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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAGGAAGCTCAAGTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgattctgagacctatatttgcttcagctttgtgttttgccgcgtcttctagtttagattttgatttctaaggatcactatgttgctttggatat...

Basic information

species Arabidopsis thaliana
transcript AT4G25370.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G25370.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA16G32910.1 (Glycine max), 5'ss of exon 3
AGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAGGAAGCTCAAGTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgattctgagacctatatttgcttcagctttgtgttttgccgcgtcttctagtttagattttgatttctaaggatcactatgttgctttggatat--
|| ||||||||||||  ||||||||| |||||||| || |||||||||||||||||||  || || ||||| ||  |||||||||| ||||| || |||||||||| | |   | |  ||   ||| | |   |||   ||  |      |    |       |  |  | ||  | ||  |  |   |       | ||  
AGGGCTATAAAGTCATATGCAATGGGGGAATTGGAAGCGAGGAAGCTCAAGTATCCAAACACGGGAACCGAGGCACTTCTCATGGGGATTTTGGTTGAAGgtttgttagtt--acaattactattggtgcctttttaatttaagtaatagccatgacaactagtccttctatcgtaagagaaaaaaaataagaaaaaaatga

upper sequence: AT4G25370.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA09G28040.1 (Glycine max), 5'ss of exon 3
AGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAGGAAGCTCAAGTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgattctgagacctatatttgcttcagctttgtgttttgccgcgtcttctagtttagattttgatttctaaggatcactatgttgctttggatat
|| |||||||| ||   ||||||||| |||||||| || |||||||||||||||||||  || || ||||| || ||||||||||| ||||| || |||||||||| | |   |  |  |  || |  ||   ||  |||        | | |  |   |||   ||   |  ||||    |  |    |      | | 
AGGGCTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAGGAAGCTCAAGTATCCAAACACGGGAACCGAGGCGATTCTCATGGGGATTTTGGTTGAAGgtttgttagttacaatcacaatttggtgtctttttaatgtcagtaatagccatgaaaactagtgcttctatcgtaagagaaaagacaaagaagaaaaaaa

upper sequence: AT4G25370.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA09G28050.1 (Glycine max), 5'ss of exon 3
AGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAGGAAGCTCAAGTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgattctgagacctatatttgcttcagctttgtgttttgccgcgtcttctagtttagattttgatttctaaggatcactatgttgctttggatat-
|| |||||||| ||   ||||||||| |||||||| || |||||||||||||||||||  || || ||||| ||  |||||||||| ||||| || |||||||||| | | ||  | |   ||||| |     |||   ||  |      |    |       |  |  | ||  | ||  |  |    |     || |  
AGGGCTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAGGAAGCTCAAGTATCCAAACACGGGAACCGAGGCACTTCTCATGGGGATTTTGGTTGAAGgtttgttagt-tgcaatcacaatttggtgtctttttaatttcagtaatagccatgaaaaccagtgcttctatcgtaagagaaaaacaaagaagaagaaaat

upper sequence: AT4G25370.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA16G32900.1 (Glycine max), 5'ss of exon 3
AGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAGGAAGCTCAAGTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgattctgagacctatatttgcttcagctttgtgttttgccgc-gtcttctagtttagattttgatttctaag---gatcactatgttgctttggatat
|| | |||||| ||   ||||||||| |||||||| || |||||||||||||||||||  || || ||||| ||  |||||||||| ||||| || |||||||| |  ||   |    || | ||| |     |||   ||  |     | | |  |   |||   ||   |  ||||   |   | || |  |    | | | 
AGGGGTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAGGAAGCTCAAGTATCCAAACACGGGAACCGAGGCGCTTCTCATGGGGATTTTGGTTGAAGgtttatatttacaa---ttacaattggtgtctttttaatttcagtaatagccatgaaaactagtccttctatcgtaagagaggaaaataagaagaaaagaaaa-

upper sequence: AT4G25370.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA02G35060.1 (Glycine max), 5'ss of exon 3
AGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAGGAAGCTCAAGTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgt-gattctgagacctatatttgc---ttcagctttgtgttttgccgcgtcttctagt--ttagattttgatttctaaggatcactatgt--tgctttggatat----------------------------------
|| ||||||||||||  |||||| || |||||||| || |||||||||||||||||||  ||  | ||  | ||  |||||||||| ||||| || ||||||||||   ||   |   ||||   ||    || |  ||      | |||| | |  |||||  ||  ||  | |     ||  || |  |     ||  |    | |                                  
AGGGCTATAAAGTCATATGCAATTGGGGAATTGGAAGCGAGGAAGCTCAAGTATCCAAACACGCGAACTAATGCACTTCTCATGGGGATTTTGGTTGAAGgtttgttagttacaattactattggtgtctttttaatttcagcaatagccgtgacaactagtccttctatcgtaagagaaaaaaataagaaaaaaatgaatcaattttttcctgtattctaaaatcaacgtatgcatttcag

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|86036181|gb|DR331934.1|DR331934
EST:     GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAG                         GCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTCTCA
genomic: GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgatt ... ttgattttagGCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
EST: gi|86036191|gb|DR331944.1|DR331944
EST:     GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAG                         GCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACAC
genomic: GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgatt ... ttgattttagGCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACAC
EST: gi|47830527|gb|CK120211.1|CK120211
EST:     GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAG                         GCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
genomic: GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgatt ... ttgattttagGCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
EST: gi|86078578|gb|DR374335.1|DR374335
EST:     GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAG                         GCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
genomic: GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgatt ... ttgattttagGCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
EST: gi|86036195|gb|DR331948.1|DR331948
EST:     GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAG                         GCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
genomic: GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgatt ... ttgattttagGCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
EST: gi|124949860|gb|EL025387.1|EL025387
EST:     TACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAG                         GCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
genomic: TACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgatt ... ttgattttagGCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
EST: gi|86036182|gb|DR331935.1|DR331935
EST:     GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAG                         GCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
genomic: GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgatt ... ttgattttagGCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
EST: gi|47828108|gb|CK117792.1|CK117792
EST:     GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAG                         GCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
genomic: GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgatt ... ttgattttagGCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
EST: gi|86036189|gb|DR331942.1|DR331942
EST:     GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAG                         GCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
genomic: GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgatt ... ttgattttagGCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
EST: gi|86036183|gb|DR331936.1|DR331936
EST:     GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAG                         GCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
genomic: GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgatt ... ttgattttagGCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
EST: gi|125270637|gb|EL284722.1|EL284722
EST:     ACCGAAGCCATTCTCATGGGTATTTTAAGTCGAAG                         GCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAA
genomic: ACCGAAGCCATTCTCATGGGTATTTT-AGTCGAAGgtttgtgatt ... ttgattttagGCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAA
EST: gi|86036190|gb|DR331943.1|DR331943
EST:     GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAG                         GCACTANCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
genomic: GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgatt ... ttgattttagGCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
EST: gi|86036188|gb|DR331941.1|DR331941
EST:     GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAG                         GCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
genomic: GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgatt ... ttgattttagGCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
EST: gi|86036196|gb|DR331949.1|DR331949
EST:     GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAG                         GCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
genomic: GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgatt ... ttgattttagGCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
EST: gi|86036193|gb|DR331946.1|DR331946
EST:     GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAG                         GCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
genomic: GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgatt ... ttgattttagGCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
EST: gi|86036186|gb|DR331939.1|DR331939
EST:     GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAG                         GCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
genomic: GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgatt ... ttgattttagGCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
EST: gi|86036194|gb|DR331947.1|DR331947
EST:     GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAG                         GCACTAGCAACAGTTGCTAAGTTCCTGAGGGGG
genomic: GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgatt ... ttgattttagGCACTAGCA-CAGTTGCTAAGTTCCTGAGGGGG
EST: gi|86036192|gb|DR331945.1|DR331945
EST:     GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAG                         GCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATG
genomic: GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgatt ... ttgattttagGCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATG
EST: gi|86036197|gb|DR331950.1|DR331950
EST:     GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAG                         GCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
genomic: GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgatt ... ttgattttagGCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
EST: gi|86036185|gb|DR331938.1|DR331938
EST:     GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAG                         GCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
genomic: GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgatt ... ttgattttagGCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
EST: gi|164199263|gb|ES041632.1|ES041632
EST:     GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAG                         GCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACA
genomic: GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgatt ... ttgattttagGCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACA
EST: gi|86036198|gb|DR331951.1|DR331951
EST:     GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAG                         GCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
genomic: GTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgatt ... ttgattttagGCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAATGGAGTCACACTTTTCA
EST: gi|124995079|gb|EL067348.1|EL067348
EST:     CGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAG                         GCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAA
genomic: CGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgatt ... ttgattttagGCACTAGCACAGTTGCTAAGTTCCTGAGGGGGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAGGAAGCTCAAGTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgattctgagacctatatttgcttcagctttgtgttttgccgcgtcttctagtttagattttgatttctaaggatcactatgttgctttggatat

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