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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGAGGCAAACAATGCACATTATAACTCAATAGCCATAATTGATGCTGATGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAGgtatgcaatattcaggtcatttatgtgtcatttagtatgcgtacatcctaactcgtccaacaaattcccctacag

Basic information

species Glycine max
transcript GLYMA08G07960.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G07960.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os02g33080.2 (Oryza sativa), 5'ss of exon 3
GAGGAGGCAAACAATGCACATTATAACTCAATAGCCATAATTGATGCTGATGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAGgtatg--caatattcaggtcatttatgtgtcatt-tagtatgcgtacatcctaactcgtccaacaaattcccctacag-------------
|||||||| |||||||||||||| || ||| ||||||| |||||||||||||| |||||||||||  | ||  | || || |||||||||||||||||||||||   | || |  || | ||    |  ||| | |||  |    |    ||| ||  |  ||  || |   |||                
GAGGAGGCGAACAATGCACATTACAATTCAGTAGCCATTATTGATGCTGATGGCACTGATCTTGGCCTGTACCGCAAATCACATATTCCAGATGGACCAGgtattgcccatgtatagtttatgacagattcactatagactagtcatggactatctgatttaaacaagttagctatttcctttttggctag

upper sequence: GLYMA08G07960.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G073950_T01 (Zea mays), 5'ss of exon 4
GAGGAGGCAAACAATGCACATTATAACTCAATAGCCATAATTGATGCTGATGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAGgtatgcaatattcaggtcatttatgtgtcatttagtatgcgtacatcctaactcgtccaacaaattccccta--cag
|| || |||||||||||||||||||| ||  | || || || |||||||||||  ||||||||||  | ||| | || || || ||||||||||||||||||| |    ||  |||   ||  |||          ||  |   |||  | ||  |  | |   |||   |   |||
GAAGAAGCAAACAATGCACATTATAATTCGGTGGCTATTATCGATGCTGATGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAGgtaaggtcaat--aggcttttcctgttctgccatacattgggttatctcatct-ataaagccgcttctgtttgtcag

upper sequence: GLYMA08G07960.1 (Glycine max), 5'ss of exon 4
lower sequence: AT2G27450.2 (Arabidopsis thaliana), 5'ss of exon 4
GAGGAGGCAAACAATGCACATTATAACTCAATAGCCATAATTGATGCTGATGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAGgtatgcaatattcag-gtcatttatgtgtcatttagtatgcgt-acatcctaactcgtccaacaaattcccctacag
||||||||||| | ||||||||| || || || || |||||||||||||||||||||||  | || |||||||| ||||| |||||||| |||||||| |||  |  |  ||  | ||     || |  | |    |    || || |  |  ||    |  |   ||  | ||   
GAGGAGGCAAATACTGCACATTACAATTCGATTGCTATAATTGATGCTGATGGAACTGACTTGGGAATTTATAGGAAGTCTCATATTCCTGATGGACCTGgtgagtcaagtttggagttggaaatatagcttgagtttcttgttacctttttgctgagacctctttttatcttaag-

upper sequence: GLYMA08G07960.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv06s0080g00560.t01 (Vitis vinifera), 5'ss of exon 4
GAGGAGGCAAACAATGCACATTATAACTCAATAGCCATAATTGATGCTGATGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAGgtatgcaatattcaggtcatttatgtgtc-atttagtatgcgtacatcctaactcg--tccaacaaat-----tcccctacag
|| |||||||||||||| ||||| || ||||| |||||| ||||||||||||| ||||||||||| || || |||||||||||||| ||||||||||||||||||  |   | |||  | | || |  | |  | |||||  | |   | |  | |  |  || ||||     |  | |||||
GAAGAGGCAAACAATGCTCATTACAATTCAATTGCCATAGTTGATGCTGATGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAGgtatgtgaatgtaaggatact-atataccgagctggtatgttttctatccattttgattataataaatagttatttcttacag

upper sequence: GLYMA08G07960.1 (Glycine max), 5'ss of exon 4
lower sequence: EFJ10979 (Selaginella moellendorffii), 5'ss of exon 4
GAGGAGGCAAACAATGCACATTATAACTCAATAGCCATAATTGATGCTGATGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAGgtatgcaatattcaggtcatttatgtgtcatttagtatgcgtacatcctaactcgtccaacaaattcccctacag
|||||||||||||||||||| |||||||| || |  || || ||||| |||||||| || |||||| | ||  |||| || || ||||| || || |||||||||||  | |||       | ||| |||   | |      |  |     || || ||                
GAGGAGGCAAACAATGCACACTATAACTCTATTGTTATCATAGATGCCGATGGAACGGACCTTGGGCTCTACCGAAAATCTCACATTCCCGACGGCCCAGgtatgcatgaatcaa------tgtgtttcacagaatcgtttcatctttcgccttgtgcag---------------

upper sequence: GLYMA08G07960.1 (Glycine max), 5'ss of exon 4
lower sequence: EFJ07601 (Selaginella moellendorffii), 5'ss of exon 4
GAGGAGGCAAACAATGCACATTATAACTCAATAGCCATAATTGATGCTGATGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAGgtatgcaatattcaggtcatttatgtgtcatttagtatgcgtacatcctaactcgtccaacaaattcccctacag
|||||||||||||||||||| |||||||| || |  || || ||||| |||||||| || |||||| | ||  |||| || || ||||| || || |||||||||||  | |||  |  |||      ||   | |      |  |     || || ||                
GAGGAGGCAAACAATGCACACTATAACTCTATTGTTATCATAGATGCCGATGGAACGGACCTTGGGCTCTACCGAAAATCTCACATTCCCGACGGCCCAGgtatgcatgaatcaatttgttt------cacaaaatcgtttcatctttcgccttgtgcag---------------

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|151410591|gb|EV280406.1|EV280406
EST:     TGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAG                         GTTATGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTCAAG
genomic: TGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAGgtatgcaata ... tcccctacagGTTATGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTCAAG
EST: gi|298199306|gb|HO042669.1|HO042669
EST:     TGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAG                         GTTACGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTCAAG
genomic: TGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAGgtatgcaata ... tcccctacagGTTATGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTCAAG
EST: gi|24135848|gb|BU926358.1|BU926358
EST:     TGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAG                         GTTACGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTCAAG
genomic: TGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAGgtatgcaata ... tcccctacagGTTATGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTCAAG
EST: gi|298184831|gb|HO030044.1|HO030044
EST:     TGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAG                         GTTACGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTCAAG
genomic: TGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAGgtatgcaata ... tcccctacagGTTATGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTCAAG
EST: gi|192328547|gb|FK023551.1|FK023551
EST:     TGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAG                         GTTATGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTCAAG
genomic: TGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAGgtatgcaata ... tcccctacagGTTATGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTCAAG
EST: gi|298167316|gb|HO010755.1|HO010755
EST:     TGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAG                         GTTACGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTCAAG
genomic: TGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAGgtatgcaata ... tcccctacagGTTATGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTCAAG
EST: gi|254330221|gb|GR839774.1|GR839774
EST:     TGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAT                         GTTATGAGGAAAAGTTCTATTTTAATCCAG-TGACACTGGATTCAAG
genomic: TGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAGgtatgcaata ... tcccctacagGTTATGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTCAAG
EST: gi|298164922|gb|HO010919.1|HO010919
EST:     TGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGGTGGACCAG                         GTTACGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTCAAG
genomic: TGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAGgtatgcaata ... tcccctacagGTTATGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTCAAG
EST: gi|298167948|gb|HO013211.1|HO013211
EST:     TGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAG                         GTTACGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATT
genomic: TGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAGgtatgcaata ... tcccctacagGTTATGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATT
EST: gi|22541663|gb|BU091506.1|BU091506
EST:     TGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAG                         GTTACGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTCAAG
genomic: TGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAGgtatgcaata ... tcccctacagGTTATGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTCAAG
EST: gi|192328548|gb|FK023552.1|FK023552
EST:     TGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAG                         GTTATGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTCAAG
genomic: TGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAGgtatgcaata ... tcccctacagGTTATGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTCAAG
EST: gi|298178170|gb|HO023905.1|HO023905
EST:     TGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAG                         GTTACGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTCAAG
genomic: TGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAGgtatgcaata ... tcccctacagGTTATGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTCAAG
EST: gi|298187812|gb|HO031769.1|HO031769
EST:     TGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAG                         GTTACGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTC
genomic: TGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAGgtatgcaata ... tcccctacagGTTATGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGAGGCAAACAATGCACATTATAACTCAATAGCCATAATTGATGCTGATGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAGgtatgcaatattcaggtcatttatgtgtcatttagtatgcgtacatcctaactcgtccaacaaattcccctacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA