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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattatataggctatttaatatatccatcatattgacaaatgtatttcaacggtagtatattgtggttctgatgtttatgtgttcatgcattttggcatattgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGA

Basic information

species Glycine max
transcript GLYMA02G47460.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os08g25734.2 (Oryza sativa), 3'ss of exon 5
gtaaattatataggctatttaatatatccatcatattgacaaatgtatttcaacggtagtatattgtggttctgatgtttatgtgttcatgcattttggcatattgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGA
|||   | |  |   | |  |   |        |   ||  |  | |||| ||   |   |  || |  || |  |  |||||   | |   ||     || | |   |||||||||||||| || ||  ||||||| || || ||||| ||| | |||||||| || ||| | |||||||||||||| || || ||||| ||||||||||| 
gtatgcttt-caatttttacaccttgctgtggctgaagattatggaatttgaagcatgtgaatttataattgtc-tccttatgatataaaatataccatcaaaatatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCCTTCGAAGGTTCTTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGT

upper sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 5
gtaaattatataggctatttaatatatccatcatattgacaaatgtatttcaacggtagtatattgtggttctgatgtttatgtgttcatgcattttggcatattgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGA
          || |   ||||   | | |||  |    |||| |   ||| ||  |  ||  |||   | |    | | |   | ||  ||          |||||  ||||| |||||||| |||||  |  |||| || || ||||| ||||| |||||||| || ||  | |||||||||||||| || || ||||||||||||||||| 
---------gtaag--gtttacattttgcatggtgaaaacaagttacttttaaaag-ggtgcatttctgctgaattttcttcctatttttgagcaaacat-tattgtgtgcagCTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCCATCAAAAGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGT

upper sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G106213_T02 (Zea mays), 3'ss of exon 5
gtaaattatataggctatttaatatatccatcatattgacaaatgtatttcaacggtagtatattgtggttctg-atgtttat-gtgttcatgcattttggcatattgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGA
                             ||  | |  |||  | ||  | || | ||  || |||   || |  |  | ||     | | |    |    |||  ||  | ||| ||||||||||||||  ||||||| || || |||||  ||||||||||||| || ||| | |||||||||||||| || || ||||||||||| ||||| 
---------------------------gtatggtttgtacatgtctacataaa-gttaagatgttgcaattttctagatctaccacttacctttgatcaaacattctgtatacagCTTCTATGATCGTTCTGCTCCAATTTATACGCAACCTAGATATTTGCCTCCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGG

upper sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G163437_T03 (Zea mays), 3'ss of exon 5
gtaaat-tatataggctatttaatata-tccatcatattgaca-aatgtatttcaacggtagtatattgtggttctgatgtttatgtgttcat---gcattttg--gcatattgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGA
|||     || |   ||  | | | |  | ||  | |  |  | || |          ||   || || |  ||   ||   |   || | ||   || |||     ||   ||| | ||| |||||||| |||||  |||||||||| || ||||| ||| || |||| || || ||| | |||||||||||||| || || |||||||||||||| |||
gtatgcacattttcacttctcactgtgctgcagtagaaagttacaacgccgcatgcgtgtcaaatcttataatttcaattagtccctgctgatttagcgtttcccttcaatctgaatacagCTTCTATGACCGTTCTGCTCCAATCTATACACAACCTCGACATCTGCCACCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAGGGA

upper sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G068506_T03 (Zea mays), 3'ss of exon 5
------gtaaattatataggctatttaatatatccatcatattgacaaatgtatttcaacggtagtatattgtggttctgatgtttatgtgttcatgcattttggcatattgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGA
       |  | |    |   |  |  |  |     |   |  |    ||| || ||||  ||  || | | |   |  | |  |  ||  ||  ||         |   ||| | ||| |||||||| ||||   ||||||| || || ||||| ||| |  |||| || || ||| | |||||||||||||| || || ||||||||||||||||||
gtatgctttcacttctcactgtgctgcagttggaagttgcaacgctgcatgcatatcaa--gtcttacaatttcaattagttcctactgatttagtgttccccttaaatctgaatacagCTTCTATGACCGTTTTGCTCCAATTTATACACAACCTCGACACCTGCCACCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGA

upper sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 5
gtaaattatataggctatttaa-tatatccatcatattgacaaatgtatttcaacggtagtat-----attgtggttctgatg---tttatg-tgttcatgcattttggcatattgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGA
|||  || || || | ||   | | ||| |     |||   |  | | || |||| ||    |     |      ||||||||   |||||| | || ||    ||| | |  |  ||||||| ||||| || ||||| |||||||||||||||||||| ||||||||||| || ||||||||||||||||||||||| || ||||||||||||||||| || 
gtag-ttttacagcccatcagactgtatactgtgaattttgatctctgtt-caacagtttctttcattaccacatttctgatgcagtttatgatattaatatggttttgaacttaaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCCATCTAAGATGCTTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGC

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|22929719|gb|BU546858.1|BU546858
EST:     GGAATCACCAAAAAGCCTGTGCCTGACTTCAG                         TTTCTATGATCGTTCATCTCCAATNNACACCCAACCACGATATTNNCCTCC
genomic: GGAATCACCAAAAAGCCTGTGCCTGACTTCAGgtaaattata ... ttgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
EST: gi|51338121|gb|CO981987.1|CO981987
EST:     TTCTATAATGCAAATCTGGGANTCACCAAAAAGCCTGTGCCTGACTTCAG                         TTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAGgtaaattata ... ttgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
EST: gi|15589858|gb|BI674474.1|BI674474
EST:     TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAG                         TTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAGgtaaattata ... ttgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
EST: gi|298174060|gb|HO017396.1|HO017396
EST:     TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAG                         TTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAGgtaaattata ... ttgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
EST: gi|20498182|gb|BQ273112.1|BQ273112
EST:     TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAG                         TTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAGgtaaattata ... ttgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
EST: gi|192316610|gb|FK006817.1|FK006817
EST:     TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGTCTGACTTCAG                         TTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAGgtaaattata ... ttgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
EST: gi|193576586|gb|FK538387.1|FK538387
EST:     TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAG                         TTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAGgtaaattata ... ttgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
EST: gi|6070729|gb|AW100116.1|AW100116
EST:     GCCTGACTTCAG                         TTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
genomic: GCCTGACTTCAGgtaaattata ... ttgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
EST: gi|207752357|gb|GD726226.1|GD726226
EST:     TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAG                         TTTCTATGATCGTTCATCTCCAATCTAC
genomic: TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAGgtaaattata ... ttgattgcagTTTCTATGATCGTTCATCTCCAATCTAC
EST: gi|16277058|gb|BI942182.1|BI942182
EST:     TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAG                         TGTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATGTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAGgtaaattata ... ttgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
EST: gi|20811566|gb|BQ296044.1|BQ296044
EST:     TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAG                         TTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAGgtaaattata ... ttgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
EST: gi|16278915|gb|BI943160.1|BI943160
EST:     TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAG                         TTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAGgtaaattata ... ttgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
EST: gi|13266691|gb|BG370154.1|BG370154
EST:     TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAG                         TTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAGgtaaattata ... ttgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
EST: gi|23728098|gb|BU762095.1|BU762095
EST:     TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAG                         TTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAGgtaaattata ... ttgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
EST: gi|15589806|gb|BI674422.1|BI674422
EST:     TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAG                         TTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAGgtaaattata ... ttgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
EST: gi|15814292|gb|BI786567.1|BI786567
EST:     TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAG                         TTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAGgtaaattata ... ttgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
EST: gi|46492701|gb|CN472257.1|CN472257
EST:     TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAG                         TTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAGgtaaattata ... ttgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatattgtggttctgatgtttatgtgttcatgcattttggcatattgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGA
                                           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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattatataggctatttaatatatccatcatattgacaaatgtatttcaacggtagtatattgtggttctgatgtttatgtgttcatgcattttggcatattgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGA

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