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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAATGATTGATCATGAGCAGCGTAAGCTTCGCCTTATAGATTGGGGGCTTGCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGCGTGGCATCAAGgtatatttgctcttatgtctcttttttttttgttttttttttttggggtgggggaggaggattcataattgaggtgggccttggggggaatcattaggag...

Basic information

species Glycine max
transcript GLYMA05G22320.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G22320.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os03g55490.1 (Oryza sativa), 5'ss of exon 4
TAATGATTGATCATGAGCAGCGTAAGCTTCGCCTTATAGATTGGGGGCTTGCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGCGTGGCATCAAGgtatatttgctcttatgtctcttttttttttgttttttttttttggggtgggggaggagga--ttcataattgaggtgggccttggggggaatcattaggag
| ||||||||||||||| | ||  ||||| | ||||| |||||||| || |||||||||||||||||   ||  |||||||||| | | || || ||||||| || |  | |||   |      ||   |  ||     || ||  | |     || ||||  ||||       |     || |  | |      ||| |  
TCATGATTGATCATGAGAAACGCCAGCTTTGTCTTATTGATTGGGGTCTAGCAGAGTTCTATCATCCCAAGATGGAATATAATGCTAGAGTTGCTTCAAGgt-tagtctcccttgcattggaagttcaatgtttcagacttgttcagcttattaagaaggaacttcacttgcatgcctaaccctctgagatccttttatgt-

upper sequence: GLYMA05G22320.1 (Glycine max), 5'ss of exon 4
lower sequence: AT2G23070.1 (Arabidopsis thaliana), 5'ss of exon 4
TAATGATTGATCATGAGCAGCGTAAGCTTCGCCTTATAGATTGGGGGCTTGCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGCGTGGCATCAAGgtatatttgctcttatgtctcttttttttttgtttttt---ttttttggggtgggggaggaggattcataattgaggtgggccttggggggaatcattaggag
| ||||||||||| |||||||| || |||||  | || || |||||  | ||||| ||||||||||||||||||||||| ||||| || || || ||||||||  |    |    | |||  |  | | |  | |      || | |  | ||  |  |    |||  |  |    | | | || |    |||   ||     
TCATGATTGATCACGAGCAGCGAAAACTTCGTTTAATTGACTGGGGTTTGGCAGAATTCTATCATCCTGGGAAAGAATACAATGTCCGTGTTGCTTCAAGgtagttccttttggctatctgctaatctctcctctgcaagattctatttgttgcagttgctaaatttctgctcatagagagtctagataagaaatgttga---

upper sequence: GLYMA05G22320.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv07s0129g00270.t01 (Vitis vinifera), 5'ss of exon 4
TAATGATTGATCATGAGCAGCGTAAGCTTCGCCTTATAGATTGGGGGCTTGCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGCGTGGCATCAAGgtatatttgctcttatgtctcttttttttttgttttttttttttggggtgggggaggaggattcataattgaggtgggccttgggggga--atcattaggag---
| ||||||||||||||||||||||| ||||| |||||||||||||| || |||||||||||||||||||| |||||||| |||||||| || || |||||||   ||  | ||     ||  |||  |      ||  || ||| |  | |   |     |||  |  |     ||    ||||  | |  | ||||        
TCATGATTGATCATGAGCAGCGTAAACTTCGTCTTATAGATTGGGGCCTGGCAGAGTTCTATCATCCTGGCAAAGAATACAATGTTCGGGTTGCTTCAAGgttctttccccct-----cttctttaatggaagcttaattattttgcatagtatatttacattttttttctccttgttttttggtagaactaccatttcctttct

upper sequence: GLYMA05G22320.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S165_107V6.1 (Physcomitrella patens), 5'ss of exon 4
TAATGATTGATCATGAGCAGCGTAAGCTTCGCCTTATAGATTGGGGGCTTGCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGCGTGGCATCAAGgtatatttgc-tcttatgtctcttttttttttgttttttttttttggggtgggggaggaggattcataattgaggt----gggccttggggggaatcattaggag
| |||||||||||||| ||||| ||  |  |  | ||||||||||||||||| || ||||||||||| || ||||| ||||| || ||||| || || ||||      || || |   |   |   |  |        |||| |  |   |       ||  ||  ||| |    |        ||||    ||||| ||     
TGATGATTGATCATGAACAGCGAAAATTAAGATTAATAGATTGGGGGCTTGCTGAATTCTATCATCCCGGAAAAGAGTATAACGTGCGCGTTGCGTCTAGgtcagcacgcatcattcctgaatgcatcatcacaaaacttttctctgtacgctcttctagtttttttaaattcactttttaacacttgacttgaatcgtt-----

upper sequence: GLYMA05G22320.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S63_208V6.1 (Physcomitrella patens), 5'ss of exon 5
TAATGATTGATCATGAGCAGCGTAAGCTTCGCCTTATAGATTGGGGGCTTGCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGCGTGGCATCAAGgtatatttgctcttatgtctcttttttttttgtttttttttt---ttggggtgggggaggaggattcataattgaggtgggccttggggggaatcattaggag
|||||||||| || ||||| || |||||  | || || |||||||| || || ||||||||||| ||||| |||||||||||||| || || || || |||||  ||       | |  |||  |     ||| ||         ||    |   | |   | ||     | ||  ||||    || ||   || ||||    
TAATGATTGACCACGAGCAACGAAAGCTGAGACTGATTGATTGGGGACTCGCTGAGTTCTATCACCCTGGCAAAGAATATAATGTGCGTGTTGCCTCCAGgtaagttc---taaaggcttctcgtggcactgtcttaacgagggattcatttcaagaaatcgtatcatagaatgtagtggttactgtggattattattaattt

upper sequence: GLYMA05G22320.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 5
TAATGATTGATCATGAGCAGCGTAAGCTTCGCCTTATAGATTGGGGGCTTGCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGCGTGGCATCAAGgtatatttg------ctcttatgtctcttttttttttgttttttttttttggggtgggggaggaggattcataattgaggtgggccttggggggaatcattaggag
| |||||||| ||||||||||| |||||| | ||||| || ||||| ||||| || |||||||||||||| ||||| |||||||| || || || || ||||   |||        ||||  | |  ||  ||         ||| | ||  | | ||    ||      | |   ||     || |    | | |   |      
TGATGATTGACCATGAGCAGCGGAAGCTTAGGCTTATTGACTGGGGACTTGCCGAATTCTATCATCCTGGCAAAGAGTATAATGTGCGTGTTGCCTCTAGgtgagtttcagaggcttcttgaggcagttacttagggaggactttatattatgtttggctgagaatccggacatcagaatcatgcttcatcgagtaagct------

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|37995826|gb|CF807415.1|CF807415
EST:     GCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGCGTGGCATCAAG                         ATATTTCAAAGGTCCTGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC
genomic: GCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGCGTGGCATCAAGgtatatttgc ... ttacatgtagATATTTCAAAGGTCCTGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC
EST: gi|15815566|gb|BI787841.1|BI787841
EST:     GCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGCGTGGCATCAAG                         ATATTTCAAAGGTCCTGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC
genomic: GCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGCGTGGCATCAAGgtatatttgc ... ttacatgtagATATTTCAAAGGTCCTGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC
EST: gi|18848708|gb|BM567820.1|BM567820
EST:     GCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGCGTGGCATCAAG                         ATATTTCAAAGGTCCTGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC
genomic: GCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGCGTGGCATCAAGgtatatttgc ... ttacatgtagATATTTCAAAGGTCCTGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC
EST: gi|20814462|gb|BQ298940.1|BQ298940
EST:     GCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGCGTGGCATCAAG                         ATATTTCAAAGGTCCTGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC
genomic: GCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGCGTGGCATCAAGgtatatttgc ... ttacatgtagATATTTCAAAGGTCCTGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC
EST: gi|16343159|gb|BI968754.1|BI968754
EST:     TATCATCCTGNNNAAGAATATAATGTTCGCGTGGCATCAAG                         ATA-TTCAAAGGTCCTGAGCTTC-TGNNNNNTCTTCAAGACTATGATTACT
genomic: TATCATCCTGGGAAAGAATATAATGTTCGCGTGGCATCAAGgtatatttgc ... ttacatgtagATATTTCAAAGGTCCTGAGCTTCTTG-TTGATCTTCAAGACTATGATTACT
EST: gi|9819518|gb|BE555031.1|BE555031
EST:     GCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGCGTGGCATCAAG                         ATATTTCAAAGGTCCTGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC
genomic: GCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGCGTGGCATCAAGgtatatttgc ... ttacatgtagATATTTCAAAGGTCCTGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC
EST: gi|7640075|gb|AW734384.1|AW734384
EST:     GCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGCGTGGCATCAAG                         ATATTTCAAAGGTCCTGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC
genomic: GCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGCGTGGCATCAAGgtatatttgc ... ttacatgtagATATTTCAAAGGTCCTGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAATGATTGATCATGAGCAGCGTAAGCTTCGCCTTATAGATTGGGGGCTTGCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGCGTGGCATCAAGgtatatttgctcttatgtctcttttttttttgttttttttttttggggtgggggaggaggattcataattgaggtgggccttggggggaatcattaggag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggggtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaggagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaggtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggggga