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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttaatttcagtcatgacctcttggaagtaattatgtcttttgcttctttggatattttgtggttcccattcctaattcattttttaatatctgccacagGGTCAAAATCAGAGTTTTGATCTTCCTATTAAGAAAAGGAGTGACATCTGTACAATAATGTATACTAGTGGAACTACTGGTGACCCCAAGGGAGTGTTGA

Basic information

species Glycine max
transcript GLYMA01G43470.5
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G43470.5 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g46750.4 (Oryza sativa), 3'ss of exon 5
---gttaatttcagtcatgacctcttggaagtaattatgtcttttgcttctttggatattttgtggttcccattcctaattcattttttaatatc-tgccacagGGTCAAAATCAGAGTTTTGATCTTCCTATTAAGAAAAGGAGTGACATCTGTACAATAATGTATACTAGTGGAACTACTGGTGACCCCAAGGGAGTGTTGA---
     ||||||      |    ||   ||  | ||| |     |   || || |||||  ||    |||  ||     |||  |    | | ||  |  |    ||   | | ||    || ||||||||  | ||   || || |||||| ||||| ||||||||||| ||||||||||||||||||||||| || ||  |||   
ctttctaatttggaaagttgtttca-agagttcattttacacctattttattaggatagctt----ttcagatattctatttttcacatgacattgtatcttcagGC--AGACCAAGAATTCGATCTTCCAGTGAAAGCAAAGACTGACATATGTACTATAATGTATACCAGTGGAACTACTGGTGACCCCAAAGGTGTACTGATCT

upper sequence: GLYMA01G43470.5 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 8
gttaatttcagtcatgacctcttggaagtaattatgt---cttttgcttctttggatattttgtggttcccattcctaattcattttttaatatctgccacagGGTCAAAATCAGAGTTTTGATCTTCCTATTAAGAAAAGGAGTGACATCTGTACAATAATGTATACTAGTGGAACTACTGGTGACCCCAAGGGAGTGTTGA
     |||| ||    || |||   || ||||| | |   | |  |     |  ||  || | |   ||   |    |  | ||| | |  | |   |  |||||     |  | |  | ||| |||||||  ||| ||| |  ||| ||||||||||||||||| || |||||||| ||||||||||| |||||||| || |
-cctgtttctgtttcaac-tctacaaaataattttatggacatcagagcaatgtgactttatattcatctggtattaagataattatctgttttac-ctgcagGGAGGTGAAGAAAAGTATGAACTTCCTACAAAGCAAAAGGATGATATCTGTACAATAATGTACACCAGTGGAACAACTGGTGACCCTAAGGGAGTTTTAA

upper sequence: GLYMA01G43470.5 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM5G861300_T01 (Zea mays), 3'ss of exon 8
gttaatttcagtcatgacctcttggaagtaattatgtcttttgcttctttggatattttgtggttcccattcctaattcattttttaatatctgccacagGGTCAA------AATCAGAGTTTTGATCTTCCTATTAAGAAAAGGAGTGACATCTGTACAATAATGTATACTAGTGGAACTACTGGTGACCCCAAGGGAGTGTTGA
  |   ||   |  ||  |   | |   ||| | | |  ||      | |    | ||||||  |   | | |  |  | |   || | ||  || | |    ||        | ||    |||||||||||  | ||| | | |   ||||| || || |||||||||||||||||||||||||||||||| || |||||  |||
--tggattagttattgtacctattggtttaactgtataattca----tataagaaatttgtgactataaatgcctacccttccatttacatgagctatatctgcagGCGGCTGACCAAGAATTTGATCTTCCAGTCAAGGAGAAGGCAGACATATGCACTATAATGTATACTAGTGGAACTACTGGTGACCCAAAAGGAGTACTGA

upper sequence: GLYMA01G43470.5 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 8
--------------------------------------------------------------------gttaatttcagtcatgacctc--ttggaagtaattatgtcttt---tgcttctttgg-------atattttgtggttcccattcctaattcattttttaat--atctgcca-cagGGTCAAAATCAGAGTTTTGATCTTCCTATTAAGAAAAGGAGTGACATCTGTACAATAATGTATACTAGTGGAACTACTGGTGACCCCAAGGGAGTGTTGA
                                                                      |   || || ||||   |   ||  || |   ||  | |||    || || |||        ||   |||   |  |  ||   || | |||||||      ||| ||| |||||    ||  |||  ||||| |||||    ||| ||| |  |||||| |||||||||||||| || |||||||| |||||||| || ||||||||  | |
gtaaggttctcctttcctgaccaaatcacacatggaatgaataagtgcttagttacaagaatattaataatgtgttaaggcatgtttttcatttcaaatttatacatttttgggggcatccttgcgagaaatatgccttgatatatcagttagaaaattattttttttctgttctaccaacagGGAGGTAAAGAGAAGTTTGAACTTCCACCCAAGGAAAAGGATGACATATGTACAATAATGTACACCAGTGGAACAACTGGTGATCCTAAGGGAGTACTAA

upper sequence: GLYMA01G43470.5 (Glycine max), 3'ss of exon 8
lower sequence: AT4G23850.1 (Arabidopsis thaliana), 3'ss of exon 8
-------------------gttaatttcagtcatgacctcttggaagtaattatgtcttttgcttctttggatat-tttgtggttcccattcctaattcattttttaatatctgccacagGGTCAAAATCAGAGTTTTGATCTTCCTATTAAGAAAAGGAGTGACATCTGTACAATAATGTATACTAGTGGAACTACTGGTGACCCCAAGGGAGTGTTGA
                    |     | |   ||      |  |   || || | ||   || |  | |   |||  || |  |    || | |   ||  ||   ||||| |  | |||||| ||    ||   | |||||| || || || || |  || ||||| || || || |||||||| |||||||| ||||||||||| ||||||||| |||
gtatgagacttgacatttgctcgtcctgaaatatactgattctgtgatatttctttccagtggtcttataactatgcttatcatgtttatactt---tccattgcgaatatttctcccagGGTGAAGGAAAGCAATATGATCTCCCAATCAAAAAGAAAAGCGACATTTGCACGATTATGTATACGAGTGGAACCACTGGTGACCCAAAGGGAGTGATGA

upper sequence: GLYMA01G43470.5 (Glycine max), 3'ss of exon 8
lower sequence: AT4G11030.1 (Arabidopsis thaliana), 3'ss of exon 8
gttaatttcagtcatgacctcttggaagtaattatgtcttttgcttctttggatattttgtggttcccattcctaattcattttttaatatctgccacagGGTCAAAATCAGAGTTTTGATCTTCCTATTAAGAAAAGGAGTGACATCTGTACAATAATGTATACTAGTGGAACTACTGGTGACCCCAAGGGAGTGTTGA
          || |    || ||    |    | |  |  | | |  ||   ||||  | ||||    | |    ||||   | | |||  |    ||||||| |   | ||   | ||| ||||| ||||| ||    || ||||| || || || ||||||||||| ||||| ||||||||||| ||||||||  |||
----------gtaagagactattatttgcttctttaacaat-gatcattcacatataatatggtat--aatgtatattc---tgtcaatgacattaacagGGTGAGGGTAAGCAATATGAGCTTCCCATTAAAAAGCCAAGCGACATATGCACGATTATGTATACTAGCGGAACAACTGGTGACCCGAAGGGAGTTATGA

upper sequence: GLYMA01G43470.5 (Glycine max), 3'ss of exon 8
lower sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 8
-gttaatttcagtcatgacctcttggaagtaattatgtcttttgcttctttggatattttgtggttcccattcctaattcattttttaatatctgc-cacagGGTCAAAATCAGAGTTTTGATCTTCCTATTAAGAAAAGGAGTGACATCTGTACAATAATGTATACTAGTGGAACTACTGGTGACCCCAAGGGAGTGTTGA
 |||   | || |  |  |   ||     ||   ||  || ||  |      | |||||||    |   |    |||  | | | ||  | | ||| |||||||  |  || | |  |||||||||||  | |  || |  |  ||||| |||||||||||||| || |||||||| || ||||||||||| || ||| |||
agttttctgcatttttccctctttattgttag--atacctatttataaacatgctattttgcctatagaaaagttaaagcttgtgtttttgtttgctcacagGGAGATGATAAAAAATTTGATCTTCCATTGACAAAGAAAAACGACATTTGTACAATAATGTACACAAGTGGAACAACCGGTGACCCCAAAGGTGTGATGA

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|19346911|gb|BM891799.1|BM891799
EST:     TTGAAAATTCTGGGTTGGAAATATATTCATGGGATGAATTCTTACAAGTG                         GGTCAAAATCAGAGTTTTGATCTTCCTATTAAGAAAAGGAGTGACATCTGT
genomic: TTGAAAATTCTGGGTTGGAAATATATTCATGGGATGAATTCTTACAAGTGgtgggttatt ... tctgccacagGGTCAAAATCAGAGTTTTGATCTTCCTATTAAGAAAAGGAGTGACATCTGT
EST: gi|209718138|gb|BW657797.1|BW657797
EST:     TTGAAAATTCTGGGTTGGAAATATATTCATGGGATGAATTCTTACAAGTG                         GGTCAAAATCAGAGTTTTGATCTTCCTATTAA
genomic: TTGAAAATTCTGGGTTGGAAATATATTCATGGGATGAATTCTTACAAGTGgtgggttatt ... tctgccacagGGTCAAAATCAGAGTTTTGATCTTCCTATTAA
EST: gi|308097989|gb|HO761160.1|HO761160
EST:     TTGAAAATTCTGGGTTGGAAATATATTCATGGGATGAATTCTTACAAGTG                         GGTCAAAATCAGAGTTTTGATCTTCCTATTAAGAAAAGGAGTGACATCTGT
genomic: TTGAAAATTCTGGGTTGGAAATATATTCATGGGATGAATTCTTACAAGTGgtgggttatt ... tctgccacagGGTCAAAATCAGAGTTTTGATCTTCCTATTAAGAAAAGGAGTGACATCTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttggatattttgtggttcccattcctaattcattttttaatatctgccacagGGTCAAAATCAGAGTTTTGATCTTCCTATTAAGAAAAGGAGTGACATCTGTACAATAATGTATACTAGTGGAACTACTGGTGACCCCAAGGGAGTGTTGA
                       attcctaattcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaatttcagtcatgacctcttggaagtaattatgtcttttgcttctttggatattttgtggttcccattcctaattcattttttaatatctgccacagGGTCAAAATCAGAGTTTTGATCTTCCTATTAAGAAAAGGAGTGACATCTGTACAATAATGTATACTAGTGGAACTACTGGTGACCCCAAGGGAGTGTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA