2|EC891566
EST:     TATCGCATGCATATGGATCTTTGGCTGAACAAGTGGCTATTATTGCCCAG                         AACGAAGGCTTGGGAAAGCGCCTTGTTCATGGATACCCATTTTTGGAAGCT
genomic: TATCGCATGCATATGGATCTTTGGCTGAACAAGTGGCTACTATTGCCCAGgtgtgttctc ... atgtttttagAACGAAGGCTTGGGAAAGCGCCTTGCTCATGGATACCCATTTTTGGAAGCT
EST: gi|71760898|gb|DR958835.1|DR958835
EST:     TATCGCATGCATATGGATCTTTGGCTGAACAAGTGGCTACTATTGCCCAG                         AACGAAGGCTTGGGAAAGCGCCTTGCTCATGGATACCCATTTTTGGAAGCT
genomic: TATCGCATGCATATGGATCTTTGGCTGAACAAGTGGCTACTATTGCCCAGgtgtgttctc ... atgtttttagAACGAAGGCTTGGGAAAGCGCCTTGCTCATGGATACCCATTTTTGGAAGCT
EST: gi|211411795|gb|FL441048.1|FL441048
EST:     TATCGCATGCATATGGATCTTTGGCTGAACAAGTGGCTACTATTGCCCAG                         AACGAAGGCTTGGGAAAGCGCCTTGCTCATGGATACCCATTTTTGGAAGCT
genomic: TATCGCATGCATATGGATCTTTGGCTGAACAAGTGGCTACTATTGCCCAGgtgtgttctc ... atgtttttagAACGAAGGCTTGGGAAAGCGCCTTGCTCATGGATACCCATTTTTGGAAGCT
EST: gi|37379892|gb|CF626714.1|CF626714
EST:     TATCGCATGCATATGGATCTTTGGCTGAACAAGTGGCTACTATTGCCCAG                         AACGAAGGCTTGGGAAAGCGCC-TGCTTCATGGATACCCATTTTTGGAAGC
genomic: TATCGCATGCATATGGATCTTTGGCTGAACAAGTGGCTACTATTGCCCAGgtgtgttctc ... atgtttttagAACGAAGGCTTGGGAAAGCGCCTTGC-TCATGGATACCCATTTTTGGAAGC

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: 45 (upstream exon), 49 (downstream exon)
Score: 28

TGGTGGCAAGGTTATTCCAGGTGCAATGGACAGTGCTGTATCGAAACATTTATCGCATGCATATGGATCTTTGGCTGAACAAGTGGCTACTATTGCCCAGgtgtgttctc ... atgtttttagAACGAAGGCTTGGGAAAGCGCCTTGCTCATGGATACCCATTTTTGGAAGCTGAAGTAGCATACTGTGCTCGTTATGAGTACTGTGAATCTGCCGTGGATT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 158

TGGTGGCAAGGTTATTCCAGGTGCAATGGACAGTGCTGTATCGAAACATTTATCGCATGCATATGGATCTTTGGCTGAACAAGTGGCTACTATTGCCCAGgtgtgttctc ... atgtttttagAACGAAGGCTTGGGAAAGCGCCTTGCTCATGGATACCCATTTTTGGAAGCTGAAGTAGCATACTGTGCTCGTTATGAGTACTGTGAATCTGCCGTGGATT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 95

TGGTGGCAAGGTTATTCCAGGTGCAATGGACAGTGCTGTATCGAAACATTTATCGCATGCATATGGATCTTTGGCTGAACAAGTGGCTACTATTGCCCAGgtgtgttctc ... atgtttttagAACGAAGGCTTGGGAAAGCGCCTTGCTCATGGATACCCATTTTTGGAAGCTGAAGTAGCATACTGTGCTCGTTATGAGTACTGTGAATCTGCCGTGGATT


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 197

TGGTGGCAAGGTTATTCCAGGTGCAATGGACAGTGCTGTATCGAAACATTTATCGCATGCATATGGATCTTTGGCTGAACAAGTGGCTACTATTGCCCAGgtgtgttctc ... atgtttttagAACGAAGGCTTGGGAAAGCGCCTTGCTCATGGATACCCATTTTTGGAAGCTGAAGTAGCATACTGTGCTCGTTATGAGTACTGTGAATCTGCCGTGGATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctgattgcacatgatatgtcgtcttcatagtatttgtacttcaatgtttttagAACGAAGGCTTGGGAAAGCGCCTTGCTCATGGATACCCATTTTTGGAAGCTGAAGTAGCATACTGTGCTCGTTATGAGTACTGTGAATCTGCCGTGGATT
 atctgat  putative branch site (score: 197)
                                              tgttttt  putative PPT
                                            aatgttttta  TA-rich tract