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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatgcttgtatggttattgaatcttattttgcctctggcttccttttgtatacaactccatatattatgatttcttatgagggaagcttaattttgcagGGAAGGATGATTTTGGCACACTTATGTGATGAACCTAAGGGTCTGAAAACTGGGATGTGCATG

Basic information

species Glycine max
transcript GLYMA02G14210.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G14210.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os06g10280.1 (Oryza sativa), 3'ss of exon 13
-acatgcttgtatggttattgaatcttattttgcctctggcttccttttgtatacaactccatatattatgatttcttatgagggaagcttaattttgcagGGAAGGATGATTTTGGCACACTTATGTGATGAACCTAAGGGTCTGAAAACTGGGATGTGCATG
   |   ||| |    || || ||  || |   |  |   | ||||| | | | |  |     || |  || |    | |   |    | |   |   ||||||||||||||  | || || |||||||||||||| || ||||| |||||||| |||||||||
gtgagatttgcaaacatagtgcataatactaatctaccatcatccttgtttttccttcctggaat-tagtgctcatattttgagttgccatgcatggacagGGAAGGATGATACTTGCTCATTTATGTGATGAACCCAAAGGTCTCAAAACTGGAATGTGCATG

upper sequence: GLYMA02G14210.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os02g02750.1 (Oryza sativa), 3'ss of exon 13
acatgcttgtatg-gttattgaatcttattttgcctctggcttccttttgtatacaactccatatattatgatttcttatgagggaagcttaat-tttgcagGGAAGGATGATTTTGGCACACTTATGTGATGAACCTAAGGGTCTGAAAACTGGGATGTGCATG
| | | || | |  |  | |  || ||  | || |       |  | ||| | |  || |  | ||| |  ||| | ||  |   |    || | |   ||||| || |||||| |||| |||||||||||||| || || |||||||| || ||||||||||||
ata-gtttatgtaagccagtatattttggtctgacatgcttcttttgttgcaaaagacactct-tatgagcattacctaatatctacttctattatgcacagGGCAGAATGATTCTGGCTCACTTATGTGATGAGCCCAAAGGTCTGAAGACAGGGATGTGCATG

upper sequence: GLYMA02G14210.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os02g02750.3 (Oryza sativa), 3'ss of exon 13
acatgcttgtatg-gttattgaatcttattttgcctctggcttccttttgtatacaactccatatattatgatttcttatgagggaagcttaat-tttgcagGGAAGGATGATTTTGGCACACTTATGTGATGAACCTAAGGGTCTGAAAACTGGGATGTGCATG-------------------------------------
| | | || | |  |  | |  || ||  | || |       |  | ||| | |  || |  | ||| |  ||| | ||  |   |    || | |   ||||| || |||||| |||| |||||||||||||| || || |||||||| || ||||||||||||                                     
ata-gtttatgtaagccagtatattttggtctgacatgcttcttttgttgcaaaagacactct-tatgagcattacctaatatctacttctattatgcacagGGCAGAATGATTCTGGCTCACTTATGTGATGAGCCCAAAGGTCTGAAGACAGGGATGTGCATGGTTGTTGCCTAATCACCTTTGTTCTTTGGTTTTGTTT

upper sequence: GLYMA02G14210.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G466281_T01 (Zea mays), 3'ss of exon 13
acatgcttgtatggttattgaatcttattttgcctctggc--ttccttttgtata-caactccatatattatgatttcttatgagggaagcttaattttgcagGGAAGGATGATTTTGGCACACTTATGTGATGAACCTAAGGGTCTGAAAACTGGGATGTGCATG
 ||||||| | |  || ||   |   |  |  |||||  |  || || | ||  |  ||    ||  |  || | ||   ||  |   |  ||   |   |||||||| |||||| |||| ||||| ||||||||||| |||||| ||||||| ||||||||||||
-catgcttattttatttttctcttacagatgccctctttcagttactgtagtgcagtaaaaatatgaac-attactttacatctgcttatattg-ctccacagGGAAGAATGATTCTGGCTCACTTGTGTGATGAACCCAAGGGTTTGAAAACAGGGATGTGCATG

upper sequence: GLYMA02G14210.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv01s0010g00950.t01 (Vitis vinifera), 3'ss of exon 14
--acatgcttgtatggttattgaatcttattttgcctctggcttc---cttttgtatacaactccat-atattatgatttcttatgagggaagcttaattttgcagGGAAGGATGATTTTGGCACACTTATGTGATGAACCTAAGGGTCTGAAAACTGGGATGTGCATG
     | ||| |    | |   ||| | || |      || |      |  |   || ||||   || ||||| ||| |      ||  |||||||  ||| |||||||||||||||| |||||||||| ||||||||||| |||||  |||||||||| |||||||||
gtggcttcttttgcaatgaa-aaatttaatatcattagtgacaatagacaatcacattcaacgttatcatattgtgacta-----gaaagaagcttgttttggcagGGAAGGATGATTCTGGCACACTTGTGTGATGAACCCAAGGGCTTGAAAACTGGAATGTGCATG

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|7028778|gb|AW458561.1|AW458561
EST:     ATCCACATTTAGTTGTCATAGGAACTGGACTTACTTTCGGTTATCTTGTG                         GGAAGGATGATTTTGGCACACTTATGTGATGAACCTAAGGGTCTGAAAACT
genomic: ATCCACATTTAGTTGTCATAGGAACTGGACTTACTTTCGGTTATCTTGTGgtaagatggt ... aattttgcagGGAAGGATGATTTTGGCACACTTATGTGATGAACCTAAGGGTCTGAAAACT
EST: gi|10252639|gb|BE820405.1|BE820405
EST:     ATCCACATTTAGTTGTCATAGGAACTGGACTTACTTTCGGTTATCTTGTG                         GGAAGGATGATTTTGGCACACTTATGTGATGAACCTAAGGGTCTGAAAACT
genomic: ATCCACATTTAGTTGTCATAGGAACTGGACTTACTTTCGGTTATCTTGTGgtaagatggt ... aattttgcagGGAAGGATGATTTTGGCACACTTATGTGATGAACCTAAGGGTCTGAAAACT
EST: gi|16995635|gb|BM085007.1|BM085007
EST:     ATCCACATTTAGTTGTCATAGGAACTGGACTTACTTTCGGTTATCTTGTG                         GGAAGGATGATTTTGGCACACTTATGTGATGAACCTAAGGGTCTGAAAACT
genomic: ATCCACATTTAGTTGTCATAGGAACTGGACTTACTTTCGGTTATCTTGTGgtaagatggt ... aattttgcagGGAAGGATGATTTTGGCACACTTATGTGATGAACCTAAGGGTCTGAAAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtatacaactccatatattatgatttcttatgagggaagcttaattttgcagGGAAGGATGATTTTGGCACACTTATGTGATGAACCTAAGGGTCTGAAAACTGGGATGTGCATG
                                         gcttaat  putative branch site (score: 4)
               atatattatgatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatgcttgtatggttattgaatcttattttgcctctggcttccttttgtatacaactccatatattatgatttcttatgagggaagcttaattttgcagGGAAGGATGATTTTGGCACACTTATGTGATGAACCTAAGGGTCTGAAAACTGGGATGTGCATG

acatgct
- - - -tgtatgg
- - - - - - - - - - - - - - - tgcctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - aactcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagggaa