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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttagttgatgttctggtcacctttattcttactcctacttttttgtttttatataaatgcccatagattgtttgtatgttatttcactcttcaatcaatttagGGAGAGAACAAGGGTTTTCTTGTCTGCAAGAAAAAGATGGCGACATCTCCGGAGTCTTTGTGTGGAATCTGTCCACAACCTTTCCGGGATTTTGTTGAGT

Basic information

species Zea mays
transcript GRMZM2G158177_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158177_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 9
gttagtttagttgatgttctggtcacctttattcttactcctacttttttgtttttatataaatgcccatagattgtttgtatgttatttcactcttcaatcaatttagGGAGAGAACAAGGGTTTTCTTGTCTGCAAGAAAAAGATGGCGACATCTCCGGAGTCTTTGTGTGGAATCTGTCCACAACCTTTCCGGGATTTTGTTGAGT
                            ||||| || || | | |  |   ||||  ||  ||||   |  ||   | ||  | ||||   | | ||   |   |  ||||||| || || || |||||||||||||||||||||||||| || ||||| ||  |||||||| |  | ||||| ||||| || ||  | |||||||| |
---------------------------gttattattccttcaaatagtc-attttagtactaatggtaaatgaaaatatgattcttatg--atttttt--ttgttacagGGAGAAAATAAAGGGTTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCAGAAACTTTGTGTTGCTTTTGTCCTCAACCATTTCGACAATTTGTTGAAT

upper sequence: GRMZM2G158177_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 9
gttagtttagttgatgttctggtcacctttattcttactcctacttttttgtttttatataaatgcccatagattgtttgtatgttatttcactcttcaatcaatttagGGAGAGAACAAGGGTTTTCTTGTCTGCAAGAAAAAGATGGCGACATCTCCGGAGTCTTTGTGTGGAATCTGTCCACAACCTTTCCGGGATTTTGTTGAGT
                            ||||| ||  | | | |  |   ||||  ||  |||    |  ||   | ||  | ||||   ||| ||       |  ||||||| || || || |||||||||||||||||||||||||| || ||||| ||  |||||||| |  | ||||| ||||| || ||| | ||||| || |
---------------------------gttattattgtttcaaatagtc-attttagtactaattgtaaatgaaaatatgactcttatgaaactttttgt----tacagGGAGAAAATAAAGGGTTTCTTGTCTGCAAGAAAAAGATGGCCACGTCTCCAGAAACTTTGTGTTGCTTTTGTCCCCAACCATTTCGGCAATTTGTGGAAT

upper sequence: GRMZM2G158177_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 9
gttagtttagttgatgttctggtcacctttattcttactcctacttttttgtttttatataaatgcccatagattgtttgtatgttatttcactcttcaatcaatttagGGAGAGAACAAGGGTTTTCTTGTCTGCAAGAAAAAGATGGCGACATCTCCGGAGTCTTTGTGTGGAATCTGTCCACAACCTTTCCGGGATTTTGTTGAGT
                            ||||| ||  ||  |  |  |  |||   ||  ||||    ||  |      |||| |  ||      |   |   |  ||||||| || || || |||||||||||||||||||||||||| || ||||| ||  |||||||| |  | ||||| ||||| || ||| | |||||||| |
---------------------------gttattattg-tctcaaatagtcatttgagtactaatg---gtaagtcaaaaatatgattcttatgagattttttgttacagGGAGAAAATAAAGGATTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCTGAAACTTTGTGTTGCTTGTGTCCTCAACCATTTCGGCAATTTGTTGAAT

upper sequence: GRMZM2G158177_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 9
gttagtttagttgatgttctggtcacctttattcttactcctacttttttgtttttatataaatgcccatagattgtttgtatgttatttcactcttcaatcaatttagGGAGAGAACAAGGGTTTTCTTGTCTGCAAGAAAAAGATGGCGACATCTCCGGAGTCTTTGTGTGGAATCTGTCCACAACCTTTCCGGGATTTTGTTGAGT------
                                            || ||||||||  |     || | |    ||  ||||   | |||    |  || ||   || ||||||||||||| ||||| ||||| |||||||| |||||||| || || || ||  || | ||  |  ||||||| |||||||| ||  | ||||| ||||      
-------------------------------------------gttatttgttttatttcc--tggcaact--ttccttgtcaatcattaacttggtctatttgtt-agggagagAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGTATGTGG

upper sequence: GRMZM2G158177_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT2G25760.1 (Arabidopsis thaliana), 3'ss of exon 9
gttagtttagttgatgttctggtcacctttattcttactcctacttttttgtttttatataaatgcccatagattgtttgtatgttatttcactcttcaatcaatttagGGAGAGAACAAGGGTTTTCTTGTCTGCAAGAAAAAGATGGCGACATCTCCGGAGTCTTTGTGTGGAATCTGTCCACAACCTTTCCGGGATTTTGTTGAGT
               |||  || |||     || ||        | |||| |||      || |  ||         ||||   | |||    |  || ||   || ||||||||||||| ||||| ||||| |||||||| |||||||| || || || ||  || | ||  |  ||||||| |||||||| ||  | ||||| ||||
---------------gttggggacactaaagttatt--------tgttttatttcctggcaactttcc---------ttgtcaatcattaacttggtctatttgtt-agGGAGAGAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGT

upper sequence: GRMZM2G158177_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 9
gttagtttagtt-gatgttctggtcacctttattcttactcct-acttttttgtttttatataaatg------------cccatagattgtttgtat--gttatttcactcttcaa---tca-atttagGGAGAGAACAAGGGTTTTCTTGTCTGCAAGAAAAAGATGGCGACATCTCCGGAGTCTTTGTGTGGAATCTGTCCACAACCTTTCCGGGATTTTGTTGAGT
||| | |   || || |||| | | |  ||| ||| | ||| | | |||   |||   ||| || |             ||  |  | | ||||  |   || |||   |||| ||    || || ||||||||||||||||| || ||||| |||||||| |||||||| |||||||||||  || ||||| |  ||||||||   |||||| |  | |||||||| |
gttggctccattcgaagttccgataaaatttgttccttctcttcaatttgaagttccgataaaatttgttccttgtcttcctttcaagtttttgacttgatttttttgttcttaaaatcccatatatagGGAGAGAACAAGGGGTTCCTTGTTTGCAAGAAGAAGATGGCAACATCTCCGGAAGCTCTGTGTTGCTTCTGTCCAATGCCTTTCAGACAGTTTGTTGAAT

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|74241723|gb|DT649637.1|DT649637
EST:     ACACGCTTATTTTTCTTCTACGTGGCCGCCTCCCTTGGCAAGGATACCAG                         GGAGAGAACAAGGGTTTTCTTGTCTGCAAGAAAAAGATGGCGACATCTCCG
genomic: ACACGCTTATTTTTCTTCTACGTGGCCGCCTCCCTTGGCAAGGATACCAGgttagtttag ... atcaatttagGGAGAGAACAAGGGTTTTCTTGTCTGCAAGAAAAAGATGGCGACATCTCCG




















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), 49 (downstream exon)
Score: 22

TCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTTGCATACACGCTTATTTTTCTTCTACGTGGCCGCCTCCCTTGGCAAGGATACCAGgttagtttag ... atcaatttagGGAGAGAACAAGGGTTTTCTTGTCTGCAAGAAAAAGATGGCGACATCTCCGGAGTCTTTGTGTGGAATCTGTCCACAACCTTTCCGGGATTTTGTTGAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 59

TCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTTGCATACACGCTTATTTTTCTTCTACGTGGCCGCCTCCCTTGGCAAGGATACCAGgttagtttag ... atcaatttagGGAGAGAACAAGGGTTTTCTTGTCTGCAAGAAAAAGATGGCGACATCTCCGGAGTCTTTGTGTGGAATCTGTCCACAACCTTTCCGGGATTTTGTTGAGT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 80

TCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTTGCATACACGCTTATTTTTCTTCTACGTGGCCGCCTCCCTTGGCAAGGATACCAGgttagtttag ... atcaatttagGGAGAGAACAAGGGTTTTCTTGTCTGCAAGAAAAAGATGGCGACATCTCCGGAGTCTTTGTGTGGAATCTGTCCACAACCTTTCCGGGATTTTGTTGAGT


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 48

TCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTTGCATACACGCTTATTTTTCTTCTACGTGGCCGCCTCCCTTGGCAAGGATACCAGgttagtttag ... atcaatttagGGAGAGAACAAGGGTTTTCTTGTCTGCAAGAAAAAGATGGCGACATCTCCGGAGTCTTTGTGTGGAATCTGTCCACAACCTTTCCGGGATTTTGTTGAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatataaatgcccatagattgtttgtatgttatttcactcttcaatcaatttagGGAGAGAACAAGGGTTTTCTTGTCTGCAAGAAAAAGATGGCGACATCTCCGGAGTCTTTGTGTGGAATCTGTCCACAACCTTTCCGGGATTTTGTTGAGT
                      tttgtatgttattt  TA-rich tract