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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatattgctccgttcctgtaaacatttttgttccaccctactgctttccctcccctgttcaagtatataacttttgtcaaacctgtggcacatctgtagGCTGCGAAAGAATATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCT

Basic information

species Zea mays
transcript GRMZM2G057576_T02
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 19
gtaaatattgctccgttcctgtaaacatttttgttccaccctactgctttccctcccctgttcaagtatataacttttgtc-aaacctgtggcacatctgtagGCTGCGAAAGAATATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCT
         |     || ||      | ||| |  |  ||||  |   |  | || |   ||   |  | | | | || || |||| |||| || ||||| ||||||| |||||||| ||||| || ||||| |||||||||||||||||| | ||||| |||||||||||||| |||||||| ||||||||||||||| | |
---------gtatttttgctacgtttagttt-gaccttcccttttttgtcacttctcacatt---ggttctgattattatcgaaacatgtgtcatatctgcagGCTGCCAAAGAATACTCTGAGCAGCTAGGGGTTGATGCTTGCATAAAACTGTTTGAGCAATTCAAATCTTACGAGGGCCTTTACTTTTTCTTGGGAGCTT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 19
gtaaatattgctccgttcctgtaaacatttttgttccaccctactgctttccctcccctgttcaagta--tataacttttgtc-aaacctgtggcacatctgtagGCTGCGAAAGAATATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCT
              ||   ||     |  |||  |  | ||| |   |||   || | | |   | |   | | | | || || |||| |||| || ||||| ||||||| |||||||| ||||| || ||||| |||||||||||||||||| | ||||| |||||||||||||| |||||||| ||||||||||||||| | |
--------------gtatttgc---tacatttagtttaaccttcccttttttgtcacttctcacattggttctgattattatcgaaacatgtgtcatatctgcagGCTGCCAAAGAATACTCTGAGCAGCTAGGGGTTGATGCTTGCATAAAACTGTTTGAGCAATTCAAATCTTACGAGGGCCTTTACTTTTTCTTGGGAGCTT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 18
gtaaatattgctccgttcctgtaaacatttttgttccaccctactgctttccctcccctgttcaagtatataacttttgtcaaacctgtggcacatctgtagGCTGCGAAAGAATATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCT
                   || ||  ||  | ||    |  ||               | ||  | |  ||||||   |  ||     |  |  || | |||| ||| |||||||||| ||||||| | || |||||||||||||||||  | ||||| || ||||  || ||||| || || || |||||| ||||||| |
----------------gtatgaaactatcatcgtctt-ctataacatggaattattaatatttgattg-ataact---gaaaacttactaactaatatttagGTTGCTAAAGAATATTGTGAACAATTGGGCGTTGATGCTTGCATAAAGCTTTTTGAGCAGTTCAGGTCATATGAAGGGCTGTATTTTTTCCTGGGATCAT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 19
--gtaaatattgctccgttcctgta-aacatttttgttccaccctactgctttccctcccctgttcaagtatataacttttgtcaaacctgtggcacatctgtagGCTGCGAAAGAATATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCT
       |  ||     ||     | || | |  ||||| |   || |  ||    ||| |  ||||  ||||  |      ||  ||  ||      | || || |||| || ||||||||||| ||  | || |||||||| ||||| ||| | ||||| ||||||||||| ||||| || || ||||||||||||||  | |
gtactgtttctggataattttgccataagagtcatgttctattttattttttgaattccgcaattcatctataagaaa---atcttactagtacatggtttgcagACTGCTAAGGAATATTCTGAGCAGTTGGGTGTTGATGCATGCATTAAACTCTTTGAGCAATTCAAATCCTATGAAGGACTATACTTTTTCTTGGGTGCAT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 17
gtaa-atattgctccgttcctgtaaacatttttgttccaccctactgctttccctcccctgttcaag-----tatataacttttgtcaaa----cctg-tggcacat---ctgtagGCTGCGAAAGAATATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCT
|||   ||||    | |    ||    ||  |  |||||   || |  |  |  |   || ||   |     | ||||| ||   | |||    | |  | | ||||    || || |||| || ||||||| |||||| || || |||||||| ||||| ||| | ||||| |||||||| || ||||| || || ||||||||||||||  | |
gtactgtattagggcttggtagtcggtataatgtttccatgatatttttaacaattatctttttttggtttttttataatttcaataaaagaatcttactagtacatgatttgcagACTGCTAAGGAATATTGTGAACAGCTGGGTGTTGATGCATGCATTAAACTCTTTGAGCAATTCAAGTCCTATGAAGGACTATACTTTTTCTTGGGTGCAT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 18
gtaaatattgctccgttcctgtaaacatttttgttccaccctactgctttccctcccctgttcaagtatataacttttgtcaaacctgtggcacatctgtagGCTGCGAAAGAATATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCT
                   | |  | | | |  ||     |||   | |    |      |    |  |  ||||   |  |      |  |   | | |||| ||| |||||||||| ||||||| | || |||||||||||||||||  | ||||| || ||||  || ||||| || || || |||||| ||||||| |
------------------gtatgga-actatcattgtcttctataacatggaattattaatatttgattgaaact---gaaagcttactaacttctgtctagGTTGCTAAAGAATATTGTGAACAATTGGGCGTTGATGCTTGCATAAAGCTTTTTGAGCAGTTCAGGTCATATGAAGGGCTGTATTTTTTCCTGGGATCAT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 19
------------------gtaaatattgctccgttcctgtaaacatttttgttccaccctactgctttccctcccctgttcaagtatataacttttgtcaaacctgtggcacatctgtagGCTGCGAAAGAATATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCT
                  |||     |     ||| |  | |  |||||| | | |   || |  |||   |    |  | |  | |||||      ||  ||  ||     || || || |||| || ||||||| |||||| || || || ||||| ||||| ||| | ||||| |||||||| || ||||| || || ||||||||||||||  | |
gtactgtattagggcttggtagtcggtataatgtttccatga-tattttt-tacaattatatttttttgggtttttttataatttctataaaaga-atcttactagtacattatttgcagACTGCCAAGGAATATTGTGAACAGCTCGGTGTAGATGCATGCATTAAACTCTTTGAGCAATTCAAGTCCTATGAAGGACTATACTTTTTCTTGGGTGCAT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 19
--gtaaatattgctc--cgttcctgtaaacatttttgttccaccctactgctttccctcccctgttcaagtatataacttttgtcaaacctgtggcacatctgtagGCTGCGAAAGAATATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCT
       |  ||      ||| |  |||  |||  ||||| |   || |  ||    ||| |  ||||  ||||  |      ||  ||  ||     || |  || |||| || ||||||||||| ||  | || |||||||| ||||| ||| | ||||||||||||||||| ||||| ||  | ||||||||||||||  | |
gtactgtttctgtataatgttgccataag-attcatgttctattttattttttgaattccacaattcatctataagaga---atcttactagtacatgatttacagACTGCTAAGGAATATTCTGAGCAGTTGGGTGTTGATGCATGCATTAAACTCTTTGAACAATTCAAATCCTATGAAGGATTATACTTTTTCTTGGGTGCAT

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|15188223|gb|BI417200.1|BI417200
EST:     AGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTGTGCAG                         GCTGCGAAAGAATATT
genomic: AGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTGTGCAGgtaaatattg ... acatctgtagGCTGCGAAAGAATATT
EST: gi|22489541|gb|BU049464.1|BU049464
EST:     AGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTGTGCAG                         GCTGCGAAAGAATATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTA
genomic: AGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTGTGCAGgtaaatattg ... acatctgtagGCTGCGAAAGAATATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTA
EST: gi|18053133|gb|BM318791.1|BM318791
EST:     AGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTGTGCAG                         GCTGCGAAAGAATATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTA
genomic: AGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTGTGCAGgtaaatattg ... acatctgtagGCTGCGAAAGAATATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTA
EST: gi|15313673|gb|BI478897.1|BI478897
EST:     AGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTGTGCAG                         GCTGCGAAAGAATAT
genomic: AGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTGTGCAGgtaaatattg ... acatctgtagGCTGCGAAAGAATAT
EST: gi|32928656|gb|CF033468.1|CF033468
EST:     AGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTGTGCAG                         GCTGCGAAAGAATATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTA
genomic: AGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTGTGCAGgtaaatattg ... acatctgtagGCTGCGAAAGAATATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTA
EST: gi|88758497|gb|DY542866.1|DY542866
EST:     AGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTGTGCAG                         GCTGCGAAAGAATATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTA
genomic: AGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTGTGCAGgtaaatattg ... acatctgtagGCTGCGAAAGAATATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTA
EST: gi|32929052|gb|CF033864.1|CF033864
EST:     AGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTGTGCAG                         GCTGCGAAAGAATATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTA
genomic: AGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTGTGCAGgtaaatattg ... acatctgtagGCTGCGAAAGAATATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTA

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: 182

TGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGCATGAAGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTGTGCAGgtaaatattg ... acatctgtagGCTGCGAAAGAATATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 168

TGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGCATGAAGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTGTGCAGgtaaatattg ... acatctgtagGCTGCGAAAGAATATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

TGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGCATGAAGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTGTGCAGgtaaatattg ... acatctgtagGCTGCGAAAGAATATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 208

TGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGCATGAAGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTGTGCAGgtaaatattg ... acatctgtagGCTGCGAAAGAATATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccctcccctgttcaagtatataacttttgtcaaacctgtggcacatctgtagGCTGCGAAAGAATATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCT
                    atataac  putative branch site (score: 208)
                aagtatataactttt  TA-rich tract