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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGTTAGTGTTATTTTAGCAAAAGAAGAATTGGCACCTGATGTTGATTTCGAAGCAATAGCAAATATGACTGATGGATATTCTGGGAGTGACCTAAAGgttgtatttctatgtatcttctacttcaattcttgatcgctggggaagatgacatgattttacatgaaatactcattgactcattgttatcttttcactgcag

Basic information

species Glycine max
transcript GLYMA10G02410.1
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G02410.1 (Glycine max), 5'ss of exon 21
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 5'ss of exon 24
AATTGTTAGTGTTATTTTAGCAAAAGAAGAATTGGCACCTGATGTTGATTTCGAAGCAATAGCAAATATGACTGATGGATATTCTGGGAGTGACCTAAAGgttgtatttctatgtatcttctacttcaattcttgatcgctggggaagatgacatgattttacatgaaatactcattgactcattgttatcttttcactgcag
 ||  | || |||||| |||||||||||||| | ||||| || || ||||| ||||| |||||||||||||| ||||| || || || |||||| |||||||      | | | || | |   ||   | |||   || |  |  || |  ||    |   ||| | | |  |  |||  |    |                 
GATCTTGAGCGTTATTCTAGCAAAAGAAGAAATAGCACCAGACGTCGATTTAGAAGCTATAGCAAATATGACAGATGGGTACTCAGGAAGTGACTTAAAGgtctcgactttctataaccttccctctcaatctccttcccctgtaaaaa-aac----tcacacacgtattcttttttgg-ttgcag-----------------

upper sequence: GLYMA10G02410.1 (Glycine max), 5'ss of exon 21
lower sequence: AT1G02890.2 (Arabidopsis thaliana), 5'ss of exon 23
AATTGTTAGTGTTATTTTAGCAAAAGAAGAATTGGCACCTGATGTTGATTTCGAAGCAATAGCAAATATGACTGATGGATATTCTGGGAGTGACCTAAAGgt-tgtatttctatgtatcttctacttcaattcttgatcgctggggaagatgacatgattttacatgaaatactcattgactcattgttatcttttcactgcag
 ||  | || || ||||| || ||||||||  |||||   || || || || |||||||||||||||||||| ||||| || || ||||||||| ||||||| ||||  |   |  |||     |   || |    | |  |     | |   |   ||| || || ||||  ||  ||  |    |                 
GATCTTGAGCGTGATTTTGGCGAAAGAAGAGATGGCAGAAGACGTAGACTTAGAAGCAATAGCAAATATGACAGATGGGTACTCAGGGAGTGACTTAAAGgtctgtaacttcctccatccaaagcacaaactgaaaacccatttcataaaaatccacattcta-atcaaattgtc--tggtttgcag-----------------

upper sequence: GLYMA10G02410.1 (Glycine max), 5'ss of exon 21
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 5'ss of exon 24
AATTGTTAGTGTTATTTTAGCAAAAGAAGAATTGGCACCTGATGTTGATTTCGAAGCAATAGCAAATATGACTGATGGATATTCTGGGAGTGACCTAAAGgttgtatttctatgtatcttctacttcaattcttgatcgctggggaagatgacatgattttacatgaaatactcattgactcattgttatcttttcactgcag
|||| | || |||||| | || ||||||||||||||||||||||||| ||| |||||| | ||||||||||||||||| |||||||| ||||||||||||||||  |    || |    |||| |  |  |  | ||  ||     | |  || |     || || |  | |   |   |  |||    | |           
AATTCTGAGAGTTATTCTGGCCAAAGAAGAATTGGCACCTGATGTTGGTTTGGAAGCAGTTGCAAATATGACTGATGGGTATTCTGGAAGTGACCTAAAGgttgcct---aatctcctctctattatatatgat-atgccttaaacatagaactttggcctatattagtttcctctaatcaaattaccgtttgcag-------

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|7234672|gb|AW570007.1|AW570007
EST:     TCGAAGCAATAGCAAATATGACTGATGGATATTCTGGGAGTGACCTAAAG                         AATCTATGTGTCACAGCAGCTCACTGTCCAATAAGAGAGATCTTGGAGAAG
genomic: TCGAAGCAATAGCAAATATGACTGATGGATATTCTGGGAGTGACCTAAAGgttgtatttc ... ttcactgcagAATCTATGTGTCACAGCAGCTCACTGTCCAATAAGAGAGATCTTGGAGAAG
EST: gi|24205678|gb|BU964931.1|BU964931
EST:     TCGAAGCAATAGCAAATATGACTGATGGATATTCTGGGAGTGACCTAAAG                         AATCTATGTGTCACAGCAGCTCACTGTCCAATAAGAGAGATCTTGGAGAAG
genomic: TCGAAGCAATAGCAAATATGACTGATGGATATTCTGGGAGTGACCTAAAGgttgtatttc ... ttcactgcagAATCTATGTGTCACAGCAGCTCACTGTCCAATAAGAGAGATCTTGGAGAAG
EST: gi|23064134|gb|BU578907.1|BU578907
EST:     TCGAAGCAATAGCAAATATGACTGATGGATATTCTGGGAGTGACCTAAAG                         AATCTATGTGTC-CAGCAGCTCACTGTCCAATAAGAGAGATCTTGGAGAAG
genomic: TCGAAGCAATAGCAAATATGACTGATGGATATTCTGGGAGTGACCTAAAGgttgtatttc ... ttcactgcagAATCTATGTGTCACAGCAGCTCACTGTCCAATAAGAGAGATCTTGGAGAAG
EST: gi|208157183|gb|GD955869.1|GD955869
EST:     TCGAAGCAATAGCAAATACGACTGATGGATATTCTGGGAGTGACCTAAAG                         AATCTATGTGTCACAGCAGCTCACTGTCCAATAAGAGAGATCTTGGAGAAG
genomic: TCGAAGCAATAGCAAATATGACTGATGGATATTCTGGGAGTGACCTAAAGgttgtatttc ... ttcactgcagAATCTATGTGTCACAGCAGCTCACTGTCCAATAAGAGAGATCTTGGAGAAG
EST: gi|33389718|gb|CA852925.1|CA852925
EST:     TCGAAGCAATAGCAAATATGACTGATGGATATTCTGGGAGTGACCTAAAG                         AATCTATGTGTCACAGCAGCTCACTGTCCAATAAGAGAGATCTTGGAGAAG
genomic: TCGAAGCAATAGCAAATATGACTGATGGATATTCTGGGAGTGACCTAAAGgttgtatttc ... ttcactgcagAATCTATGTGTCACAGCAGCTCACTGTCCAATAAGAGAGATCTTGGAGAAG
EST: gi|208169524|gb|GD972329.1|GD972329
EST:     TCGAAGCAATAGCAAATATGACTGATGGATATTCTGGGAGTGACCTAAAG                         AATCTATGTGTCACAGCAGCTCACTGTCCAATAAGAGAGATCTTGGAGAAG
genomic: TCGAAGCAATAGCAAATATGACTGATGGATATTCTGGGAGTGACCTAAAGgttgtatttc ... ttcactgcagAATCTATGTGTCACAGCAGCTCACTGTCCAATAAGAGAGATCTTGGAGAAG
EST: gi|58023725|gb|CX710466.1|CX710466
EST:     TCGAAGCAATAGCAAATATGACTGATGGATATTCTGGGAGTGACCTAAAG                         AATCTATGTGTCACAGCAGCTCACTGTCCAATAAGAGAGATCTTGGAGAAG
genomic: TCGAAGCAATAGCAAATATGACTGATGGATATTCTGGGAGTGACCTAAAGgttgtatttc ... ttcactgcagAATCTATGTGTCACAGCAGCTCACTGTCCAATAAGAGAGATCTTGGAGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTGTTAGTGTTATTTTAGCAAAAGAAGAATTGGCACCTGATGTTGATTTCGAAGCAATAGCAAATATGACTGATGGATATTCTGGGAGTGACCTAAAGgttgtatttctatgtatcttctacttcaattcttgatcgctggggaagatgacatgattttacatgaaatactcattgactcattgttatcttttcactgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA