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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGATGGCTTTATTGATTTGGATTCATATGATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACGgtgagtgaaatttttcattgtcagggccaaaattttatgctaggaaatctagagggcttaaatttcatttctttggtggtcttgtgagtattgtgaccgggatgattttggtgcag

Basic information

species Glycine max
transcript GLYMA07G04830.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G04830.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os01g52720.1 (Oryza sativa), 5'ss of exon 6
TTTGATGGCTTTATTGATTTGGATTCATATGATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACGgtgagtgaaatttttcattgtcagggccaaaattttatgctaggaaatctagagggcttaaatttcatttctttggtggtcttgtgagtattgtgaccgggatgattttggtgcag
||| |||| || |||||| | ||| ||||||||||||| || |||||||| | ||| ||||||||||| || |||||||| ||  ||     |  ||||  | ||   ||  |||  ||| |  || ||| ||     ||||  | | || || |  |  |||      || |   || |                 
TTTAATGGTTTCATTGATCTTGATGCATATGATACTATAGCGATGAAACTCAGAGGGGATGGAAGATGCTACATATCTACTgtatgta----tcctcatcctgaga--cagtattgaatg-tgcgatatcaag-----ttaa--tacgttgctata-taatctgaatcttaattaaacag-----------------
















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|298165347|gb|HO011396.1|HO011396
EST:     ATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACT                         ATCTACACGGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCA
genomic: ATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACGgtgagtgaaa ... tttggtgcagATCTACACAGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCA
EST: gi|192323993|gb|FK018684.1|FK018684
EST:     ATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACG                         ATCTACACGGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCA
genomic: ATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACGgtgagtgaaa ... tttggtgcagATCTACACAGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCA
EST: gi|298194118|gb|HO040766.1|HO040766
EST:     ATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACT                         ATCTACACGGAGAATTGGGTCAATTCACC
genomic: ATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACGgtgagtgaaa ... tttggtgcagATCTACACAGAGAATTGGGTCAATTCACC
EST: gi|298184473|gb|HO029686.1|HO029686
EST:     ATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACG                         ATCTACACAGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCA
genomic: ATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACGgtgagtgaaa ... tttggtgcagATCTACACAGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCA
EST: gi|298163373|gb|HO012106.1|HO012106
EST:     ATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACG                         ATCTACACAGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCA
genomic: ATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACGgtgagtgaaa ... tttggtgcagATCTACACAGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCA
EST: gi|193637998|gb|FK585372.1|FK585372
EST:     ATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACT                         ATCTACACGGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAAT
genomic: ATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACGgtgagtgaaa ... tttggtgcagATCTACACAGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAAT
EST: gi|192318066|gb|FK007180.1|FK007180
EST:     ATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACG                         ATCTACACAGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCA
genomic: ATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACGgtgagtgaaa ... tttggtgcagATCTACACAGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCA
EST: gi|298179745|gb|HO024960.1|HO024960
EST:     ATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACT                         ATCTACACGGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCA
genomic: ATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACGgtgagtgaaa ... tttggtgcagATCTACACAGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCA
EST: gi|192322997|gb|FK016728.1|FK016728
EST:     TTATATATCTACG                         ATTCTACACAGAGAATTTGGTCAATTTCACCTGGACAGATGGAAGATAATT
genomic: TTATATATCTACGgtgagtgaaa ... tttggtgcagA-TCTACACAGAGAATTGGGTCAA-TTCACCTGGACAGATGGAAGATAATT
EST: gi|58014519|gb|CX701261.1|CX701261
EST:     ATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACG                         ATCTACACAGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCA
genomic: ATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACGgtgagtgaaa ... tttggtgcagATCTACACAGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCA
EST: gi|192318065|gb|FK007179.1|FK007179
EST:     ATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACG                         ATCTACACAGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCA
genomic: ATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACGgtgagtgaaa ... tttggtgcagATCTACACAGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCA
EST: gi|298168411|gb|HO009341.1|HO009341
EST:     ATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACG                         ATCTACACAGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCA
genomic: ATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACGgtgagtgaaa ... tttggtgcagATCTACACAGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCA
EST: gi|192325825|gb|FK018047.1|FK018047
EST:     ATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACG                         ATCTACACAGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCA
genomic: ATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACGgtgagtgaaa ... tttggtgcagATCTACACAGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCA
EST: gi|298177341|gb|HO027122.1|HO027122
EST:     ATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACG                         ATCTACACAGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCA
genomic: ATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACGgtgagtgaaa ... tttggtgcagATCTACACAGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGATGGCTTTATTGATTTGGATTCATATGATACTATTGCTATGAAACTTAAAGGAGATGGAAGATGTTATATATCTACGgtgagtgaaatttttcattgtcagggccaaaattttatgctaggaaatctagagggcttaaatttcatttctttggtggtcttgtgagtattgtgaccgggatgattttggtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG