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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttatatttaagcctttatgtccgcataccacccgatactcacaaaatacaaagcaaaagaaaacttttggaagacattttaatcaatatatttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAGCTTGCTGAGGATAGGCATTGGAGGGTCCGGCTTGCAATTATAGAATATA

Basic information

species Glycine max
transcript GLYMA10G42250.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 8
----------cttatatttaagcctttatgtccgcataccacccgatactcacaaaatacaaagcaaaagaaaacttttggaagacattttaatcaatatatttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAGCTTGCTGAGGATAGGCATTGGAGGGTCCGGCTTGCAATTATAGAATATA
          || | || |||   || |  |  || | ||    ||  || | ||| | |   |  | |||||| |  |          | | ||  | |  | || |||||||| ||||||||| || | || || ||  ||||||| || || || || ||||| ||||||||||| |||||||| ||||||||||| || || || |
agtcccacagctca-atataacatttcaattttgcttccctaatga--ctgataaattccttggtcatagaaaattcatta-------ctgagtccttttgatctttcagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAACTTGCAGAGGATAGGCACTGGAGGGTTCGGCTTGCAATAATTGAGTACA

upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 8
-----------------------------------------------------------------------------------cttatatttaagcctttatgtccgcataccacccgatactcacaaaa----tacaaagcaaaagaaaacttttggaagacattttaatc--aatatatttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAGCTTGCTGAGGATAGGCATTGGAGGGTCCGGCTTGCAATTATAGAATATA
                                                                                   ||     |||      ||  |     ||  |   |||   |   |||    | |    |     |||| | |  || ||    | | |     | |  | || |||||||| ||||||||  || ||||||| ||  || ||||||| ||||| || ||||| ||||||||||| ||||| |||||||||||||| || || || |
gtcagtaccattttttttgttattagatttatttgccttttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagattttttta--agttgatgtccttgaaagccttgcctttctcttcaaaattatctgatgattgctgatttttgttttgatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA

upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 8
-------------------------------------------------------------------------------cttatatttaagcctttatgtccgcataccacccgatactcacaaaatacaaag-caaaagaaaacttttggaagacattttaatcaatatatttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAGCTTGCTGAGGATAGGCATTGGAGGGTCCGGCTTGCAATTATAGAATATA
                                                                                |  |||    |  ||| | |  |   ||   ||  ||  |      | |     ||||| |   || |||   |     ||  |   | |  | || |||||||| || |||||  | ||||| ||  |  || ||||||||||||| || ||||| ||||||||||| ||||| |||||||||||||| || || || |
gtcagtaccattttttgttactggatttctttgccttttccttgccgttttggatctttgaagtcttgtttaccagctattagtatgctggaatttttttaagt-cactgtcctgtaagcctggcctccctcttcaaaaaagttctgttgattggtgaatt--ttgttttgatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA

upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 8
cttatatttaagcctttatgtccgcataccacccgatactcacaaaatacaaagcaaaagaaaacttttggaagacattttaatcaatatatttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAGCTTGCTGAGGATAGGCATTGGAGGGTCCGGCTTGCAATTATAGAATATA
  | | ||  | |  |  |||  || |   |  | |   | |     | |  |             ||| |  |     | ||| | | | ||   ||||||||| |||||||||||  ||||||| || |||||||| |||||||| || |||||||||||| |||| ||||| ||||| |||||||| ||||| ||| 
-gtttgttgcatctctcttgtgtgctttagatactacttttattgcttcctta-------------tttagttggtgactgaatta-tcttttacggcagGTTATTGGAATTGATCTACTATCTCAATCCTTGTTACCGGCCATTGTAGAACTTGCTGAGGATCGGCACTGGAGAGTCCGACTTGCAATAATAGAGTATG

upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 7
cttatatttaagcctttatgtccgcataccacccgatactcacaaaatacaaagcaaaagaaaacttt--tggaagacattttaatcaatatatttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAGCTTGCTGAGGATAGGCATTGGAGGGTCCGGCTTGCAATTATAGAATATA
  |  ||   |  ||| | | |   | |     | || |     | |        |   | |   |    |   |||||||||||  ||   ||| ||||||||||| |||| |||||| || || || ||  | ||||| ||||||||||||||||| |||||||| ||||||||||| || |||||||| ||||| ||||
--tccatgacaagcttcagggctttaaagatgtccatgcatgtgagaggagtcttatgtgcatgttcccctttcagacattttaaataagcgattcttgcagGTTATTGGAACTGATCTATTGTCCCAATCCCTATTACCGGCCATTGTTGAGCTTGCAGAGGATAGACATTGGAGGGTTCGACTTGCAATAATAGAGTATA

upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S117_137V6.1 (Physcomitrella patens), 3'ss of exon 7
------------------------------------------------------------------------------------cttatatttaagcctttatgtc-cgcataccaccc-gatactcacaaaatacaa-agcaaaagaaaacttttggaagac--attttaatcaatatatttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAGCTTGCTGAGGATAGGCATTGGAGGGTCCGGCTTGCAATTATAGAATATA
                                                                                    ||    |||   | |  ||||        | |  | |   |  ||    |   | | |     | ||  |  || |  |  |  ||| | | | | | ||||||||| ||||| |||||| | || ||||||||  |||||||||||||||| ||| | ||||||||  | |||||| | || || || || || || ||||| |
gtaagtagttaattctgtcaacaaaggatattatgatacatgtcgagatcctttcattgtgatgggtgtgttgacttcatgtctctccggtttgttcatgaatgtggtttgctctattctggcgccgacggtctttgacaacggggaagaatatccgggaatctgaagttagt-actttttgtttgcagGTGATAGGCATTGATTTATTGTCTCAGTCACTGTTACCAGCCATTGTCGAGTTGGCTGAGGACCGACATTGGCGCGTTCGTCTGGCCATAATTGAATACA

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|151403929|gb|EV273739.1|EV273739
EST:     TTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAG                         GTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
genomic: TTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgttgttatag ... atttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
EST: gi|151407658|gb|EV277473.1|EV277473
EST:     TTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAG                         GTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
genomic: TTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgttgttatag ... atttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
EST: gi|17153685|gb|BM143618.1|BM143618
EST:     TTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAG                         GTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
genomic: TTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgttgttatag ... atttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
EST: gi|254331030|gb|GR842295.1|GR842295
EST:     TTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAG                         GTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
genomic: TTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgttgttatag ... atttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
EST: gi|19270079|gb|BM886335.1|BM886335
EST:     ATCAAGTGAATCAG                         GTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
genomic: ATCAAGTGAATCAGgttgttatag ... atttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
EST: gi|16105352|gb|BI893092.1|BI893092
EST:     CGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAG                         GTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
genomic: CGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgttgttatag ... atttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
EST: gi|7926502|gb|AW832528.1|AW832528
EST:     TTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAG                         GTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
genomic: TTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgttgttatag ... atttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
EST: gi|208055523|gb|GD854618.1|GD854618
EST:     CAAGTGAATCAG                         GTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
genomic: CAAGTGAATCAGgttgttatag ... atttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
EST: gi|26057519|gb|CA800433.1|CA800433
EST:     TTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAG                         GTTATAGGAATTGATCTGTTATCTCAATCTTTGTTACCAGCCATTGTTGAG
genomic: TTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgttgttatag ... atttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
EST: gi|254343473|gb|GR857229.1|GR857229
EST:     TTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAG                         GTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
genomic: TTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgttgttatag ... atttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatacaaagcaaaagaaaacttttggaagacattttaatcaatatatttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAGCTTGCTGAGGATAGGCATTGGAGGGTCCGGCTTGCAATTATAGAATATA
                                ttttaat  putative branch site (score: 3)
                                            tattttt  putative PPT
                          aagacattttaatcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttatatttaagcctttatgtccgcataccacccgatactcacaaaatacaaagcaaaagaaaacttttggaagacattttaatcaatatatttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAGCTTGCTGAGGATAGGCATTGGAGGGTCCGGCTTGCAATTATAGAATATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - -gccttta
- - - - - - - - - - - -gcatacc
- - - - - - - - - - - - - - - - - - -actcaca
- - - - - - - - - - - - - - - - - - - - - - - - -caaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa