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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacataatttcttgaatatttttgcagctttctgatgtttctgttttcttcatgtaaaatatgttgatgtgatttgtcatgccaattgtagCCTGATTTTCATGTCAAAGAAAAGATACTGGTTCTTGTAGATACTTGGCAAGAAGCTTTTGGAGGCCCAAGGGCAAGATATCCACAATATTATGCTGCAT

Basic information

species Glycine max
transcript GLYMA17G26440.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G26440.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g22650.1 (Oryza sativa), 3'ss of exon 3
gtatacataatttcttgaatatttttgcagctttctgatgtttctgttttcttcatgtaaaatatgttgatgtgatttgtcatgccaattgtagCCTGATTTTCATGTCAAAGAAAAGATACTGGTTCTTGTAGATACTTGGCAAGAAGCTTTTGGAGGCCCAAGGGCAAGATATCCACAATATTATGCTGCAT
                   | |  |  || || | ||||||   |   | ||  | |   || || ||||| |   ||||  ||    || |||||||||| |||||| ||||| ||||||||  ||||  |||| |||||||||||||||||||| ||  |  | ||||||||||| ||||||||||  ||||
------------------gtctgctaaca-ctgtttgatgtccttccatgctgaaagattaagatattgattta--ttgttttgtt--ttctagCCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTTCCCGTGCAAGATATCCGCAATATTATGTAGCAT

upper sequence: GLYMA17G26440.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g17350.2 (Oryza sativa), 3'ss of exon 3
gtatacataatttcttgaatattt----ttgcagctttctgatgtttctgttttcttcatgtaaaatatgttgatgtgatttgtcatgccaattgtagCCTGATTTTCATGTCAAAGAAAAGATACTGGTTCTTGTAGATACTTGGCAAGAAGCTTTTGGAGGCCCAAGGGCAAGATATCCACAATATTATGCTGCAT
||||  |||     || ||  ||     ||  |  | |||| | |   |||   ||   | |||| | |   |   |  | | |   ||   || ||||||||||||||||| ||||| ||||| ||   |||  |||| ||||||||||||| |||||| ||   | | ||||||||||||||||| || || ||||
gtatgtatataagtttaaaccttaaaagttaaaattgtctggt-tagttgtaaactc--tttaaattttaacgccttattcttttgagc---ttttagCCTGATTTTCATGTGAAAGAGAAGATCCTCACTCTGATAGACACTTGGCAAGAAGTTTTTGGCGGGGTACGTGCAAGATATCCACAATACTACGCAGCAT

upper sequence: GLYMA17G26440.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G053925_T01 (Zea mays), 3'ss of exon 3
gtatacataatttcttgaatatttttgcagctttctgatgtttctgttttcttcatgtaaaatatgttgatgtgatttgtcatgccaattgtagCCTGATTTTCATGTCAAAGAAAAGATACTGGTTCTTGTAGATACTTGGCAAGAAGCTTTTGGAGGCCCAAGGGCAAGATATCCACAATATTATGCTGCAT
           |   || |||  |||  | | ||   |  || ||| ||  |  ||   ||||   || |||   | | |  ||  |||| |||| ||||| |||||| ||||| ||||| ||    ||  |||||||||||||||||| |||||| ||  || | ||||||||||||||||||||||| ||||
----------gtatgtgcatacattttaaacctt---aatttactgattg-tcaatagcaaatcc-ttaatgct-tctcttttgaaaattttagCATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAAGAAGTTTTTGGTGGTGCACGTGCAAGATATCCACAATATTATGCAGCAT

upper sequence: GLYMA17G26440.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G153138_T01 (Zea mays), 3'ss of exon 3
gtatacataatttcttgaatatttttgcagctttctgatgtttctgttttcttcatgtaaaata-----tgttgatgtgatttgtcatgccaattgtagCCTGATTTTCATGTCAAAGAAAAGATACTGGTTCTTGTAGATACTTGGCAAGAAGCTTTTGGAGGCCCAAGGGCAAGATATCCACAATATTATGCTGCAT
              || ||||| |||   |||| |  |  | |   | || |||   | || |      |  |||||   |||    | |   ||  || |||||  || ||| ||||| ||  || |||| ||  ||||||| ||||||||||| ||||| || ||| | ||||||||||||||||| ||||| ||||
-------------gttcaatatgtttcatgcttgcaaaactctacttcttattctaatgaactgctggcttatgatggtgttttgttttcatgttacagTCTGATCCTCGTGTTAAAGAGAAAGTATTGGTGCTGATAGATACATGGCAAGAAGCATTTGGGGGACCACGTGCAAGATATCCACAATACTATGCAGCAT

upper sequence: GLYMA17G26440.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G077844_T01 (Zea mays), 3'ss of exon 3
-----------------------------------------------------------------------------gtatacataatttcttgaatatttttgcagctttctgatgtttctgttttcttcatgtaaaatatgt-tgatgtgatttgtcatgccaattgtagCCTGATTTTCATGTCAAAGAAAAGATACTGGTTCTTGTAGATACTTGGCAAGAAGCTTTTGGAGGCCCAAGGGCAAGATATCCACAATATTATGCTGCAT
                                                                             | | ||| | ||  | |  | | |||     |   | |   |     ||   | ||  |||  |||| | || |  | | || |   |  |||||||||| | ||| |||||||| |||||| |  ||||  |||| |||||||||||||||||||| ||  |  | ||||||||||| || ||||| || ||||
gtgcaaatgccttttaatattctcctttatcattattacttgccacttcgacatgggcatgcatatttgaatcatgggcaaacaaatttcttggcttgtgtttatgagtaagtaacccta----ttcagtaataaaaataatgtctaatctactatttcgtttgatctgtagCCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTGCCCGTGCAAGATATCCCCAGTATTACGCAGCAT

upper sequence: GLYMA17G26440.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G32760.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatacataatttcttgaatatttttgcagctttctga-tgtttctgttttcttcatgtaaaatatgttgatgtgatttgtcatgccaattgtagCCTGATTTTCATGTCAAAGAAAAGATACTGGTTCTTGTAGATACTTGGCAAGAAGCTTTTGGAGGCCCAAGGGCAAGATATCCACAATATTATGCTGCAT
               | |   || || ||  ||  |   | ||||| | | | |         | | |     | ||| ||| ||     | ||||| || || ||||||||||| ||||| ||||| ||| | ||||| |||||||| || ||||| ||||| |||||||||||||||||||| ||||| | ||
--------------gtaatggttcttccaaattggtctctctttctctctcccttgctctgcctctctaatcctaattggtc-tgatgcatatagCCGGACTTCCATGTCAAAGAGAAGATTCTGGTCCTTATCGATACATGGCAAGAGGCCTTTGGTGGCCCTAGGGCAAGATATCCACAATACTATGCAGGAT

upper sequence: GLYMA17G26440.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 3
gtatacataatttcttgaatat--ttttgcagctttctgatgtttctgttttcttcat--gtaaaatatgttgatgtgatttgtcatgccaa-ttgtagCCTGATTTTCATGTCAAAGAAAAGATACTGGTTCTTGTAGATACTTGGCAAGAAGCTTTTGGAGGCCCAAGGGCAAGATATCCACAATATTATGCTGCAT
||  | |   |   |  | ||   ||||   | |  ||  | |   |  |||  | ||  |  |||  |||| ||   |||| |  ||| || ||| |||||||||| ||||||| ||| |||||| || ||||  |||||||||||||||||||||||||||| ||||||||||||||||||||||| ||||||||||
gt-cagactgtcattcaagtaccatttttttgttccctagtttcatttatttacttatccgagaaacctgttcatagtatttattctgcaaaattgcagCCTGATTTGCATGTCAGAGAGAAGATATTGATTCTGATAGATACTTGGCAAGAAGCTTTTGGAGGACCAAGGGCAAGATATCCACAATACTATGCTGCAT

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|9987051|gb|BE661159.1|BE661159
EST:     TTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAG                         CCTGATTTTCATGTCAAAGAAAAGATACTGGTTCTTGTAGATACTTGGCAA
genomic: TTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAGgtatacataa ... ccaattgtagCCTGATTTTCATGTCAAAGAAAAGATACTGGTTCTTGTAGATACTTGGCAA
EST: gi|254344824|gb|GR855588.1|GR855588
EST:     TTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAG                         CCTGATTTTCATGTCAAAGAAAAGATACTGGTTCTTGTAGATACTTGGCAA
genomic: TTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAGgtatacataa ... ccaattgtagCCTGATTTTCATGTCAAAGAAAAGATACTGGTTCTTGTAGATACTTGGCAA
EST: gi|17021949|gb|BM092983.1|BM092983
EST:     TTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAG                         CCTGATTTTCATGTCAAAGAAAAGATACTGGTTCTTGTAGATACTTGGCAA
genomic: TTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAGgtatacataa ... ccaattgtagCCTGATTTTCATGTCAAAGAAAAGATACTGGTTCTTGTAGATACTTGGCAA
EST: gi|23064188|gb|BU578961.1|BU578961
EST:     TTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAG                         CCTGATTTTCATGTCAAAGAAAAGATACTGGTTCTTGTAGATACTTGGCAA
genomic: TTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAGgtatacataa ... ccaattgtagCCTGATTTTCATGTCAAAGAAAAGATACTGGTTCTTGTAGATACTTGGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttctgttttcttcatgtaaaatatgttgatgtgatttgtcatgccaattgtagCCTGATTTTCATGTCAAAGAAAAGATACTGGTTCTTGTAGATACTTGGCAAGAAGCTTTTGGAGGCCCAAGGGCAAGATATCCACAATATTATGCTGCAT
                         tgttgat  putative branch site (score: 4)
            ttcatgtaaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacataatttcttgaatatttttgcagctttctgatgtttctgttttcttcatgtaaaatatgttgatgtgatttgtcatgccaattgtagCCTGATTTTCATGTCAAAGAAAAGATACTGGTTCTTGTAGATACTTGGCAAGAAGCTTTTGGAGGCCCAAGGGCAAGATATCCACAATATTATGCTGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC