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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatatttcaaatgctatcttttgtgttgatgccgtcggtaatacaaattttatttctaagattgttggcttcatatgatctgttgaatttatgttcattttgggtttcatatgatctgttgaatttatgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA

Basic information

species Zea mays
transcript GRMZM2G070273_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 18
gtgaatatttcaaatgctatcttttgtgttgatgccgtcggtaatacaaattttatttctaagattgttggcttcatatgatctgttgaatttatgttcattttgggtttcatatgatc-tgttgaatttatgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA
|| | ||||| || || || | | | ||| || | | |||| | || || || | ||| || | | ||||||| ||||||||||||||| || ||||| || ||||||||||||||||| ||||||||||| ||||| ||||||||||||||||| ||||| || |||||||| || |||||||
----------------------------------------gtgaccttttttttaacacttc--tttttaacat-acatgtgctcattagattatttgcaatt-ggactccatgtgtttatcatgaattt-tgtgatgcagTATCTAGTTCAATCGGCCGTTGATGGATATAATGTTTGTATATTTGCTTATGGGCAAACTGGTTCTGGAAAAACTTTTACAATTTATGGATCTGAAAACA

upper sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 19
--gtgaatatttcaaatgctatcttttgtgttgatgccgtcggtaatacaaattttatttctaagattgttggcttcatatgatctgttgaatttatgttcattttgggtttcatatgatctgttgaatttatgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA-------
| | ||| ||||| || | | || ||| | | || | | | || | || | || | || | | ||||| ||||| | | | ||| ||| | | || |||||||| | || ||||| ||||| ||||| |||||||| || |||||||| ||||| ||||||||||||||||||||||| || || ||||| |||||||
gtcttagtataacaaattatagatcatagttttttgctttagatagcatatacatt------gaaatgg--------atttaatattt----tttatactcattaccaatgtttt----tcttttggaaatttgcaatgcagtacttagTGCAATCTGCTGTGGATGGTTATAATGTTTGCATATTTGCTTATGGTCAAACTGGTTCTGGAAAGACTTTTACAATCTATGGAGTTGAAAACAATCCTGG

upper sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA11G09480.1 (Glycine max), 3'ss of exon 19
gtgaatatttcaaatgctatcttttgtgttgatgccgtcggtaatacaaattttatttctaagattgttggcttcatatgatctgttgaatttatgttcattttgggt-ttcatatgat-ctgttgaatttatgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA
|| | || || | | || | | |||| | | |||| | | | || || ||| | | | || | | | || | | || ||| | | || |||||||| | || ||||| ||||| ||||| |||||||| || |||||||| || || |||||||||||||| |||||||| || || ||||| | |||||||
---------------gcaagtcttagtataacaa--attaaagatcctagttttttgctttagataatatgtacattgaaatagatttaatatttttctatactcattactaatgtttttcttttggacatttgcaatgcagTACTTAGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTACGGTCAAACTGGTTCTGGGAAGACTTTTACAATCTATGGAGCTGAAAACA

upper sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 19
gtgaatatttcaaatgctatcttttgtgttgatgccgtcggtaatacaaattttatttctaagattgttggcttcatatgatctgttgaatttatgttcattttgggtttcatatgatctgttgaatttatgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA
| | || ||| | || || || | | || | | ||| | | || | | | || ||| ||||| | |||| || | || ||||||||| |||| || || ||||| ||||| |||||||| || |||||||| ||||| |||||||| ||||||||||| || || || ||||| || || ||||
---------------------gtatttgaggatacaaa-ggcaagtcatttatcatattt---atttcttgtttatgggaacatatataacttacactcattatcaatttctcgtggatt----------tgcaatgcagTATTTGGTGCAGTCTGCTGTAGATGGTTATAATGTTTGCATATTTGCCTATGGTCAAACTGGCTCTGGAAAGACATTTACAATCTATGGATCTGACAACA

upper sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 22
gtgaatatttcaaatgctatcttttgtgttgatgccgtcggtaatacaaattttatttctaagattgttggcttcatatgatctgttgaatttatgttcattttgggtttcatatgatctgttgaatttatgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA
| || ||| |||| ||||| ||| | |||| | | | || ||| ||||| |||| || | | || ||||||||| |||| ||||| ||||| ||||| |||||||| || |||||||| ||||| |||||||| ||||||||||| || || || ||||| || || | ||
------------------------------------gcaagtcata--aattgtattt-----atttcttgcttatggaaacatatataacttacactcattaccaatttctcgtg----------tatttgcaatgcagTATTTGGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTATGGTCAAACTGGATCTGGAAAGACATTTACAATCTATGGATCGGACATCA

upper sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 17
lower sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 16
gtgaatatttcaaatgctatcttttgtgttgatgccgtcggtaatacaaattttatttctaagattgttggcttcatatgatctgttgaatttatgttcattttgggtttcatatgatctgttgaatttatgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA
| ||||| || | | || ||||| | | ||| | | | ||| | || || ||| ||| || | |||||| ||||||| || ||||| ||||| ||||| || || || ||||| ||||| ||||||||||||||||| ||||||||||| ||||| || | ||
-------------------------------------------------gtattattgatatg-taactgtgttcatttacctttcatcctttgttattttcttgtggttactaacatc-gttttcctttta----acagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA

upper sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 17
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 18
gtgaatatttcaaatgctatcttttgtgttgatgccgtcggtaatacaaattttatttctaagattgttggcttcatatgatctgttgaatttatgttcattttgggtttcatatgatctgttgaatttatgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA
| || ||| | | | | ||||| || | || | || ||| || | || ||| | || | | |||||| |||||||| |||| ||||| ||||| |||||||||||||| || |||||||| ||||| || ||||||||||||||||| ||||| ||||||||||| || |
----------------------------------------gcaagtcaacatc---atgaatgtttgttagca--acttgtttgattacattaattagtagttcaagttgtgtgatattttctatgtttatg-attgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA

upper sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 17
lower sequence: PP1S199_47V6.1 (Physcomitrella patens), 3'ss of exon 20
-------------------------------gtg-aatatttcaa--atgctatcttttgtgttgatgccgtcggt---aatacaaattttattt-ctaagattgttggcttcatatgatctgttgaatttatgtt------cattttgggtttcatatgatctgttgaatttatgtg-atgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA
||| ||| ||| | ||| || || |||| | | | || ||| | |||| | | | || || |||| | || | | | |||| || | ||| | || || |||||||| |||| |||||||| |||| ||||| ||||||||||||||||| || || |||||||| || || || || || || ||||| ||||| || ||||
gtatagttggtcagagtaattgagtcaatccgtgcaatctttttatcatggaatggctttggttgtaactactgatcccgatgagaataaaaccaactaaaagaccttgattagatcgacttgtttatttggtatcattgaatactttgtcttctgcgcg-tctaacgtgctttaatgtgtgcagTATTTGGTCCAATCAGCAATTGACGGATACAATGTCTGTATATTTGCATACGGGCAAACTGGGTCAGGCAAAACGTTTACGATTTACGGTTCTGACAACA

upper sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 17
lower sequence: PP1S83_25V6.1 (Physcomitrella patens), 3'ss of exon 19
gtgaatatttcaaatgctatcttttgtgttgatgccgtcggtaatacaaattttatttctaagattgttggcttcatatgatctgttg--aatttatgttcattttgggtttcatatgatctgt-tgaatttatgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA
| || | || | || | |||| | | ||| | | || | ||| || || ||||| || |||||||| |||| |||||||| ||||||| || ||||||||||| ||||| || || |||||||| || || || ||||| |||||||||||||| ||||| |
-------------------------------------------acacctagttgtcctgctgttttagggtattcaaaaacttcattgttattcaataatgattctgtattctgcgcagctaacatgaatgtaacgtgtgcagTATTTGGTCCAATCAGCGATTGATGGGTACAATGTCTGTATTTTTGCATACGGACAAACTGGATCAGGGAAAACTTTTACTATTTATGGTTCTGAAAATA

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|211116600|gb|FL350312.1|FL350312
EST:     GTGTTTTTGATGCAAACACAAGTCAAGAAGAAGTCTTTGAGGATACTAAG                         TATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTAT
genomic: GTGTTTTTGATGCAAACACAAGTCAAGAAGAAGTCTTTGAGGATACTAAGgtgaatattt ... tgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTAT




















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: 48 (upstream exon), 48 (downstream exon)
Score: 84

AATTTCACATCCATGGAAAGATGAAAAGTCAAAGCAACATATATATGATCGTGTTTTTGATGCAAACACAAGTCAAGAAGAAGTCTTTGAGGATACTAAGgtgaatattt ... tgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 11

AATTTCACATCCATGGAAAGATGAAAAGTCAAAGCAACATATATATGATCGTGTTTTTGATGCAAACACAAGTCAAGAAGAAGTCTTTGAGGATACTAAGgtgaatattt ... tgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 15

AATTTCACATCCATGGAAAGATGAAAAGTCAAAGCAACATATATATGATCGTGTTTTTGATGCAAACACAAGTCAAGAAGAAGTCTTTGAGGATACTAAGgtgaatattt ... tgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 36

AATTTCACATCCATGGAAAGATGAAAAGTCAAAGCAACATATATATGATCGTGTTTTTGATGCAAACACAAGTCAAGAAGAAGTCTTTGAGGATACTAAGgtgaatattt ... tgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaatttatgttcattttgggtttcatatgatctgttgaatttatgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA
     tttatgttcatttt  TA-rich tract