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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCACTATCACCGCCGCCACAAGGTGTGCGAGTTTCACTCCAAAGCCGCCACCGTCATCGCCGCCGGCTTGACTCAGCGATTCTGCCAGCAATGCAGCAGgttgtggtggtgctagtttgttcctcaccgtcggaaattgcatcaatcattgagttcagctccctcgggggcactttcgtctttttacacacctaccttt...

Basic information

species Glycine max
transcript GLYMA07G14610.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G14610.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os02g08070.1 (Oryza sativa), 5'ss of exon 1
AGCACTATCACCGCCGCCACAAGGTGTGCGAGTTTCACTCCAAAGCCGCCACCGTCATCGCCGCCGGCTTGACTCAGCGATTCTGCCAGCAATGCAGCAGgttg----tggtg--gtgctagtttgttcctcaccgtcggaaattgcatcaatcattgagttcagctccctcgggggcactttcgtctttttacacacctaccttt
||||||| ||||||||||||||||| ||||| || ||| |||| |||||| ||||| |||||||||||  |   ||||| ||||||||||| |||||||||||      | |   | || |   |||  ||  | |  || |    || ||  ||    ||   ||| ||  | |||  |    |       ||||||  ||    
AGCACTACCACCGCCGCCACAAGGTCTGCGACTTCCACGCCAAGGCCGCCGCCGTCCTCGCCGCCGGCAAGCAGCAGCGCTTCTGCCAGCAGTGCAGCAGgttagctccgatcccgcgcaaccatgtcgctgccaggtgggacc--cagcaggcac-acgtgtcgctgccaggtgggacccagggcacagccacacacgcact---

upper sequence: GLYMA07G14610.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os06g44860.1 (Oryza sativa), 5'ss of exon 1
AGCACTATCACCGCCGCCACAAGGTGTGCGAGTTTCACTCCAAAGCCGCCACCGTCATCGCCGCCGGCTTGACTCAGCGATTCTGCCAGCAATGCAGCAGgttgtggtggtgctagtttgtt-cctcaccgtcggaaattgc-atcaatcattgagttcagctccctcgggggcactttcgtctttttacacacctaccttt
||||||| ||||||||||||||||| |||||||  ||| |||| ||| ||  ||||  |||| |||||  |   ||||| ||||||||||||||||||||||   | |  ||||      |  ||   |    |    | || || | ||  ||   |  |||  || |    |  | ||      | ||    ||     |
AGCACTACCACCGCCGCCACAAGGTCTGCGAGTACCACGCCAAGGCCTCCGTCGTCGCCGCCTCCGGCAAGCAGCAGCGCTTCTGCCAGCAATGCAGCAGgtaa-gctactgctccgccatcaccgtgctacagcgtgtcgccatgattcgctgtactt-gctttcttgaattctttctctcgccatgaccggtctcgggat

upper sequence: GLYMA07G14610.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G168229_T02 (Zea mays), 5'ss of exon 1
AGCACTATCACCGCCGCCACAAGGTGTGCGAGTTTCACTCCAAAGCCGCCACCGTCATCGCCGCCGGCTTGACTCAGCGATTCTGCCAGCAATGCAGCAGgttgtggtggtgctagtttgttcctcaccgtcggaaattgcatcaatcattgagttcagctccctcgggggcactt-tcgtctttttaca-cacctaccttt
||||||| ||||||||||||||||| |||||||| ||| |||| |||  | |||||  ||||||||||  |   ||||| ||||||||||||||||||||||   ||   ||        | |     |  |  | |   || |  || |||   ||   | |       | || | |||  ||   |   ||| || | | 
AGCACTACCACCGCCGCCACAAGGTCTGCGAGTTCCACACCAAGGCCAGCGCCGTCGCCGCCGCCGGCAAGCAGCAGCGCTTCTGCCAGCAATGCAGCAGgtacgggcactgtcgacagctactagctcagctcagac-acacctttccttgttgtctattgcacgtactgtacctgtcgctttgccatgtcacgtaacgt-

upper sequence: GLYMA07G14610.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G111136_T01 (Zea mays), 5'ss of exon 1
AGCACTATCACCGCCGCCACAAGGTGTGCGAGTTTCACTCCAAAGCCGCCACCGTCATCGCCGCCGGCTTGACTCAGCGATTCTGCCAGCAATGCAGCAGgttgtggtggtgctagtttgttcctcaccgtcggaaattgcatcaatcattgagttcagctccctcgggggcactttcgtctttttacacacctaccttt-
||||||| ||||||||||||||||| |||||||  ||| |||| |||  | |||||  ||||||||||  |   ||||| ||||||||||| ||||||||||   |   || |     ||| |||| |   |    ||     ||  |||  |   | |  ||   |   |      || || |  | |||| | ||    
AGCACTACCACCGCCGCCACAAGGTCTGCGAGTACCACGCCAAGGCCAGCGCCGTCGCCGCCGCCGGCAAGCAGCAGCGTTTCTGCCAGCAGTGCAGCAGgt-acgtacgtacgtacgtgtccctccctcccctgcatgcgtgcatgcatgcatgcccggccctgggtcaggtggcccgcctgtcaagacacgtgcccact

upper sequence: GLYMA07G14610.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G101499_T01 (Zea mays), 5'ss of exon 1
AGCACTATCACCGCCGCCACAAGGTGTGCGAGTTTCACTCCAAAGCCGCCACCGTCATCGCCGCCGGCTTGACTCAGCGATTCTGCCAGCAATGCAGCAGgttgtggtggtgc-tagtttgttcctcaccgtcggaaattgcatcaatcattgagttcagctccctcgggggc--actttcgtctttttacacacctaccttt---
||||||| ||||||||||||||||| |||||||  ||| |||| ||| ||  ||||  | ||| ||||  |   ||||| ||||||||||||||||||||||      | ||| ||| | |   | |  ||||      |   ||  ||         |||   |   |  ||  |     | | |   ||  ||  |  | |   
AGCACTACCACCGCCGCCACAAGGTCTGCGAGTACCACGCCAAGGCCTCCGTCGTCGCCACCGGCGGCAAGCAGCAGCGCTTCTGCCAGCAATGCAGCAGgtacgtacgttgcctagctagccgcgcgtcgtc------tctctcgctctacctagctagcgtgcgaagaagctgaaaaaaggcatagcacgtacggaagtatcag

upper sequence: GLYMA07G14610.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv15s0021g02300.t01 (Vitis vinifera), 5'ss of exon 2
AGCACTATCACCGCCGCCACAAGGTGTGCGAGTTTCACTCCAAAGCCGCCACCGTCATCGCCGCCGGCTTGACTCAGCGATTCTGCCAGCAATGCAGCAGgttgtggtgg--tgctagtttgttcctcaccgtcg-gaaattgcatcaatcattgagttcagctccctcgggggc--actttcgtctttttacacacctaccttt
|||| || ||||||||||||||||| |||||||| |||||||||||| | || ||| |||||||||| ||||||||||| |||||||| ||||| |||||||| | |     | | |       | |   |     |||| | |  ||   ||| | |  |                ||      |    | || | | |     
AGCATTACCACCGCCGCCACAAGGTCTGCGAGTTCCACTCCAAAGCCTCTACAGTCTTCGCCGCCGGGTTGACTCAGCGCTTCTGCCAACAATGTAGCAGgttctcgcaaattaccaaaacacccttattcacaacgaaacttc--cagctatttaatctaataaaaaataaaatcaacgcaaaccaaaattcaaagcaagt---

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|208317630|gb|GE116243.1|GE116243
EST:     ACCGTCATCGCCGCCGGCTTGACTCAGCGATTCTGCCAGCAATGCAGCAG                         GTTCCATCTTCTTTCTGAGTTTGATAACGGAAAACG
genomic: ACCGTCATCGCCGCCGGCTTGACTCAGCGATTCTGCCAGCAATGCAGCAGgttgtggtgg ... tgacgtgcagGTTCCATCTTCTTTCTGAGTTTGATAACGGAAAACG
EST: gi|6964578|gb|AW433271.1|AW433271
EST:     ACCGTCATCGCCGCCGGCTTGACTCAGCGATTCTGCCAGCAATGCAGCAG                         GTTCCATCTTCTTTCTGAGTTTGATAACGGAAAACGTAGCTGCAGGAAGAG
genomic: ACCGTCATCGCCGCCGGCTTGACTCAGCGATTCTGCCAGCAATGCAGCAGgttgtggtgg ... tgacgtgcagGTTCCATCTTCTTTCTGAGTTTGATAACGGAAAACGTAGCTGCAGGAAGAG
EST: gi|193648679|gb|FK598406.1|FK598406
EST:     ACCGTCATCGCCGCCGGCTTGACTCAGCGATTCTGCCAGCAATGCAGCAG                         GTTCCATCTTCTTTCTGAGTTTGATAACGGAAAACGTAGCTGCAGGAAGAG
genomic: ACCGTCATCGCCGCCGGCTTGACTCAGCGATTCTGCCAGCAATGCAGCAGgttgtggtgg ... tgacgtgcagGTTCCATCTTCTTTCTGAGTTTGATAACGGAAAACGTAGCTGCAGGAAGAG
EST: gi|4300337|gb|AI443033.1|AI443033
EST:     ACCGTCATCGCCGCCGGCTTGACTCAGCGATTCTGCCAGCAATGCAGCAG                         GTTCCATCTTCTTTCTGAGTTTGATAACGGAAAACGTAGCTGCAGGAAGAG
genomic: ACCGTCATCGCCGCCGGCTTGACTCAGCGATTCTGCCAGCAATGCAGCAGgttgtggtgg ... tgacgtgcagGTTCCATCTTCTTTCTGAGTTTGATAACGGAAAACGTAGCTGCAGGAAGAG
EST: gi|9440063|gb|BE440574.1|BE440574
EST:     ACCGTCATCGCCGCCGGCTTGACTCAGCGATTCTGCCAGCAATGCAGCAG                         GTTCCATCTTCTTTCTGAGTTTGATAACGGAAAACGTAGCTGCAGGAAGAG
genomic: ACCGTCATCGCCGCCGGCTTGACTCAGCGATTCTGCCAGCAATGCAGCAGgttgtggtgg ... tgacgtgcagGTTCCATCTTCTTTCTGAGTTTGATAACGGAAAACGTAGCTGCAGGAAGAG
EST: gi|19053431|gb|BM732098.1|BM732098
EST:     ACCGTCATCGCCGCCGGCTTGACTCAGCGATTCTGCCAGCAATGCAGCAG                         GTTCCATCTTCTTTCTGAGTTTGATAACGGAAAACGTAGCTGCAGGAAGAG
genomic: ACCGTCATCGCCGCCGGCTTGACTCAGCGATTCTGCCAGCAATGCAGCAGgttgtggtgg ... tgacgtgcagGTTCCATCTTCTTTCTGAGTTTGATAACGGAAAACGTAGCTGCAGGAAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCACTATCACCGCCGCCACAAGGTGTGCGAGTTTCACTCCAAAGCCGCCACCGTCATCGCCGCCGGCTTGACTCAGCGATTCTGCCAGCAATGCAGCAGgttgtggtggtgctagtttgttcctcaccgtcggaaattgcatcaatcattgagttcagctccctcgggggcactttcgtctttttacacacctaccttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccctc