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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggaatctctttctgtatgtggggctagatcaagggagatagcatttagtgtaatgttgtattcttgcttttatttgttcaaatgatgataacactgcccgactcttgtaaatatataattatgttctatttttgttcaattcctcacaaaataattgttattcttacatggtcatattcaaatgtaacagATTCCAGAAGAAGAGAAAAATCTTGGTTCTCATGATCGTCTAATTCATGTTTACCATTTCAATAAAGAGACAGCTCAAAACCAAATG

Basic information

species Glycine max
transcript GLYMA20G11330.1
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 19
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 27
gtaggaatctctttctgtatgtggggctagatcaagggagatagcatttagtgtaatgttgtattcttgcttttatttgttcaaatgatgataacactgcccgactcttgtaaatatataattatgttctatttttgttcaattcctcacaaaataattgttattctta-catggtcatattcaaatgtaacagATTCCAGAAGAAGAGAAAAATCTTGGTTCTCATGATCGTCTAATTCATGTTTACCATTTCAATAAAGAGACAGCTCAAAACCAAATG
                                                                           || |||  ||      |    ||| | |||  |  | |    ||||||   ||   ||  | | | | |  |||  | || |||| | | | || |||  |      ||| || ||||||| ||||| |||||||| || |||||  | ||||||||  | |||||||||||||||||||  |||||  |   |||||| ||    
--------------------------------------------------------------------------gttcgtttgaacatctttt---ctgactgacgatattga---cataattccatttagttagtatactactg-tcattatattattgatttgcataacatttttgctaccaattgaaacagATACCAGAGGAAGAGAAGAACCTTGGCCCACATGATCGGTTGATTCATGTTTACCATTTCATGAAAGATCCTAATCAAAATCAG---

upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 19
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 23
gtaggaatctctttctgtatgtggggctagatcaagggagatagcatttagtgtaatgttgtattc--ttgcttttatttgttcaaatgatgataacactgcccgactcttgtaaatatataattatgttctatttttgttcaattcctcacaaaataattgttattcttacatggtcatattcaaatgtaacagATTCCAGAAGAAGAGAAAAATCTTGGTTCTCATGATCGTCTAATTCATGTTTACCATTTCAATAAAGAGACAGCTCAAAACCAAATG
                                                   ||||||||| | ||   |||| |||  |  | ||  |  |||    ||||      |      ||| |||  | || | ||  || |||  || |   | |     | |   |  || ||  || |  |  | |   ||| ||||||||||| || ||||||||||| ||| |  |||||||  ||||||||||||| || ||||  |||||  |   ||| || ||    
------------------------------------------------gtatgtaatgttctttttggttgcatttggtgctccatttcgtga----actgtaaagttgc----aatctatt-tcatttcctgcttgtgtcaaaatgtgcgcctt-cattctatcctcatatctgcttctgcttattggta-cagATTCCAGAGGAGGAGAAAAATCTCGGTCCAAATGATCGGTTAATTCATGTTTATCACTTCATGAAAGACCCTCTTCAGAATCAG---

upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 19
lower sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 17
gtaggaatctctttctgtatgtggggctagatcaagggagatagcatttagtgtaatgttgtattcttgcttttatttgttcaaatgatgataacactgcccgactcttgtaaatatataattatgttctatttttgttcaattcctcacaaaataattgttattcttacatggtcatattcaaatgtaacagATTCCAGAAGAAGAGAAAAATCTTGGTTCTCATGATCGTCTAATTCATGTTTACCATTTCAATAAAGAGACAGCTCAAAACCAAATG-------------
                                               || || |  | |  | |||||| | ||     ||| |   ||  ||| |       | |  | |  |   | | | || |   ||  || |  ||           ||||   |   |||      ||||  ||    || ||||||| ||||| |||||||| ||||||||  | ||||||||  | |||||||||||||||||||  |||||  |    || || |||                
----------------------------------------------gtttgtattgtttcattttcttgatgttgacccttcgatctattctaaaaaaaatacaattatatttacgaagattcatctgtgatacttatgtaaagttgtcttgcataacactgcatct------gtcaattt----tggaacagATCCCAGAGGAAGAGAAGAATCTTGGCCCACATGATCGATTGATTCATGTTTACCATTTCATGAAAGACCCTAACCAGAATCAACAAATTCAAAATTTTG

upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 19
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 27
gtaggaatctctttctgtatgtggggctagatcaagggagatagcatttagtgtaatgttgtattcttgcttttatttgttcaa---atgatgataacactgcccgactcttgtaaatatataattatgttctatttttgttcaattcctcacaaaataattgt-tattcttacatggtcatattcaaatgtaacagATTCCAGAAGAAGAGAAAAATCTTGGTTCTCATGATCGTCTAATTCATGTTTACCATTTCAATAAAGAGACAGCTCAAAACCAAATG-------------
                                               || || | || |  | |||||| | ||     ||  |   ||  |  | | |     | |||  | ||  || || | | ||   || || |||  | ||         ||  | ||  ||      |  ||||  ||  ||    |||||||||||| |||||||| ||||||||  | ||||| ||| | ||||||||||| ||||| |  |||||  |   ||| || ||   |             
----------------------------------------------gttcgtattatttcattttcttgatgttgaccctttgacctattctattgaaaaaatacaactaatttatgtagattaatctgcgatacttctgtatagttgtc-----gattgtcgtgcatgacactactgtcaattttgaa----acagATTCCAGAGGAAGAGAAGAATCTTGGCCCACATGACCGTTTGATTCATGTTTATCATTTTATGAAAGACCCTAATCAGAATCAGCAGATTCAGAATTTCG

upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 27
gtaggaatctctttctgtatgtggggctagatcaagggagatagcatttagtgtaatgttgtattcttgcttttatttgttcaaatgatgataacactgcccgactcttgtaaatatataattatgttctatttttgttcaattcctcacaaaataattgttattcttacatggtcatattcaaatgtaacagATTCCAGAAGAAGAGAAAAATCTTGGTTCTCATGATCGTCTAATTCATGTTTACCATTTCAATAAAGAGACAGCTCAAAACCAAATG
                                                                                           | |          || || ||| | | |||||  | |  |  |    |  |       || | |  |  | | | || ||   | |  || |||| |  |||||||| ||||||||||||||||||||  | || |||||  | |||||||| ||||| || |  ||||| |||||||| |||||||||
-------------------------------------------------------------------------------------------ttagttaatttttcttttttaattttctaatttagatgaaagtaaaatgtacatgatccagatt--tgatcaattttccaatttaacttttaaatattgcagATTCCTGAAGAAGAGAAAAATCTTGGACCACAGGATCGCTTGATTCATGTATACCACTTTACAAAAGACACAGCTCAGAACCAAATG

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|18690763|gb|BM519611.1|BM519611
EST:     AAAAGATTGAAAGCATTAATGATCAATACTGGACACTACGAGCAGAGGAG                         ATTCCAGAAGAAGAGAAAAATCTTGGTTCTCATGATCGTCTAATTCATGTT
genomic: AAAAGATTGAAAGCATTAATGATCAATACTGGACACTACGAGCAGAGGAGgtaggaatct ... aatgtaacagATTCCAGAAGAAGAGAAAAATCTTGGTTCTCATGATCGTCTAATTCATGTT
EST: gi|17153585|gb|BM143518.1|BM143518
EST:     AAAAGATTGAAAGCATTAATGATCAATACTGGACACTACGAGCAGAGGAG                         ATTCCAGAAGAAGAGAAAAATCTTGGTTCTCATGATCGTCTAATTCATGTT
genomic: AAAAGATTGAAAGCATTAATGATCAATACTGGACACTACGAGCAGAGGAGgtaggaatct ... aatgtaacagATTCCAGAAGAAGAGAAAAATCTTGGTTCTCATGATCGTCTAATTCATGTT
EST: gi|308098749|gb|HO760490.1|HO760490
EST:     AAAAGATTGAAAGCATTAATGATCAATACTGGACACTACGAGCAGAGGAG                         ATTCCAGAAGAAGAGAAAAATCTTGGTTCTCATGATCGTCTAATTCATGTT
genomic: AAAAGATTGAAAGCATTAATGATCAATACTGGACACTACGAGCAGAGGAGgtaggaatct ... aatgtaacagATTCCAGAAGAAGAGAAAAATCTTGGTTCTCATGATCGTCTAATTCATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaattcctcacaaaataattgttattcttacatggtcatattcaaatgtaacagATTCCAGAAGAAGAGAAAAATCTTGGTTCTCATGATCGTCTAATTCATGTTTACCATTTCAATAAAGAGACAGCTCAAAACCAAATG
                         ttcttac  putative branch site (score: 2)
            aaaataattgttattc  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggaatctctttctgtatgtggggctagatcaagggagatagcatttagtgtaatgttgtattcttgcttttatttgttcaaatgatgataacactgcccgactcttgtaaatatataattatgttctatttttgttcaattcctcacaaaataattgttattcttacatggtcatattcaaatgtaacagATTCCAGAAGAAGAGAAAAATCTTGGTTCTCATGATCGTCTAATTCATGTTTACCATTTCAATAAAGAGACAGCTCAAAACCAAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA