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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatatttcaaatgctatcttttgtgttgatgccatcagtaatataaattttatttctaggactgttcactgagggtttcatatgatgtgttgaatttatgtgatgcagTACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATATGGTCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGATAACA

Basic information

species Zea mays
transcript GRMZM2G423861_T01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 18
gtgaatatttcaaatgctatcttttgtgttgatgccatcagtaatataaattttatttctaggactgttcactga-gggtttcatatgat-gtgttgaatttatgtgatgcagTACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATATGGTCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGATAACA
               |  | ||||| | |        |   ||| ||| || |  |   ||| | | ||  |    ||  | ||| || |  |  ||||||| |||||||||||| || || ||||| || |||||||||||||| ||||| |||||||| ||||| ||||||||||||||||| ||||| || |||||||| || || ||||
---------------gtgaccttttttttaacacttctttttaacatacatgtgctcattag-attatttgcaattggactccatgtgtttatcatgaattt-tgtgatgcagTATCTAGTTCAATCGGCCGTTGATGGATATAATGTTTGTATATTTGCTTATGGGCAAACTGGTTCTGGAAAAACTTTTACAATTTATGGATCTGAAAACA

upper sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 19
--------gtga-atatttcaaatgcta-tcttttgtgtt-gatgccat---cagtaatataaattt--tatttctaggactgttcactgagggtttcatatgatgtgttgaatttatgtgatgcagTACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATATGGTCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGATAACA-------
         | | | |||  | ||  || | |||||  || |||  |||   || | | ||  ||||  ||||| |   |||  | ||  | | |||       | | ||| |  | ||  ||||||||| | || ||||| ||||| ||||| ||||| |||||||||||||| ||||||||||||||||||||||||||||| || || |||||    || ||||       
gtcttagtataacaaattatagatcatagttttttgctttagatagcatatacattgaaatggatttaatattttttatactcattaccaatgtttt-------tcttttggaaatttgcaatgcagtacttagTGCAATCTGCTGTGGATGGTTATAATGTTTGCATATTTGCTTATGGTCAAACTGGTTCTGGAAAGACTTTTACAATCTATGGAGTTGAAAACAATCCTGG

upper sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA11G09480.1 (Glycine max), 3'ss of exon 19
------------gtga-atatttcaaatgcta-tcttttgtgtt-gatgccat---cagtaatataaattttatttctaggactgttcactgagggtttcatatgatgtgttgaatttatgtgatgcagTACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATATGGTCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGATAACA
             | | | |||  | || ||| | |||||  || |||   ||   || | | ||| |||| || | |     |  ||| |     | |  |    | | ||| |  | ||  ||||||||| | || ||||| ||||| ||||| ||||| |||||||||||||| || ||||||||||||||||| |||||||| || || |||||  | || ||||
gcaagtcttagtataacaaattaaagatcctagttttttgctttagataatatgtacattgaaatagatttaatatttttctatactcattactaatgtttt----tcttttggacatttgcaatgcagTACTTAGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTACGGTCAAACTGGTTCTGGGAAGACTTTTACAATCTATGGAGCTGAAAACA

upper sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 19
gtgaatatttcaaatgctatcttttgtgttgatgccatcagtaatataaattt--tatttctaggactgt---tcactgagggtttcatatgatgtgttgaatttatgtgatgcagTACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATATGGTCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGATAACA
             ||   |   |        | | |||   | ||||  ||||  | ||| | |||   |   | ||| |   |        || | | |    | ||  ||||||||  |||| || || ||||| ||||| ||||| |||||||||||||| |||||||||||||| ||||||||||| || || || ||||| || || ||||
-----------gtatttgaggatacaaaggcaagtcatttatcatatttatttcttgtttatgggaacatatataacttacactcattatcaatttctcgtggatttgcaatgcagTATTTGGTGCAGTCTGCTGTAGATGGTTATAATGTTTGCATATTTGCCTATGGTCAAACTGGCTCTGGAAAGACATTTACAATCTATGGATCTGACAACA

upper sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 22
gtgaatatttcaaatgctatcttttgtgttgatgccatcagtaatataaattttatttctaggactgttcactgagggtttcatatgatgtgttgaatttatgtgatgcagTACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATATGGTCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGATAACA
             | |  ||   |||| || ||  | |   ||    ||  | |||  ||   |||  | ||  |   ||||   |  ||| ||       ||  ||||||||  |||| ||||| ||||| ||||| ||||| |||||||||||||| |||||||||||||| ||||||||||| || || || ||||| || || | ||
-----------gcaagtcataaattgtatttatttcttgcttatggaaacatatataacttacactcattaccaa---tttc---tcgtgtatt-------tgcaatgcagTATTTGGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTATGGTCAAACTGGATCTGGAAAGACATTTACAATCTATGGATCGGACATCA

upper sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 17
lower sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 16
gtgaatatttcaaatgctatcttttgtgttgatgccatcagtaatataaattttatttctaggactgttcactgagggtttcatatgatgtgttgaatttatgtgatgcagTACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATATGGTCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGATAACA
                 |||  ||  | |   |  |     | || ||  ||| ||   | |   | ||  ||   |||| |  |    || ||   ||||       |||||  ||||||| || ||||| ||||| |||||||||||||| ||||||||||||||||||||||||||||| ||||||||||| |||||    || | ||
----------------gtattattgatat--gtaactgtgttcatttacctttcatcctttg--ttattttcttgtggttactaacatcgttttcctttta------acagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA

upper sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 17
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 18
gtgaatatttcaaat-gctatcttttgtgttgatgccatcagtaatataaattttatttctaggactgttcactgagggtttcatatgatgtgttgaatttatgtgat-gcagTACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATATGGTCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGATAACA
          ||| |    ||| |   ||||       | || ||  |   ||| ||| |    | |  |   | | |   |  | |||| | ||  || | | |||| ||||||  |||| ||||| ||||| ||||||||||| || |||||||||||||||||||| ||||||||||||||||| ||||| ||||||||||| |||   |
---------gcaagtcaacatcatgaatgtt-----tgttagcaacttg--tttgattacattaattagtagttcaag---ttgtgtgatattttctatgtttatgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA

upper sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 17
lower sequence: PP1S83_25V6.1 (Physcomitrella patens), 3'ss of exon 19
gtgaatatttcaaatgctatcttttgtgttgatgccatcagtaatataaattttatttctaggactgttcactgagggtttcatatgatgtgttgaatttatgtgatgcagTACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATATGGTCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGATAACA
      |   | | |  |  ||  ||| ||   |   |||  ||  | | | |||||   |  | || |  |||     | |  | | |    ||||| ||     |||||||  |||| ||||||||  ||||||| || || || || || |||||||| || |||||||| || || || ||||| |||||||||||||| || || |
------acacctagttgt-cctgctgttttagggtattcaaaaacttcattgttattc--aataatgatt-ctgtattctgcgca-gctaacatgaatgtaacgtgtgcagTATTTGGTCCAATCAGCGATTGATGGGTACAATGTCTGTATTTTTGCATACGGACAAACTGGATCAGGGAAAACTTTTACTATTTATGGTTCTGAAAATA

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|18384228|gb|BM417427.1|BM417427
EST:     GTGTTTTTGATGCAAACACAAGTCAAGAAGAAATATTTGAGGATACTAAG                         TACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATAT
genomic: GTGTTTTTGATGCAAACACAAGTCAAGAAGAAATATTTGAGGATACTAAGgtgaatattt ... tgtgatgcagTACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATAT
EST: gi|67042488|gb|CO468743.1|CO468743
EST:     TGTTTTTGATGCAAACACAAGTCAAGAAGAAATATTNTCACGATACTAAG                         TACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATAT
genomic: TGTTTTTGATGCAAACACAAGTCAAGAAGAAATATT-TGAGGATACTAAGgtgaatattt ... tgtgatgcagTACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATAT
EST: gi|22489624|gb|BU049547.1|BU049547
EST:     GTGTTTTTGATGCAAACACAAGTCAAGAAGAAATATTTGAGGATACTAAG                         TACCTGGTACAATCAGCTGTTGATGGATATAACGATTTGCATATTTGCATA
genomic: GTGTTTTTGATGCAAACACAAGTCAAGAAGAAATATTTGAGGATACTAAGgtgaatattt ... tgtgatgcagTACCTGGTACAATCAGCTGTTGATGGATATAACG-TTTGCATATTTGCATA
EST: gi|211404724|gb|FL347368.1|FL347368
EST:     GTGTTTTTGATGCAAACACAAGTCAAGAAGAAATATTTGAGGATACTAAG                         TACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATAT
genomic: GTGTTTTTGATGCAAACACAAGTCAAGAAGAAATATTTGAGGATACTAAGgtgaatattt ... tgtgatgcagTACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATAT
EST: gi|18649770|gb|BM498589.1|BM498589
EST:     GTGTTTTTGATGCAAACACAAGTCAAGAAGAAATATTTGAGGATACTAAG                         TACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATAT
genomic: GTGTTTTTGATGCAAACACAAGTCAAGAAGAAATATTTGAGGATACTAAGgtgaatattt ... tgtgatgcagTACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATAT
EST: gi|22489601|gb|BU049524.1|BU049524
EST:     GTGTTTTTGATGCAAACACAAGTCAAGAAGAAATATTTGAGGATACTAAG                         TACCTGGTACAATCAGCTGTTGATGGATATAACGATAGCATATTTGCATAT
genomic: GTGTTTTTGATGCAAACACAAGTCAAGAAGAAATATTTGAGGATACTAAGgtgaatattt ... tgtgatgcagTACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATAT

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: 99

AATTGCACATCCATGGAAAGATGAGAAGTCGAAGCAACATATATATGATCGTGTTTTTGATGCAAACACAAGTCAAGAAGAAATATTTGAGGATACTAAGgtgaatattt ... tgtgatgcagTACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATATGGTCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGATAACA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 20

AATTGCACATCCATGGAAAGATGAGAAGTCGAAGCAACATATATATGATCGTGTTTTTGATGCAAACACAAGTCAAGAAGAAATATTTGAGGATACTAAGgtgaatattt ... tgtgatgcagTACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATATGGTCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGATAACA


Block sizes: 44 (upstream exon), 42 (downstream exon)
Score: 9

AATTGCACATCCATGGAAAGATGAGAAGTCGAAGCAACATATATATGATCGTGTTTTTGATGCAAACACAAGTCAAGAAGAAATATTTGAGGATACTAAGgtgaatattt ... tgtgatgcagTACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATATGGTCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGATAACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 39

AATTGCACATCCATGGAAAGATGAGAAGTCGAAGCAACATATATATGATCGTGTTTTTGATGCAAACACAAGTCAAGAAGAAATATTTGAGGATACTAAGgtgaatattt ... tgtgatgcagTACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATATGGTCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGATAACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctaggactgttcactgagggtttcatatgatgtgttgaatttatgtgatgcagTACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATATGGTCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGATAACA
                                    ttgaatttat  TA-rich tract