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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgagatctgttgttcttattctcgccttccgtaattccagaactttcttcttctttttcatcttctattgttgtttgtttgcagACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAG

Basic information

species Glycine max
transcript GLYMA17G18200.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G18200.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g60790.1 (Oryza sativa), 3'ss of exon 1
gttcgagatctgttgttcttattctcgccttccgtaa----ttccagaactttcttcttctttttcatcttctattgttgtttgtttgcagACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAG
     ||  ||    | | ||| ||   |  |   |     || | | | |     ||    |  | |||  | ||| ||  |    |||||| ||||||||| | ||||| || |||||||| ||||| || ||||||||||| | |||||| ||||||||||| | ||| ||||||||||||
--gtaaggccttgcttccctatgcttaacgcctagattgctttgcgggattcagcgctgaactgacctctcttcttgctgcatcggcgcagACCTTCAAGCGCCGCAATGGCGGCCGCAACAAGCACGGTCGCGGCCACGTCAAGTACATCCGCTGCTCCAACTGCGCCAAGTGCTGCCCCAAG

upper sequence: GLYMA17G18200.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g39960.2 (Oryza sativa), 3'ss of exon 1
-------------------------------------------gttcgagatctgttgttcttattctcgccttccgt--aattccagaactttcttcttctttttcatcttctattgttgtttgtttgcagACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAG
                                           |   | |  |  ||   | | ||||     ||||   |||  |     |     |||||  ||  | | ||  |    ||   | |||||| |||||||||||||| || || |||||||| || ||||| ||||| || || | |||||| ||||||||||| | ||| ||||||||||||
gtaaggagctcgccgcttccggatccaccctagccgccgcggcggcggcggccgcttcggcgtcttcttcttctccgctcaatctcccggttagtcccttctgattggtttcctcct----ttccctcgcagACCTTCAAGCGCAGGAACGGCGGCCGCAACAAGCATGGCCGCGGCCATGTGAAGTACATCCGCTGCTCCAACTGCGCCAAGTGCTGCCCCAAG

upper sequence: GLYMA17G18200.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G899149_T02 (Zea mays), 3'ss of exon 1
gttcgagatctgttgttcttattctcgccttccgtaattccagaactttcttcttctttttcatcttctattgttgtttgtttgcagACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAG-------
    ||| ||| | |     | |||| | |  ||     ||     |  | |||    |||  | || | | ||||       |||||| |||||||| |||||||| || |||||||| ||||| || ||||||||||| | |||||| ||||||||||| | ||| ||||||||||||       
--gtgagttct-tcgagaccaatctcccttctcg-----ccgacgttgccgtctaacctttgttgttgtctggttgccg--ccgcagACGTTCAAGCGGAGGAATGGCGGACGCAACAAGCACGGGCGCGGCCACGTCAAGTACATCCGCTGCTCCAACTGCGCCAAGTGCTGCCCCAAGGTAACAC

upper sequence: GLYMA17G18200.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G899149_T01 (Zea mays), 3'ss of exon 1
gttcgagatctgttgttcttattctcgccttccgtaattccagaactttcttcttctttttcatcttctattgttgtttgtttgcagACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAG
    ||| ||| | |     | |||| | |  ||     ||     |  | |||    |||  | || | | ||||       |||||| |||||||| |||||||| || |||||||| ||||| || ||||||||||| | |||||| ||||||||||| | ||| ||||||||||||
--gtgagttct-tcgagaccaatctcccttctcg-----ccgacgttgccgtctaacctttgttgttgtctggttgccg--ccgcagACGTTCAAGCGGAGGAATGGCGGACGCAACAAGCACGGGCGCGGCCACGTCAAGTACATCCGCTGCTCCAACTGCGCCAAGTGCTGCCCCAAG

upper sequence: GLYMA17G18200.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G129015_T02 (Zea mays), 3'ss of exon 1
gttcgagatctgttgttc-ttattctcgccttccgtaattccagaactttcttcttctttttcatcttctattgttgtttgt-----ttgcagACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAG
    | || || | |      ||   || | ||||| |  ||    |     |  | | |  |   |||| |||||| ||||       |||||| |||||||| ||||| || || |||||||| ||||| || ||||||||||| | ||| || ||||||||||| | ||| ||||| || |||
----gtgagctatcggagaccatctccgtcctccgtcacgcctcgccgccgctgctgtctaaccctttcttttgttggttgtggttgccgcagACGTTCAAGCGGAGGAACGGCGGACGCAACAAGCACGGGCGCGGCCACGTCAAGTACATACGCTGCTCCAACTGCGCCAAGTGCTGTCCAAAG

upper sequence: GLYMA17G18200.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G827266_T03 (Zea mays), 3'ss of exon 1
--------gttcgagatctgttgttcttattctcgccttccgtaattccagaactttcttcttctttttcatcttctattgttgtttgtttgcagACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAG
           | |   |||  ||||    |  | || |  | |  | ||   |     |  ||  ||| |    ||   ||| | | |  |||||| ||||||||| | || || || |||||||| || ||||| || |||||||| | |||||| ||||| ||||| | ||| ||||||||||||
gcgagtcctaaccaagcctgaagttcgatcttcctccctgtgcatgtacatctcgaatctaatccattttactccct---gttctctctccgcagACCTTCAAGCGCCGCAACGGCGGCCGCAACAAGCATGGCCGCGGTCACGTCAAGTACATCCGGTGCTCAAACTGCGCCAAGTGCTGCCCCAAG

upper sequence: GLYMA17G18200.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G40510.1 (Arabidopsis thaliana), 3'ss of exon 1
gttcgagatctgttgttcttattctcgccttccgtaattccag-aactttcttcttctttttcatcttctattgttgtttgt-ttgcagACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAG
       |    || |  ||  | | |  |  |  | || ||  ||           ||  | ||| || |||||||||||| |||||||| |||||||| ||||| || ||  | ||||| |||  | | || ||||||||    ||| |||||||||||||||||||||| |||||||||
-----gtactcattttctttgattttgattatcagatttgcaataaaagatagagaattgatgatcatccattgttgtttgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTCAACCCAATCAGATGCTCCAACTGTGGCAAATGTTGCCCCAAG

upper sequence: GLYMA17G18200.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0004g07940.t01 (Vitis vinifera), 3'ss of exon 1
gttcgagatctgttgttcttattctcgccttccgtaattccagaactttcttcttctttttcatcttctattgttgtttgtttgcagACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAG
    ||| | | |  |    | | || | || |    || |      |  ||  ||       | ||   |  |||| | ||||||||| |||||||| |||||||| ||||||||||| |||||||| ||||||||||| ||||| || |||||||||||||||||||||||||| |||
--gtgaggttt-tcctcgaaaatttcacttttcaatcttgcttgctatcatttctcaccgatttttttggtaattgtgtttttgcagACGTTCAAGCGAAGGAATGGTGGTCGCAACAAGCACGGCCGCGGCCACGTCAAGTTCATTCGCTGCTCCAACTGTGGCAAATGCTGCCCTAAG

upper sequence: GLYMA17G18200.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv13s0067g02700.t01 (Vitis vinifera), 3'ss of exon 2
gttcgagatctgttgttcttattctcgccttccgtaattccagaactttcttcttcttt-----------ttcatcttctattgttgtttgt-ttgcagACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAG
     |||||| |    |  ||   |     ||  || || |     ||||||| | ||           ||||  ||   || ||  ||||  || |||| ||||||||||| || || || |||||||| ||||||||||| || ||||| |||||||| ||||| ||||| || ||||||||||| |||
--gtaagatctctcaacc--atcaccattaccctcaactcaatcttcttcttctccgttgtgatgtaaccttcaaatttcgttattacttgtgctgtagACGTTCAAGCGCAGAAACGGCGGCCGCAACAAGCACGGCCGTGGACATGTCAAGTTCATCCGCTGCTCAAACTGCGGAAAATGCTGCCCAAAG

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|16346765|gb|BI972360.1|BI972360
EST:     CAGACAAAACCCTAGTGAGCAGAGCGTGAAAGCACCGGCCACCGGCCATG                         ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTC
genomic: CAGACAAAACCCTAGTGAGCAGAGCGTGAAAGCACCGGCCACCGGCCATGgttcgagatc ... ttgtttgcagACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTC
EST: gi|10848274|gb|BF070805.1|BF070805
EST:     CAGACAAAACCCTAGTGAGCAGAGCGTGAAAGCACCGGCCACCGGCCATG                         ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTC
genomic: CAGACAAAACCCTAGTGAGCAGAGCGTGAAAGCACCGGCCACCGGCCATGgttcgagatc ... ttgtttgcagACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTC
EST: gi|22933841|gb|BU550980.1|BU550980
EST:     CAGACAAAACCCTAGTGAGCAGAGCGTGAAAGCACCGNNCACCGGCCATG                         ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTC
genomic: CAGACAAAACCCTAGTGAGCAGAGCGTGAAAGCACCGGCCACCGGCCATGgttcgagatc ... ttgtttgcagACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTC
EST: gi|209723888|gb|BW675234.1|BW675234
EST:     CAGACAAAACCCTAGTGAGCAGAGCGTGAAAGCACCGGCCACCGGCCATG                         ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTC
genomic: CAGACAAAACCCTAGTGAGCAGAGCGTGAAAGCACCGGCCACCGGCCATGgttcgagatc ... ttgtttgcagACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtaattccagaactttcttcttctttttcatcttctattgttgtttgtttgcagACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAG
             ctttcttcttcttttt  CT-rich tract
                     ttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgagatctgttgttcttattctcgccttccgtaattccagaactttcttcttctttttcatcttctattgttgtttgtttgcagACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC