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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcaaactgaactcagctcccttttgtatattatgttttaatttagtggaacaagaatctcttaggttcttactgtgttagactatttttgaacttgcagCCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAAT

Basic information

species Glycine max
transcript GLYMA16G08200.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G08200.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G17730.2 (Arabidopsis thaliana), 3'ss of exon 1
tgcaaactgaactcagctcccttttgtatattatgttttaatttagtggaacaagaatctcttaggttcttactgtgttagactatttttgaacttgcagCCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAAT
 | ||      ||||         | ||| |  | ||| | |||   || ||  |||  | |    |||| | || || |   |  || |     |  || || ||||||||| || ||||||| || || ||||||||||||||||||||||||||  |||| ||||| | |||||| ||    |  || |||
-gtaagtacttctcaaagttaaagt-tatctcctttttgagttttagggtacttgaaattgt----ttctaattgagtcaatttgcttgt-----tttagGCATAAGACAAGATTATATATTGGACAGTTAGTGAAAGATACATCAGCTAAACTTAAAGAAGCTAGTGAAACTGATCATCAAAGAGGTGTAAAT

upper sequence: GLYMA16G08200.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv02s0012g01850.t01 (Vitis vinifera), 3'ss of exon 1
----tgcaaactgaactcagctcccttttgtatattatgttttaatttagtggaacaagaatctcttaggttcttactgtgttagactatttttgaacttgcagCCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAAT
    | |    |||||  |  | |     | | |||   |  ||||||  |          |  ||   ||  ||    | ||||  |  |  ||| || |||| |||||||| || |||||||||||||| || || || ||||| || ||||||||||||||||| || || |  ||||| ||||||||||||| |
gcatttctttttgaac--aatttcaacaagaagatttcatgataatttttttttttttttttacctcttgtgattctcatattag--ttctgctgatctggcagGCACAAGACGAGGCTACATATTGGGCAGTTAGTCAAGGATACCTCTGCTAAACTTAAGCAAGCTAGCGAAACAGATCATCATGCTGAAGTTAGT
















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|193597169|gb|FK549667.1|FK549667
EST:     GTCAACACCCTCGGAACCCC-AAAGACACCCC-GACCTCCGCGAAAAACT                         CCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
genomic: GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACTgttagttctt ... gaacttgcagCCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
EST: gi|298189796|gb|HO038199.1|HO038199
EST:     GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACT                         CCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
genomic: GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACTgttagttctt ... gaacttgcagCCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
EST: gi|298185952|gb|HO031113.1|HO031113
EST:     GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACT                         CCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
genomic: GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACTgttagttctt ... gaacttgcagCCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
EST: gi|15662381|gb|BI699752.1|BI699752
EST:     GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACT                         CCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
genomic: GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACTgttagttctt ... gaacttgcagCCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
EST: gi|193552638|gb|FK506161.1|FK506161
EST:     TCAACACCCTCGGAA-CCCCAAACGACACCCCCGACCTCCGCGAAAAACT                         CCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
genomic: TCAACACCCTCGGAACCCCCAAA-GACACCCCCGACCTCCGCGAAAAACTgttagttctt ... gaacttgcagCCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
EST: gi|37994080|gb|CF805826.1|CF805826
EST:     GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACT                         CCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
genomic: GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACTgttagttctt ... gaacttgcagCCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
EST: gi|7686453|gb|AW757101.1|AW757101
EST:     GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACT                         CCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
genomic: GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACTgttagttctt ... gaacttgcagCCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
EST: gi|209725412|gb|BW651556.1|BW651556
EST:     GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACT                         CCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
genomic: GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACTgttagttctt ... gaacttgcagCCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
EST: gi|298196583|gb|HO041326.1|HO041326
EST:     GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACT                         CCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
genomic: GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACTgttagttctt ... gaacttgcagCCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
EST: gi|193483117|gb|FK448440.1|FK448440
EST:     GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACT                         CCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
genomic: GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACTgttagttctt ... gaacttgcagCCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
EST: gi|154204866|gb|EV555128.1|EV555128
EST:     GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACT                         CCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGACACATCAGCTAA
genomic: GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACTgttagttctt ... gaacttgcagCCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
EST: gi|193708294|gb|FK643202.1|FK643202
EST:     GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACT                         CCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
genomic: GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACTgttagttctt ... gaacttgcagCCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
EST: gi|208150896|gb|GD946013.1|GD946013
EST:     GTCAACACCCTCGGAACCCCCAAAGGCACCCCCGACCTCCGCGAAAAACT                         CCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
genomic: GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACTgttagttctt ... gaacttgcagCCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
EST: gi|208330637|gb|GE126366.1|GE126366
EST:     GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACT                         CCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
genomic: GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACTgttagttctt ... gaacttgcagCCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
EST: gi|192299164|gb|FG992895.1|FG992895
EST:     GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACT                         CCACAAGACAAGACTACATACTGGGCAATTGGTGAAAGATACATCAGCTAA
genomic: GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACTgttagttctt ... gaacttgcagCCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
EST: gi|209702008|gb|BW683185.1|BW683185
EST:     GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACT                         CCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
genomic: GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACTgttagttctt ... gaacttgcagCCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
EST: gi|208144811|gb|GD941204.1|GD941204
EST:     GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACT                         CCACAAGACAAGACTACATATTGGGCAATT
genomic: GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACTgttagttctt ... gaacttgcagCCACAAGACAAGACTACATATTGGGCAATT
EST: gi|192296912|gb|FG990258.1|FG990258
EST:     GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACT                         CCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
genomic: GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACTgttagttctt ... gaacttgcagCCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
EST: gi|193488148|gb|FK453185.1|FK453185
EST:     GTCAACACCCTCGGAACCCCCAAAGACA-CCCCGACCTCCGCGAAAAACT                         CCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
genomic: GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACTgttagttctt ... gaacttgcagCCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
EST: gi|19452417|gb|BM953827.1|BM953827
EST:     GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACT                         CCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
genomic: GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACTgttagttctt ... gaacttgcagCCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
EST: gi|9565390|gb|BE474899.1|BE474899
EST:     GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACT                         CCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA
genomic: GTCAACACCCTCGGAACCCCCAAAGACACCCCCGACCTCCGCGAAAAACTgttagttctt ... gaacttgcagCCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggaacaagaatctcttaggttcttactgtgttagactatttttgaacttgcagCCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAAT
                     ttcttac  putative branch site (score: 2)
                                      tatttttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcaaactgaactcagctcccttttgtatattatgttttaatttagtggaacaagaatctcttaggttcttactgtgttagactatttttgaacttgcagCCACAAGACAAGACTACATATTGGGCAATTGGTGAAAGATACATCAGCTAAACTTAAGCAAGCCAGTGACATTGATCACCATGCTGAAGTTAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
tgcaaac
- - - - - - - - ctccctt
- - - - - - - - - - - - - - - - - - - - - - - - -aacaagaa