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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCACACCATCTGTAGTTTCGCTGATGGGAGGACTGCTTCCCTTTGGCAGCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgagttaaaatgcaattacttttctgggccataaaagattattttttcttccctttgtttggtacaaggtttacttttacttttttagagccgagccaa...

Basic information

species Glycine max
transcript GLYMA08G20100.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G20100.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os12g07670.1 (Oryza sativa), 5'ss of exon 10
CCTCACACCATCTGTAGTTTCGCTGATGGGAGGACTGCTTCCCTTTGGCAGCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgagt--taaaatgcaattacttt--tctgggccataaaagattattttttcttccctttgtttg-gtacaaggtttacttttacttttttagagccgagccaa
||| ||||| ||||| | || ||||||| || ||||||||||||||||| || ||||| |||||||| ||||| ||||| || |||||||| |||||||| | | || || || | || ||| | | || | | | | || ||| | | | | || || | | |
CCTTACACCTTCTGTTATCTCATTGATGGGTGGGCTGCTTCCCTTTGGCAGTATCTTCATTGAGATGTACTTTGTGTTCACGTCATTCTGGAACTACAAGgtaaacagtttaacttaagtatccaagtttgttttggaaacagaagtagtgcctatggtgtactggtgttcaacctcttatatggctgcttcataaatta-----

upper sequence: GLYMA08G20100.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os11g07910.1 (Oryza sativa), 5'ss of exon 10
CCTCACACCATCTGTAGTTTCGCTGATGGGAGGACTGCTTCCCTTTGGCAGCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgagttaaa-atgcaatt--acttttctgggccataaaagattattttttcttccctttgtttggt----acaaggtttacttttacttttttagagccgagccaa-------------------------------------------------------
|| ||||| ||||| | || ||||||| ||||| || ||||| |||||||| |||||||||||||| ||||| || ||||| |||||||| |||||||| | ||| || | | || | || || | | || || | || ||| | ||| | || | | | | || | | ||
TCTTACACCCTCTGTTATCTCATTGATGGGTGGACTACTCCCCTTCGGCAGCATCTTCATCGAGATGTACTTTGTGTTTACTTCATTCTGGAACTACAAGgtaaagaaaacatatcagtgaacactaatgtgcttctcagttctcacttctcaacaaattattttgctagaacagatggcatttacagtagatgtgtaccaacctaaaactctttttaatttgatggatagatagtaaccctatttctttggtatttggcag

upper sequence: GLYMA08G20100.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os02g34690.1 (Oryza sativa), 5'ss of exon 10
CCTCACACCATCTGTAGTTTCGCTGATGGGAGGACTGCTTCCCTTTGGCAGCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgagttaaaatgcaattacttttctgggccataaaagatt-attttttcttccctttgtttggtacaaggtttacttttacttttttagagccgagccaa--
|||||| || ||||| || | || ||||||||||||||||| ||||| ||||| ||||| |||||||| ||||| ||||| || || ||||| |||||||| | | || | | ||| | |||| | | || ||| | | || | | || ||| | ||| | | | | |
CCTCACGCCTTCTGTCATTGCCCTCATGGGAGGACTGCTTCCTTTTGGTAGCATCTTCATTGAGATGTACTTTGTCTTCACATCATTTTGGAACTACAAGgtaaaacaggcaacactaattttcc-----catacaggcttcattactaaggagccctgagagttg--agacttatgcatccttcctgatcatctattgacag

upper sequence: GLYMA08G20100.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G087212_T01 (Zea mays), 5'ss of exon 10
CCTCACACCATCTGTAGTTTCGCTGATGGGAGGACTGCTTCCCTTTGGCAGCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgagttaaa------------atgcaattact----------tttctgggccataaaagattattttttcttccctttgtt-tggta-caaggtttacttttacttttttagagccgagccaa---------------------
||| ||||| ||||| |||| |||||||| ||||| || ||||| |||||||| ||||| |||||||| || |||||||||||||||||||| |||||||| | ||| || || |||| | | | ||| || | | | | ||| || ||| ||| |||| || | | ||| || |
CCTTACACCTTCTGTTATTTCACTGATGGGTGGACTTCTCCCCTTCGGCAGCATCTTCATTGAGATGTACTTCGTATTCACTTCCTTCTGGAACTACAAGgtaaaaaaaaaacatagtggtgattgaagtactaaagatccaatcaccagcatatagaatgatctgcactactttcttggtcacagtagcaaagtttctttcttttagtttcaaggaatattgactccacttggtgccttggcag

upper sequence: GLYMA08G20100.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G026231_T01 (Zea mays), 5'ss of exon 10
CCTCACACCATCTGTAGTTTCGCTGATGGGAGGACTGCTTCCCTTTGGCAGCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgagtta--aaatgcaatt--acttttctgggccataaaagattattttttcttccctt--tgtttggtac---aaggtttactt--ttacttttttagagccgagccaa
||| ||||| ||||| | || ||||||| || ||||||||||||||||| || ||||| |||||||| || || ||||| || |||||||| || ||||| | | |||||| || || ||| || || | || || | | || | | | |||| ||||| | | | || || ||
CCTTACACCTTCTGTCATCTCATTGATGGGTGGCCTGCTTCCCTTTGGCAGTATCTTCATTGAGATGTACTTCGTGTTCACATCATTCTGGAACTATAAGgtaaacgagcaaatgctttttaacatttttgtaccccgtgacatcgcttctcttaccactgtcatcttgtactgtaaggtgtgcatggttggttactttt-----------

upper sequence: GLYMA08G20100.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G420310_T01 (Zea mays), 5'ss of exon 10
CCTCACACCATCTGTAGTTTCGCTGATGGGAGGACTGCTTCCCTTTGGCAGCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgagtta--aaatgcaat--tacttttctgggc--cataaaagattattttttct-----tccctttgtttggtacaaggtttacttttacttttttagagccgagccaa
||| ||||| ||||| | || ||||||| || ||||||||||| || ||||| ||||| |||||||| ||||| ||||| || |||||||| || ||||| | | |||||| | ||| || || | | | | | || || || | | ||| |||| || | ||| ||||||
CCTTACACCTTCTGTCATCTCATTGATGGGTGGCCTGCTTCCCTTCGGTAGCATCTTCATTGAGATGTACTTTGTGTTCACATCATTCTGGAACTATAAGgtaaacaagcaaatgcttttttacagttttgacctccttgagaccttgacattgctcactgtgctcctgtactgtacgttgtgcatgtttggtttttttt-----------

upper sequence: GLYMA08G20100.1 (Glycine max), 5'ss of exon 10
lower sequence: AT1G10950.1 (Arabidopsis thaliana), 5'ss of exon 10
CCTCACACCATCTGTAGTTTCGCTGATGGGAGGACTGCTTCCCTTTGGCAGCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgagttaaaatgcaattacttttctgggccataaaagattattttttcttccctttgtttggtacaaggtttacttttacttttttagagccgagccaa
| | || ||||| || || || |||||||| || |||| |||||||| ||||| ||||| |||||||| ||||| ||||| |||||||||||||||||||| | | | | | ||| | || ||| ||||| || | | | | | ||| || | |||| | | |
CTTGACTCCATCAGTCGTCTCCCTGATGGGGGGTTTGCTACCCTTTGGAAGCATCTTCATTGAGATGTACTTTGTCTTCACATCCTTCTGGAATTACAAGgtaaatatagtttctcttaataagaacaaagttatggaattgcaaattcttattccaattggccaaaccggagagatttgattagtgagagactctcaac

upper sequence: GLYMA08G20100.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv18s0041g00680.t01 (Vitis vinifera), 5'ss of exon 10
CCTCACACCATCTGTAGTTTCGCTGATGGGAGGACTGCTTCCCTTTGGCAGCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgagttaaa--atgcaattacttttctgggccataaaagattattttttcttccctttgtttggtacaaggtttacttttacttttttagagccgagccaa
||||||||||||||||| || || ||||||||||||||||| ||||| || || ||||| |||||||||||||| ||||| |||||||||||||| ||||| | | | || | | | | | || ||| | || || |||| | |||| ||| | | | | |
TCTCACACCATCTGTAGTCTCTCTCATGGGAGGACTGCTTCCTTTTGGGAGTATTTTCATTGAGATGTATTTTGTCTTCACATCCTTCTGGAATTATAAGgtaaatatgaccatttcttcaataatttaaat-gcaagtgatgagaattgttttccttgagtattgtcaagattttccccagtgctgctgcacctttattt-

upper sequence: GLYMA08G20100.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv12s0035g00280.t01 (Vitis vinifera), 5'ss of exon 10
CCTCACACCATCTGTAGTTTCGCTGATGGGAGGACTGCTTCCCTTTGGCAGCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgagttaaaatgcaattacttttctgggccataaaagattattttttcttccctttgtttggtacaaggtttacttttacttttt--tagagccgagccaa-------
|||||||||||||| || || |||||||||| ||||| ||||||||||||||||| || |||||||| ||||| ||||| |||||||||||||||||||| |||| ||| ||| || | | | | | | | || || | | | ||||| || | | | | ||
TCTCACACCATCTGTTGTCTCAATGATGGGAGGTCTGCTACCCTTTGGCAGCATATTTATTGAGATGTACTTTGTCTTCACATCCTTCTGGAATTACAAGgt------aaatataatgactcttt---ggtttgagtggcttgctaaaaagatactggtgtgagcaaggccatttttttatttgtaaatgaaaacattgcagtgtcttg

upper sequence: GLYMA08G20100.1 (Glycine max), 5'ss of exon 10
lower sequence: PP1S438_29V6.1 (Physcomitrella patens), 5'ss of exon 3
CCTCACACCATCTGTAGTTTCGCTGATGGGAGGACTGCTTCCCTTTGGCAGCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgagttaaaat----gcaattacttttctgggccataaaagattattttttcttccctttgtttggtaca--aggtttacttttacttttttagagccgagccaa
| | | || || || || | ||| ||||||| || | || || || ||||| |||||||||||||| ||||| ||||| || |||||| | ||||||||| || | | | | | | ||| | || | | || || | || ||| | |||| | || | ||| | |
CTTGAAGCCTTCGGTGGTGGCACTGCTGGGAGGGTTGTTGCCGTTCGGGAGCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAGgtgggtggaggttggagggagcgggtggcagggtcggaagtgtgtgttggttgagcagagtgcatggggctttgggttgatggagacgtgtttgagggca------

upper sequence: GLYMA08G20100.1 (Glycine max), 5'ss of exon 10
lower sequence: EFJ37593 (Selaginella moellendorffii), 5'ss of exon 11
CCTCACACCATCTGTAGTTTCGCTGATGGGAGGACTGCTTCCCTTTGGCAGCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgagttaaaatgcaattacttttctgggccataaaagattattttttcttccctttgtttggtacaaggtttacttttacttttttagagccgagccaa
|||| ||||| | || |||| |||||||| | || || || || ||||| ||||| ||||||||||| || ||||| ||||| ||||| |||||||| | | | |||| | | | | | | | | || ||| |
TCTCAAGCCATCCATCGTGGCGCTTATGGGAGGCTTACTCCCATTCGGGAGCATCTTCATAGAGATGTATTTCGTGTTCACGTCCTTTTGGAACTACAAGgt-aacccggtcgagcccagttttttcagtc------tgctgatctgagtccgtggtgcatggcag----------------------------------

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|10847708|gb|BF070348.1|BF070348
EST:     GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAG                         GTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATT
genomic: GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgagttaaa ... tgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATT
EST: gi|19935331|gb|BQ080361.1|BQ080361
EST:     GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAG                         GTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATT
genomic: GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgagttaaa ... tgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATT
EST: gi|9565317|gb|BE474826.1|BE474826
EST:     GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAG                         GTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTATCATT
genomic: GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgagttaaa ... tgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATT
EST: gi|58015230|gb|CX701972.1|CX701972
EST:     GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAG                         GTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATT
genomic: GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgagttaaa ... tgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATT
EST: gi|16105838|gb|BI893578.1|BI893578
EST:     GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAG                         GTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTATCATT
genomic: GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgagttaaa ... tgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATT
EST: gi|192331779|gb|FK024883.1|FK024883
EST:     GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAG                         GTGTACTATGTCTATGGCTTCATACTACTGGTTTTTCTGATTCTTATCATT
genomic: GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgagttaaa ... tgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTCACACCATCTGTAGTTTCGCTGATGGGAGGACTGCTTCCCTTTGGCAGCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgagttaaaatgcaattacttttctgggccataaaagattattttttcttccctttgtttggtacaaggtttacttttacttttttagagccgagccaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcttccc