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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaaaatttcccccatctgtaaccatgattaattcttttcatagtttgtcttagaatgacatatttttttggctttttattccgttcagCAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGAAGCTGCAGGATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGA

Basic information

species Glycine max
transcript GLYMA04G33180.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G33180.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g24540.1 (Oryza sativa), 3'ss of exon 1
gtagaaaatttcccccat--------ctgtaaccatgattaattc--ttttcatagtttgtcttagaatgacatatttttttggctttttattccgttcagCAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGAAGCTGCAGGATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGA
 |  |||  |       |         | |   | || | ||||   | ||  |  ||| | || |  |     | |  | ||   ||        |||||| |||||  |  | || ||||| ||||| |||||||||||||| ||||||||| |||||||||| ||| |   |||||| || |||||||| || || ||
-tttaaagctcttttggttaggattattctgttcgtggtaaatttcatgttgtttttttttttttgggtacttgactgctgtgttgttactggtttttcagCTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGAAGTTGCAGGATGGCTGGTTGGACAACGGGGACAAGGTCCCTCCTGCCGA

upper sequence: GLYMA04G33180.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G048277_T03 (Zea mays), 3'ss of exon 1
-------gtagaaaatttc-ccccatctgtaaccatgattaattcttt--tcatagtttgtcttagaatgacatatttttttggctttttattccgttcagCAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGAAGCTGCAGGATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGA
       || | || |  |  | |   |||  | ||| |||  | |||  |   |  |      |   |||  |||  || ||   |  |    | | |||| |||||  | || |||||||| || || |||||||||||||| || |||||| |||||||||| |||||    || || || || || || || |||||
aaattgagttgcaactaacgtcactcttgtgtctatgcttagctttttggttgcaagtaaagaaaagctgatttatgattatgttgtcctgcatc-tgcagCTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGAAGTTGCAGGATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGA

upper sequence: GLYMA04G33180.2 (Glycine max), 3'ss of exon 2
lower sequence: AT1G26550.1 (Arabidopsis thaliana), 3'ss of exon 2
----------------------------------------------gtagaaaatttcccccatc---tgtaaccatgattaattcttttcatagtttgtcttagaatgacatatttt--------tttggctttttattccgttcagCAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGAAGCTGCAGGATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGA
                                              ||| |||||       | |   | |       |    |   || ||   ||||| |||| |  | |   ||         | |    || | ||   ||||||||| ||| | || || ||||| ||||| |||||||| || |||||||| ||| |||||||||||||| |  |||||||||| ||||| || || |||||
gtgtgttttttggattcgtttctgtgcctgttacctttgttcatgagtaaaaaatactggtaaacaaatatggatccaaaagttctcttacaacttttgtattagtacaatagcattaaagtcaaatctccaattgtttttgtttcagCAAGACATGTTTTGTGCGAGAAGCAAGGAAAGATCAACGAGGCCTACAAAAAGTTGCAGGATGGTTGGTTGAGCAACGGAGACAAGGTTCCTCCTGCTGA

upper sequence: GLYMA04G33180.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv17s0000g06430.t01 (Vitis vinifera), 3'ss of exon 2
gtagaaaatttcccccatctgtaaccatgattaattcttttcatagtttgtcttagaatgacat--atttttttggcttttta--ttccgttcagCAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGAAGCTGCAGGATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGA
         |  || |||||| |     | |  | |  ||   |    | | | |   | |  |  ||| || |||| ||| |  | || | ||||||| ||||||||||||||||| ||||| || || |||||||| ||||||||||| || ||||| |||||| | || ||||| ||||| |||||||||||
--------gtctcctcatctgcattttagttggaattgttaatttaagtatttgatcttcatgttgattgttctggcctttcaattcccttccagCAAGACATATCTTATGTGAGAAGCAAGGCAAAATTAATGAAGCATACAAGAAGCTACAAGATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGA

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|298180788|gb|HO022227.1|HO022227
EST:     AAAGGGTGGGAAAGGTGGAGATGGGCTTGGTACTTGCACCTATGTCAAAG                         CAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGA
genomic: AAAGGGTGGGAAAGGTGGAGATGGGCTTGGTACTTGCACCTATGTCAAAGgtagaaaatt ... ttccgttcagCAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGA
EST: gi|192310836|gb|FK000322.1|FK000322
EST:     AAAGGGTGGGAAAGGTGGAGATGGGCTTGGTACTTGCACCTATGTCAAAG                         CAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGA
genomic: AAAGGGTGGGAAAGGTGGAGATGGGCTTGGTACTTGCACCTATGTCAAAGgtagaaaatt ... ttccgttcagCAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGA
EST: gi|192310835|gb|FK000321.1|FK000321
EST:     AAAGGGTGGGAAAGGTGGAGATGGGCTTGGTACTTGCACCTATGTCAAAG                         CAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGA
genomic: AAAGGGTGGGAAAGGTGGAGATGGGCTTGGTACTTGCACCTATGTCAAAGgtagaaaatt ... ttccgttcagCAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGA
EST: gi|209720765|gb|BW677555.1|BW677555
EST:     AAAGGGTGGGAAAGGTGGAGATGGGCTTGGTACTTGCACCTATGTCAAAG                         CAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGA
genomic: AAAGGGTGGGAAAGGTGGAGATGGGCTTGGTACTTGCACCTATGTCAAAGgtagaaaatt ... ttccgttcagCAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGA
EST: gi|10255640|gb|BE823406.1|BE823406
EST:     AAAGGGTGNNAAAGGTGGAGATGGGCTTGGTACTTGCACCTATGTCAAAG                         CAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGA
genomic: AAAGGGTGGGAAAGGTGGAGATGGGCTTGGTACTTGCACCTATGTCAAAGgtagaaaatt ... ttccgttcagCAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGA
EST: gi|9986791|gb|BE660899.1|BE660899
EST:     AAAGGGTGGGAAAGGTGGAGATGGGCTTGGTACTTGCACCTATGTCAAAG                         CAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGA
genomic: AAAGGGTGGGAAAGGTGGAGATGGGCTTGGTACTTGCACCTATGTCAAAGgtagaaaatt ... ttccgttcagCAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGA
EST: gi|192328239|gb|FK020458.1|FK020458
EST:     AAAGGGTGGGAAAGGTGGAGATGGGCTTGGTACTTGCACCTATGTCAAAG                         CAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGA
genomic: AAAGGGTGGGAAAGGTGGAGATGGGCTTGGTACTTGCACCTATGTCAAAGgtagaaaatt ... ttccgttcagCAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGA
EST: gi|298165798|gb|HO008769.1|HO008769
EST:     AAAGGGTGGGAAAGGTGGAGATGGGCTTGGTACTTGCACCTATGTCAAAG                         CAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGA
genomic: AAAGGGTGGGAAAGGTGGAGATGGGCTTGGTACTTGCACCTATGTCAAAGgtagaaaatt ... ttccgttcagCAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGA
EST: gi|298182306|gb|HO026481.1|HO026481
EST:     AAAGGGCGGGAAAGGTGGAGATGGGCTTGGTACTTGCACCTATGTCAAAG                         CAAGGCATATCTTATGTGAGAAGCAAGGTAAGATCAATGAAGCCTACAAGA
genomic: AAAGGGTGGGAAAGGTGGAGATGGGCTTGGTACTTGCACCTATGTCAAAGgtagaaaatt ... ttccgttcagCAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGA
EST: gi|23731993|gb|BU764147.1|BU764147
EST:     AAAGGGTGGGAAAGGTGGAGATGGGCTTGGTACTTGCACCTATGTCAAAG                         CAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGA
genomic: AAAGGGTGGGAAAGGTGGAGATGGGCTTGGTACTTGCACCTATGTCAAAGgtagaaaatt ... ttccgttcagCAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGA
EST: gi|298168618|gb|HO009548.1|HO009548
EST:     AAAGGGTGGGAAAGGTGGAGATGGGCTTGGTACTTGCACCTATGTCAAAG                         CAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGA
genomic: AAAGGGTGGGAAAGGTGGAGATGGGCTTGGTACTTGCACCTATGTCAAAGgtagaaaatt ... ttccgttcagCAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGA
EST: gi|9820183|gb|BE555693.1|BE555693
EST:     AAAGGGTGGGAAAGGTGGAGATGGGCTTGGTACTTGCACCTATGTCAAAG                         CAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGA
genomic: AAAGGGTGGGAAAGGTGGAGATGGGCTTGGTACTTGCACCTATGTCAAAGgtagaaaatt ... ttccgttcagCAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGA
EST: gi|27423863|gb|CA935383.1|CA935383
EST:     AAAGGGTGGGAAAGGTGGAGATGGGCTTGGTACTTGCACCTATGTCAAAG                         CAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGA
genomic: AAAGGGTGGGAAAGGTGGAGATGGGCTTGGTACTTGCACCTATGTCAAAGgtagaaaatt ... ttccgttcagCAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGA
EST: gi|41145676|gb|CK605887.1|CK605887
EST:     AAAGGGTGGGAAAGGTGGAGATGGGCTTGGTACTTGCACCTATGTCAAAG                         CAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGA
genomic: AAAGGGTGGGAAAGGTGGAGATGGGCTTGGTACTTGCACCTATGTCAAAGgtagaaaatt ... ttccgttcagCAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttcatagtttgtcttagaatgacatatttttttggctttttattccgttcagCAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGAAGCTGCAGGATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGA
                                      ctttttattccgttc  CT-rich tract
                          atatttttttggcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagaaaatttcccccatctgtaaccatgattaattcttttcatagtttgtcttagaatgacatatttttttggctttttattccgttcagCAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGAAGCTGCAGGATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA