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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattccccttccatacctttggtgagcagttattgttgtttacatggacagaagtaactaatgtttcttctttgctcattctatttagATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAG

Basic information

species Glycine max
transcript GLYMA09G12420.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G12420.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g42380.1 (Oryza sativa), 3'ss of exon 4
gtattccccttccatacctttggtgagcagttat-tgttgtttacatggacagaa-gtaactaatgtttcttctttgctcattct-atttagATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAG
           ||       |||  | ||||| | |  ||  |   ||| | |   ||   |||  ||  ||  ||  | || || ||  || || || ||| | || |||||||||||||| || |  ||||| || ||||||||||| ||||||||||| || || |||||||| |||||
--gcaagttaacctggttgctgggtatcagttctataatgcctcattgggctgtttgttcataaaattaatt--ttattgatgctgatgcagGTACGAGAAGAGGCACTCCAATATTCCTGCTCACATTTCACCGTGCTTCCGTGTTAAGGAAGGAGATCACGTGATCATTGGCCAGTGCAG

upper sequence: GLYMA09G12420.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0118g00680.t01 (Vitis vinifera), 3'ss of exon 4
gtattccccttccatacctttggtgagcagttattgttgtttacatggacag---------aagtaactaatgtttcttctttgctcattctatttagATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAG
| ||   ||| |  |     | ||||   | |||| ||  || |      |          |||||  | |   || ||  ||  |   |  ||| |||||||| ||| | || || || |||||||| || ||||| || || |||||||| || |||||||||||||||||||||||||| |||||
gcatgttcctccagttatagttgtgaatgggtatttttactttccccagaatttgcttttcaagtagttgaccattttttcttctttgctgcattcagATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCGTGTGAAGGAAGGAGATCATGTTATTATTGGCCAGTGCAG
















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|192295631|gb|FG990485.1|FG990485
EST:     ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAG                         ATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
genomic: ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAGgtattcccct ... ttctatttagATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
EST: gi|192327596|gb|FK020643.1|FK020643
EST:     ACCATTATTGTAAGGAGGAATTATTTTCATTTTATTAAGAAATACCAGAG                         ATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
genomic: ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAGgtattcccct ... ttctatttagATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
EST: gi|213610237|gb|DB980823.1|DB980823
EST:     ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAG                         ATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
genomic: ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAGgtattcccct ... ttctatttagATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
EST: gi|31474232|gb|CD416260.1|CD416260
EST:     ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAG                         ATATGAAAAGCGACATTCCAATATTCCTGCACATATATCACCTTGTTTCCG
genomic: ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAGgtattcccct ... ttctatttagATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
EST: gi|298193555|gb|HO040203.1|HO040203
EST:     ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAG                         ATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
genomic: ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAGgtattcccct ... ttctatttagATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
EST: gi|213612020|gb|DB964856.1|DB964856
EST:     ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAG                         ATATGAAAAGCGACATTCCAATATTCCTGCACATACATNCACCTTGTTTCC
genomic: ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAGgtattcccct ... ttctatttagATATGAAAAGCGACATTCCAATATTCCTGCACATACAT-CACCTTGTTTCC
EST: gi|151409325|gb|EV279133.1|EV279133
EST:     ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAG                         ATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
genomic: ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAGgtattcccct ... ttctatttagATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
EST: gi|192334070|gb|FK026227.1|FK026227
EST:     ACCATTATTGTAAGGAGGAATTATTTTCATTTTATTAAGAAATACCAGAG                         ATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
genomic: ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAGgtattcccct ... ttctatttagATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
EST: gi|298192237|gb|HO036319.1|HO036319
EST:     ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAG                         ATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
genomic: ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAGgtattcccct ... ttctatttagATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
EST: gi|192329280|gb|FK020199.1|FK020199
EST:     ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAG                         ATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
genomic: ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAGgtattcccct ... ttctatttagATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
EST: gi|192323316|gb|FK017422.1|FK017422
EST:     ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAG                         ATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
genomic: ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAGgtattcccct ... ttctatttagATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
EST: gi|10256428|gb|BE824194.1|BE824194
EST:     ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAG                         ATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
genomic: ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAGgtattcccct ... ttctatttagATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
EST: gi|151410570|gb|EV280385.1|EV280385
EST:     ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAG                         ATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
genomic: ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAGgtattcccct ... ttctatttagATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
EST: gi|7145646|gb|AW507568.1|AW507568
EST:     ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAG                         ATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
genomic: ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAGgtattcccct ... ttctatttagATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
EST: gi|38192824|gb|CF922030.1|CF922030
EST:     ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAG                         ATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
genomic: ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAGgtattcccct ... ttctatttagATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
EST: gi|192327595|gb|FK020642.1|FK020642
EST:     ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAG                         ATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
genomic: ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAGgtattcccct ... ttctatttagATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
EST: gi|38193079|gb|CF922285.1|CF922285
EST:     ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAG                         ATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
genomic: ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAGgtattcccct ... ttctatttagATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
EST: gi|298185805|gb|HO030966.1|HO030966
EST:     ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAG                         ATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
genomic: ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAGgtattcccct ... ttctatttagATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
EST: gi|151412049|gb|EV281861.1|EV281861
EST:     ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAG                         ATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
genomic: ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAGgtattcccct ... ttctatttagATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
EST: gi|213610749|gb|DB963135.1|DB963135
EST:     ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAG                         ATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
genomic: ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAGgtattcccct ... ttctatttagATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
EST: gi|192334069|gb|FK026226.1|FK026226
EST:     ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAG                         ATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
genomic: ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAGgtattcccct ... ttctatttagATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
EST: gi|18040050|gb|BM308344.1|BM308344
EST:     ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAG                         ATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG
genomic: ACCATTATTGTAAGGAGGAATTATCTTCATTTTATTAAGAAATACCAGAGgtattcccct ... ttctatttagATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgtttacatggacagaagtaactaatgtttcttctttgctcattctatttagATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAG
                      aactaat  putative branch site (score: 2)
                              tttcttctttgctcat  CT-rich tract
                                            attctattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattccccttccatacctttggtgagcagttattgttgtttacatggacagaagtaactaatgtttcttctttgctcattctatttagATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA