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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattgcctatttgatatatccatcatattgacaaatgtatttcaatgatagtgttttgtggttctgatgtttatgtgttcatgcgttttggcatattgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGA

Basic information

species Glycine max
transcript GLYMA14G01290.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os08g25734.2 (Oryza sativa), 3'ss of exon 5
gtaaattgcctatttg-atatatccatcatattgacaaatgt---atttcaatgatagtgttttgtggttctgatgtttatgtgttcatgcgttttggcatattgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGA
|||   |  | ||||  | |  |   |     |||  | | |   |||| ||  ||     ||| |  || |  |  |||||   | |    |     || | |   |||||||||||||| || ||  ||||||| || || ||||| ||| | |||||||| || ||| | |||||||||||||| || || ||||| ||||||||||| 
gtatgctttcaatttttacaccttgctgtggctgaagattatggaatttgaagcatgtgaatttataattgtc-tccttatgatataaaatataccatcaaaatatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCCTTCGAAGGTTCTTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGT

upper sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 5
gtaaattgcctatttgatatatccatcatattgacaaatgtatttcaatgatagtgttttgtggttctgatgtttatgtgttcatgcgttttggcatattgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGA
||||  |    ||||      | |||  |    |||| | || ||  |  |  |||  ||   | |    | | |   | ||  || |        |||||  ||||| |||||||| |||||  |  |||| || || ||||| ||||| |||||||| || ||  | |||||||||||||| || || ||||||||||||||||| 
gtaaggtttacattt------tgcatggtgaaaacaagt-tacttttaaaagggtgcatttctgctgaattttcttcctatttttgagcaaacat-tattgtgtgcagCTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCCATCAAAAGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGT

upper sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G106213_T02 (Zea mays), 3'ss of exon 5
gtaaattgcctatttgatatatccatcatattgacaaatgtatttcaatgatagtgttttgtggttctgatgtttatgtgttcatgcgttttggcatattgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGA
            | || | | | |||  | |  | |||    ||   ||| |    |||| | | |||     |||  | |      | |    |||  ||  | ||| ||||||||||||||  ||||||| || || |||||  ||||||||||||| || ||| | |||||||||||||| || || ||||||||||| ||||| 
-----------gtatggtttgtacat-gtctacataaa---gttaagatgttgcaattttctagatctaccacttaccttt------gatcaaacattctgtatacagCTTCTATGATCGTTCTGCTCCAATTTATACGCAACCTAGATATTTGCCTCCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGG

upper sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G163437_T03 (Zea mays), 3'ss of exon 5
----gtaaattgcctatttgatatatccatcatattgacaaatgtatttcaatgatagtgtt-----ttgtggttctgatgtttatgtgttcat---gcgttttg--gcatattgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGA
    | | |||  |  ||     | | |  ||  | || |  |  |   |       ||||      || |  ||   ||   |   || | ||   ||||||     ||   ||| | ||| |||||||| |||||  |||||||||| || ||||| ||| || |||| || || ||| | |||||||||||||| || || |||||||||||||| |||
gtatgcacattttcacttctcactgtgctgca-gtagaaagttacaacgccgcatgcgtgtcaaatcttataatttcaattagtccctgctgatttagcgtttcccttcaatctgaatacagCTTCTATGACCGTTCTGCTCCAATCTATACACAACCTCGACATCTGCCACCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAGGGA

upper sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G068506_T03 (Zea mays), 3'ss of exon 5
gtaaattgcctatttgatatatccatcatattgacaaatgtatttcaatg-----atagtgttttgtggttctgat--gtttatg-tgttcatgcgttttggc--atattgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGA
|||   |  |  ||     | | |  ||  |||  |  || |   |         ||   || ||    ||   ||  |||  |  || |   | |||       |   ||| | ||| |||||||| ||||   ||||||| || || ||||| ||| |  |||| || || ||| | |||||||||||||| || || ||||||||||||||||||
gtatgctttcacttctcactgtgctgca-gttggaagttgcaacgctgcatgcatatcaagtcttacaatttcaattagttcctactgatttagtgttccccttaaatctgaatacagCTTCTATGACCGTTTTGCTCCAATTTATACACAACCTCGACACCTGCCACCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGA

upper sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 5
gtaaatt----gcctatttga---tatatccatcatattgacaaatgtatttcaatgatagtgttt--tgtggttctgatg---tttatg-tgttcatgcgttttggcatattgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGA
|||  ||    ||| ||  ||   ||||      || ||||    |||    || |     |  ||       ||||||||   |||||| | || ||  | ||| | |  |  ||||||| ||||| || ||||| |||||||||||||||||||| ||||||||||| || ||||||||||||||||||||||| || ||||||||||||||||| || 
gtagttttacagcccatcagactgtatactgtgaattttgatctctgttcaacagtttctttcattaccacatttctgatgcagtttatgatattaatatggttttgaacttaaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCCATCTAAGATGCTTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGC

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|120494929|gb|EH223096.1|EH223096
EST:     GCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAG                         TTTCTATGATCGTTCATCTCCAATCTACACCCAACCACTATATTTGCCTCC
genomic: GCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAGgtaaattgcc ... ttgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
EST: gi|22522873|gb|BU081684.1|BU081684
EST:     TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAG                         TTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAGgtaaattgcc ... ttgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
EST: gi|15287005|gb|BI470896.1|BI470896
EST:     TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAG                         TTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAGgtaaattgcc ... ttgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
EST: gi|10238679|gb|BE807567.1|BE807567
EST:     GGCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAG                         TTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAGgtaaattgcc ... ttgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
EST: gi|17518996|gb|BM188038.1|BM188038
EST:     TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAG                         TTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAGgtaaattgcc ... ttgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
EST: gi|51335512|gb|CO979378.1|CO979378
EST:     TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAG                         TTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAGgtaaattgcc ... ttgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
EST: gi|10232477|gb|BE801365.1|BE801365
EST:     AAAAAGCCTGTGCCTGACTTCAG                         TTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
genomic: AAAAAGCCTGTGCCTGACTTCAGgtaaattgcc ... ttgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
EST: gi|5770728|gb|AI973902.1|AI973902
EST:     CAAAAAGCCTGTGCCTGACTTCAG                         TTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
genomic: CAAAAAGCCTGTGCCTGACTTCAGgtaaattgcc ... ttgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
EST: gi|7640498|gb|AW734799.1|AW734799
EST:     TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAG                         TTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAGgtaaattgcc ... ttgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttttgtggttctgatgtttatgtgttcatgcgttttggcatattgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGA
                                           tattgat  putative branch site (score: 3)
                                          atattgatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattgcctatttgatatatccatcatattgacaaatgtatttcaatgatagtgttttgtggttctgatgtttatgtgttcatgcgttttggcatattgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT