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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattgttttcatttggttgatatttttgtttatgaaatttgaatgtagtttaattgggtctagaacacttaatttcctctttctcactttcaatatgtagATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGG

Basic information

species Glycine max
transcript GLYMA16G27020.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G27020.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G891739_T01 (Zea mays), 3'ss of exon 4
tattgttttcatttggttgatatttttgtttatgaaatttgaatgtagtttaattgggtctagaacacttaatttcctctttctcactttcaatatgtagATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGG
              | | | |  | |||        || |  || || |   |||   | | || ||  | ||  ||| |||||     |   | || ||||| |  | | |||   ||| |||||  | |||||||| |||||||| ||||||||||||||||| || || ||||
--------------gttcggtcatcttga----aggatgtatatataatcctattaatttt-gatcaactgataacctatttctgctgctt--tctgaagATTTCATTGAGTGGGCCTCATTCCATTCTGGGAAGGGCAGTTGTTGTACATGCTGATCCTGATGACCTAGGGAGGG

upper sequence: GLYMA16G27020.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G18100.2 (Arabidopsis thaliana), 3'ss of exon 4
---------------------------------tattgttttcatttggttgatatttttgtttatgaaatttgaatgtagtttaattgggtctagaacacttaa----tttcctctttctcactttcaatatgtagATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGG
                                 | |  | ||        | |   ||   ||| |    | | |   | ||| |  |   ||| | ||  || |    ||  ||| |  |  |||| |||    |||| || || | |||     | |||||| | || ||||| |||||||||||||| ||||||||||| ||||| |  |
gtatatgatcttcttttttcacttcttcaatcatttaatgtttggcaaaataaacattacatttttcggttcttag-attgttcatatatctctcggacgtttcaccatttatctcatcttgtctttgaattcacagATACCGCTTAGTGGGCAGTATTCCATACTCGGGAGGGCGGTTGTTGTGCATGCGGATCCTGATGACCTTGGGAAAG

upper sequence: GLYMA16G27020.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0007g07280.t01 (Vitis vinifera), 3'ss of exon 4
tattgttttcatttggttgatatttttg--tttatga-aatttgaatgtagtttaattgggtctaga----acacttaatttcctc--tttctcactttcaatatgtagATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGG
         |||||    | | | | |   ||| ||| ||| ||||     ||| ||||  | ||||    | | || ||| | ||   |  |  |||  ||| |||||||| |  ||| |||    || |||||  | |||||||| ||||||||||||||||||||||||||||||||||| |
---------catttataaggtttctctagttttgtgataatgtgaaaactttttgattgattatagacttaaaagtttattccttcaactctttccttcaaatttgtagATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGAG

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|23058846|gb|BU578339.1|BU578339
EST:     GAGTTGCTGAGATTTCTATTAAAGATAGACAG                         ATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCAT
genomic: GAGTTGCTGAGATTTCTATTAGAGATAGACAGgtaaagaatt ... caatatgtagATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCAT
EST: gi|31470014|gb|CD412042.1|CD412042
EST:     GAGTTGCTGAGATTTCTATTAGAGATAGACAG                         ATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCAT
genomic: GAGTTGCTGAGATTTCTATTAGAGATAGACAGgtaaagaatt ... caatatgtagATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCAT
EST: gi|31470725|gb|CD412753.1|CD412753
EST:     GAGTTGCTGAGATTTCTATNAGAGATAGACAG                         ATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCAT
genomic: GAGTTGCTGAGATTTCTATTAGAGATAGACAGgtaaagaatt ... caatatgtagATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCAT
EST: gi|7146773|gb|AW508695.1|AW508695
EST:     GAGTTGCTGAGATTTCTATTAGAGATAGACAG                         ATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCAT
genomic: GAGTTGCTGAGATTTCTATTAGAGATAGACAGgtaaagaatt ... caatatgtagATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCAT
EST: gi|209702151|gb|BW677951.1|BW677951
EST:     GAGTTGCTGAGATTTCTATTAGAGATAGACAG                         ATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCAT
genomic: GAGTTGCTGAGATTTCTATTAGAGATAGACAGgtaaagaatt ... caatatgtagATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCAT
EST: gi|192334422|gb|FK024115.1|FK024115
EST:     GAGTTGCTGAGATTTCTATTAGAGATAGACAG                         ATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCAT
genomic: GAGTTGCTGAGATTTCTATTAGAGATAGACAGgtaaagaatt ... caatatgtagATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCAT
EST: gi|6747004|gb|AW317460.1|AW317460
EST:     GAGTTGCTGAGATTTCTATTAGAGATAGACAG                         ATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCAT
genomic: GAGTTGCTGAGATTTCTATTAGAGATAGACAGgtaaagaatt ... caatatgtagATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCAT
EST: gi|31472202|gb|CD414230.1|CD414230
EST:     GAGTTGCTGAGATTTCTATTAGAGATAGACAG                         ATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCAT
genomic: GAGTTGCTGAGATTTCTATTAGAGATAGACAGgtaaagaatt ... caatatgtagATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCAT
EST: gi|209702150|gb|BW677950.1|BW677950
EST:     GAGTTGCTGAGATTTCTATTAGAGATAGACAG                         ATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCAT
genomic: GAGTTGCTGAGATTTCTATTAGAGATAGACAGgtaaagaatt ... caatatgtagATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCAT
EST: gi|298171130|gb|HO016162.1|HO016162
EST:     GAGTTGCTGAGATTTCTATTAGAGATAGACAG                         ATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCAT
genomic: GAGTTGCTGAGATTTCTATTAGAGATAGACAGgtaaagaatt ... caatatgtagATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCAT
EST: gi|10255867|gb|BE823633.1|BE823633
EST:     GAGTTGCTGAGATTTCTATTAGAGATAGACAG                         ATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCAT
genomic: GAGTTGCTGAGATTTCTATTAGAGATAGACAGgtaaagaatt ... caatatgtagATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCAT
EST: gi|298197096|gb|HO041839.1|HO041839
EST:     GAGTTGCTGAGATTTCTATTAGAGATAGACAG                         ATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCAT
genomic: GAGTTGCTGAGATTTCTATTAGAGATAGACAGgtaaagaatt ... caatatgtagATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCAT
EST: gi|15200962|gb|BI424621.1|BI424621
EST:     GAGTTGCTGAGATTTCTATTAGAGATAGACAG                         ATTCCTCTAACTGGAGTTCACTCCATAATCGGAAGGGCCGTTGTTGTGCAT
genomic: GAGTTGCTGAGATTTCTATTAGAGATAGACAGgtaaagaatt ... caatatgtagATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtttaattgggtctagaacacttaatttcctctttctcactttcaatatgtagATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGG
                                   ttctcac  putative branch site (score: 2)
                      cttaatttcctctttc  CT-rich tract
                     acttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattgttttcatttggttgatatttttgtttatgaaatttgaatgtagtttaattgggtctagaacacttaatttcctctttctcactttcaatatgtagATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - gaatgta