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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAATTTTTGAGGGACATTCACACTATGTGATGCAGGTTACTTTCAACCCAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttgacaatattatggagcaagatgttagttgcgactgagtcaagatgtgatcttgttcattcatacttctcactctgaaattgtag

Basic information

species Zea mays
transcript GRMZM2G095348_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 6
TCAAATTTTTGAGGGACATTCACACTATGTGATGCAGGTTACTTTCAACCCAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttgacaata--ttatggagcaagatgttagttgcgac---tgagtcaagatgtgat--cttgttcattcatacttctcactctgaaattgtag
|||||| |||||||||||||||||||| |||||||| ||||||||||| |||||||||| ||||||||||||||||||||||||||| || |||||||||||  |  |  |||||   ||||| ||   ||||||| |  | |    ||  |    ||| | |   |||| || | ||  |||| |  ||||||    ||
TCAAATCTTTGAGGGACATTCACACTACGTGATGCAAGTTACTTTCAATCCAAAGGATACTAACACTTTTGCAAGTGCATCTCTTGACCGAACTACAAAGgtctgtttc-acaatctcttatgcagtg-gatgttattcacaatatatggctttttatgaggtgatttgtgcactaatggttctaaaactgaaacaacag

upper sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA07G03890.1 (Glycine max), 5'ss of exon 6
TCAAATTTTTGAGGGACATTCACACTATGTGATGCAGGTTACTTTCAACCCAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgcct-tgacaatattatggagcaag----atgttagttgcgactgagtcaagatgtg-atcttgttcattcatacttctcactctgaaattgtag----------
 || || |||||||||||||| || ||||| ||||| || || || || || || || |  ||||| ||||| |||||||||||||||||||| | ||||||   | | ||    | ||         |       ||   |  |  |   || | |     ||  |    ||| | |  |       | |  || |            
CCAGATATTTGAGGGACATTCTCATTATGTCATGCAAGTGACATTTAATCCTAAAGACACAAACACCTTTGCCAGTGCATCTCTTGATCGCACCATAAAGgtatacatgtgttcttcttgctagttgtgtcctgcattttctttgtttatttccaaacacctatgataaaaattaaaaagtaatgtattaatgttatcttttcttgcag

upper sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 6
TCAAATTTTTGAGGGACATTCACACTATGTGATGCAGGTTACTTTCAACCCAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgcct-tgacaatattatggagcaagatgtt-----agttgcgactgagtcaagatgtgatct-tgttcat-tcatacttctcactc-tgaaattgtag--------------
 || || ||||| || ||||| || ||||| ||||| || || || || || || || |  ||||| ||||||||||||||||||||||| || | |||||||    | ||    | ||   |         ||     |      |   ||| || |    | || || || | | |||     || |  || || |||                
CCAGATATTTGAAGGTCATTCTCATTATGTCATGCAAGTAACATTTAATCCCAAAGACACAAACACCTTTGCAAGTGCATCTCTTGATCGGACAATAAAGgtgtaattatgttcttgttcctggatgtttcttttttaaaaaaaaaaaaaagtaaaaagaaaaactatgatcctatgatataatgcattgatgcaactgttatcatctcttttcag

upper sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 6
TCAAATTTTTGAGGGACATTCACACTATGTGATGCAGGTTACTTTCAACCCAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgc---------cttgacaata-ttatggagcaagat------gttagttgcgactgagtcaagatgtgatcttgt---tcattcatacttctcactctgaaattgtag
 || || |||||||||||||| || ||||| ||||| || || || || || || || |  ||||| ||||| |||||||||||||||||||| | ||||||             |||  |  || || ||     |  |      |||  || | |   |   | |||   |  ||     | ||  ||   | | | |||  ||||| ||
CCAGATATTTGAGGGACATTCTCATTATGTCATGCAAGTGACATTTAATCCTAAAGACACAAACACCTTTGCCAGTGCATCTCTTGATCGCACCATAAAGgtatatacatgtgttcttctcgctagttgtgtcctgaattttctttgtttatttccatacatctatgataaaaatttaaaagtaatgtattaatgtta-tcttcaattgcag

upper sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 5'ss of exon 6
TCAAATTTTTGAGGGACATTCACACTATGTGATGCAGGTTACTTTCAACCCAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgc-gccttgacaatattatggagcaagatgttagttgcgactgagtcaagatgtgatcttgttcattcatacttctcactctgaaattgtag
||| || || |||||||| ||||||||||||||||| || || || || ||||| || |  ||||||||||| |||||||| |||||||| || | |||||||| |   ||     |   || | ||  ||  | |||  | | |  |       | ||  |     | ||| | | |   |||  |       
TCAGATATTCGAGGGACACTCACACTATGTGATGCAAGTCACATTTAATCCAAAAGACACCAACACTTTTGCCAGTGCATCCCTTGATCGTACCATAAAGgtgctgaaatggtctaacattgaaacatcattatggtttagtccgcttagtccgctcattctacgtttacatgcatgttcatcttcag------

upper sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT3G15980.3 (Arabidopsis thaliana), 5'ss of exon 6
TCAAATTTTTGAGGGACATTCACACTATGTGATGCAGGTTACTTTCAACCCAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttgacaatattatggagcaagatgttagttgcgactgagtcaagatgtgatcttgttcattcatacttctcactctgaaattgtag---------------
||| || |||||||||||||| |||||||||||||| ||    || || ||||| ||||  ||||||||||| ||||| || |||||||| || | ||||||| |   | | |     | | |   || | |||     | || ||| |  | | | |  | || |       |||| |  || |  ||   |               
TCAGATATTTGAGGGACATTCGCACTATGTGATGCAAGTGGTATTTAATCCAAAAGATACCAACACTTTTGCCAGTGCTTCGCTTGATCGTACCATAAAGgtgtg---taagaggtccaagcactgagctttta----tggcttagttagcacgaggtacttttaaaagggttttcttagactaattttcatgcttgttcatattcag

upper sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 6
TCAAATTTTTGAGGGACATTCACACTATGTGATGCAGGTTACTTTCAACCCAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttgacaatattatggagcaagatgttagttgcgactgagtcaagatgtgatcttgttcatt-----catacttctcactctgaaattgtag------------
||| || |||||||| || || || ||||||||||| || || || || ||||| ||||  ||||||||||| ||||||||||| |||||||| |  |||||  |   ||    |  | | | ||||  |||||  |||   |   |    || |    |  |  | |       | ||  | |  ||   ||  ||             
TCAGATCTTTGAGGGCCACTCTCATTATGTGATGCAAGTGACATTTAATCCAAAAGATACCAACACTTTTGCTAGTGCATCTCTGGATCGCACCATTAAGgtatgatctggattttctgttg-gcaacttgttaactgcatttttttaccaattttgcttcatcaagtatgagtgtgctatttatgctctgatgatatctccttttccag

upper sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 6
TCAAATTTTTGAGGGACATTCACACTATGTGATGCAGGTTACTTTCAACCCAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttgacaatattatggagcaagatgtt----agttgcgactgagtcaagatgtgatcttgttcattcatactt--ctcactctga-aattgtag-
||| |||||||| || ||||| ||||| |||||||| || || || || ||||| || |  ||||| ||||||||||| || || |||||||||| ||||||| |  | || ||| ||       ||  ||||    | |||    || ||    ||||  |  |||| || | | | |   | | | |    |||||   
TCAGATTTTTGAAGGGCATTCTCACTACGTGATGCAAGTGACATTTAATCCAAAAGACACCAACACCTTTGCAAGTGCCTCCCTCGATCGCACTATAAAGgtgtgagtgga-aatgtttcttgataacctgttgtgaacttgaagatgtgtttcaatgtcctaatgttgatccttccatagttgattttattgattgtgtg

upper sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 5
lower sequence: PP1S61_1V6.1 (Physcomitrella patens), 5'ss of exon 6
TCAAATTTTTGAGGGACATTCACACTATGTGATGCAGGTTACTTTCAACCCAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttga------caatattatggagcaagatgttagttgc--gactgagt---caagatgtgatcttgttcattcatacttctcactctgaaattgtag
 ||||| |||||||| |||||||| ||||| ||||| || ||  ||||||| ||||| |  |||||||| |||||||||||| | |||||||| |  ||||| |  ||  |      ||    |   | ||| | |  |  |||   ||  ||||   ||    |  |  ||||      ||| || | | | |   | |    
CCAAATCTTTGAGGGGCATTCACATTATGTCATGCAAGTGACCATCAACCCGAAGGACAACAACACTTTCGCAAGTGCATCTTTAGATCGCACCATCAAGgtacttctgaagtgatgcagcgcttctgggcatgtttatgcttgtttgaaagagtattcactcagctaaattgtgtcaaaatatttttgattttattact----

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|78122343|gb|DV540727.1|DV540727
EST:     CAAAGGATATTAACACTTTTGCGAGTGCATCTCTTGATCGCACTACAAAG                         ATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAA
genomic: CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttg ... gaaattgtagATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAA
EST: gi|18654986|gb|BM499791.1|BM499791
EST:     CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGACCGCACTACAAAG                         ATATGGAGTTTAGGTTCTCCAGATCCAAACTTCA
genomic: CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttg ... gaaattgtagATATGGAGTTTAGGTTCTCCAGATCCAAACTTCA
EST: gi|22489991|gb|BU049914.1|BU049914
EST:     CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGACCGCACTACAAAG                         ATATGGAGTTTAGGTTCTCCAGATCCAA-CTTCAC-CTTGA
genomic: CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttg ... gaaattgtagATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGA
EST: gi|18655044|gb|BM499849.1|BM499849
EST:     CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGACCGCACTACAAAG                         ATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAA
genomic: CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttg ... gaaattgtagATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAA
EST: gi|18655016|gb|BM499821.1|BM499821
EST:     CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGACCGCACTACAAAG                         ATATGGAGTTTAG
genomic: CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttg ... gaaattgtagATATGGAGTTTAG
EST: gi|32930849|gb|CF035661.1|CF035661
EST:     CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAG                         ATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAA
genomic: CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttg ... gaaattgtagATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAA
EST: gi|89106409|gb|DY576626.1|DY576626
EST:     CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGACCGCACTACAAAG                         ATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAA
genomic: CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttg ... gaaattgtagATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAA
EST: gi|22489999|gb|BU049922.1|BU049922
EST:     CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGACCGCACTACAAAG                         ATATGGAGTTTAGGTTCTCCAGATCCAAACTTCAC-CTTGATGGACATCAA
genomic: CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttg ... gaaattgtagATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAA
EST: gi|18649626|gb|BM498445.1|BM498445
EST:     CAAAGGATATTAACACTTTAGCAAGTGCATCTCTTGACCGCACTACAAAG                         ATATGGAGTTTAGGTTCT
genomic: CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttg ... gaaattgtagATATGGAGTTTAGGTTCT
EST: gi|32933566|gb|CF038378.1|CF038378
EST:     CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAG                         ATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAA
genomic: CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttg ... gaaattgtagATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAA
EST: gi|18661996|gb|BM501688.1|BM501688
EST:     CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGACCGCACTACAAAG                         ATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTGGATGGACATCAA
genomic: CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttg ... gaaattgtagATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAA
EST: gi|18450688|gb|BM428966.1|BM428966
EST:     CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGC-CGCACTACAAAG                         ATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAA
genomic: CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttg ... gaaattgtagATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAA

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), 49 (downstream exon)
Score: 184

TCAAATTTTTGAGGGACATTCACACTATGTGATGCAGGTTACTTTCAACCCAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttg ... gaaattgtagATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAAAAGGGTGTCAATTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 156

TCAAATTTTTGAGGGACATTCACACTATGTGATGCAGGTTACTTTCAACCCAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttg ... gaaattgtagATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAAAAGGGTGTCAATTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 172

TCAAATTTTTGAGGGACATTCACACTATGTGATGCAGGTTACTTTCAACCCAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttg ... gaaattgtagATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAAAAGGGTGTCAATTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 141

TCAAATTTTTGAGGGACATTCACACTATGTGATGCAGGTTACTTTCAACCCAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttg ... gaaattgtagATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAAAAGGGTGTCAATTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT