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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattttacatgaacgtttgatgtacagtcttctttttcttttcccctttgtctagttcatgaagtatttttgtgatttaaattccagtgttcctgtttatacaatattctgcctgaacactgttctaaatttatgtattttatgtcttgaggtaaacaaccataatacatgtaataattttgttatgttaccatatagGCTAAAAAAAGAGTGTTATGGGGAACAGCTCAGTTGTTCATGCATCCTCGTTACATGCATGGTGCTGCTACTAG

Basic information

species Glycine max
transcript GLYMA17G07380.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G07380.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G335948_T01 (Zea mays), 3'ss of exon 5
gtaattttacatgaacgtttgatgtacagtcttctttttcttttcccctttgtctagttcatgaagtatttttgtgatttaaattccagtgttcctgtttatacaatattctgcctgaacactgttctaaa-tttatgtattttatgtcttgaggtaaacaaccataatacatgtaataattttgttatgtta---ccatatagG------CTAAAAAAAGAGTGTTATGGGGAACAGCTCAGTTGTTCATGCATCCTCGTTACATGCATGGTGCTGCTACTAG
                                                                                                                          |  | |||  ||||  |   |      | |  |||  | |||||  | |||      ||||  || | |||   |||| ||||      | || | ||     || ||||| || || ||| | || |||||||||||||||||||| || |||||||||||
------------------------------------------------------------------------------------------------------------------------gttagtttaacctttaaattgctggcacttagctgtaccccaccattttgcattaccctatttgctttttttaattccatttagGGTGAGACCAATATAAAGCCATTGTGGGGTACTGCACAGCTCTTTATGCATCCTCGTTACATGCACGGAGCTGCTACTAG

upper sequence: GLYMA17G07380.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G005493_T01 (Zea mays), 3'ss of exon 7
gtaattttacatgaacgtttgatgtacagtcttctttttcttttcccctttgtctagttcatgaagtatttttgtgatttaaattccagtgttcctgtttatacaatattctgcctgaacactgttctaaatttatgtattttatgtcttgaggtaaacaaccataatacatgtaataattttgttatgttaccatatagGCTAAAAAAAGAGTGTTATGGGGAACAGCTCAGTTGTTCATGCATCCTCGTTACATGCATGGTGCTGCTACTAG
                                                                                        ||     |     || | | ||    || | | | |  | |  ||  || |||       |||           |||| |   | |   | ||   |||||||       || | || | ||     || ||||| || || ||| | || |||||||||||||||||||| || |||||||||||
----------------------------------------------------------------------------------------gttagggtaaccttaaactgttggcacttagctccgcaccaccttcttgcattaccctgtttgc---------tcatattttttctttcatttaaattatgtttagGGTGAGACCAATATAAAGCCATTGTGGGGTACTGCACAGCTCTTTATGCATCCTCGTTACATGCACGGAGCTGCTACTAG

upper sequence: GLYMA17G07380.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G57655.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaattttacatgaacgtttgatgtacagtcttctttttcttttcccctttgtctagttcatgaagtatttttgtgatttaaattccagtgttcctgtttatacaatatt-ctgcctgaacactgttctaaatttatgtattttatgtcttgaggtaaacaaccataatacatgtaataattttgttatgttaccatatagGCTAAAAAAAGAGTGTTATGGGGAACAGCTCAGTTGTTCATGCATCCTCGTTACATGCATGGTGCTGCTACTAG-----------------------
                                                                               || | |  | | ||  | |   |  || | | ||  ||    ||  |||     |||    ||| ||||  | ||  ||| |             |  |  |||| ||    | |     ||   ||||  | |   || ||||||||||||||| | ||| ||||||||||||| ||||| || |  || || ||                       
-------------------------------------------------------------------------------tataattgaatctttttatcactgaaacagtactatcttgttaccattc----ctta---gtttgatgtgctaagaaaaaaaggt----------tcttcgttttcttcaaatgcagGGGAG--CAAAATCAAACCATTGTGGGGAACAGCTCAGCTTTTCTTGCATCCTCGTTATATGCACGGAGGAGCGACCAGCTCTGAAGTTGGAGTGTATGCTT

upper sequence: GLYMA17G07380.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv11s0052g01710.t01 (Vitis vinifera), 3'ss of exon 8
gtaattttacatgaacgtttgatgtacagtcttctttttcttttcccctttgtctagttcatgaagtatttttgtgatttaaattccagtgttcctgtttatacaatattctgcctgaacactgttctaaatttatgtattttatgtcttgaggtaaacaaccataatacatgtaataattttgttatgttaccatatagGCTAAAAAAAGAGTGTT-ATGGGGAACAGCTCAGTTGTTCATGCATCCTCGTTACATGCATGGTGCTGCTACTAG
                                                                                       | ||  | || |  |   |  ||||   || |  |   |        |||| |  ||||||      |   ||  | | |||| |   ||| ||   ||   |    | |  |   ||| |   |   ||  ||||| |||||||||||||||   |||||||| || |||||||||| |||||||||
-------------------------------------------------------------------------------------tgaatggccatgctgttgtcactttct--ttggatgccaat--------atgtttgatatgtccaatctttgtcaggcctgatacct---atacttcccttgcatctttacagGGAAAAAAGATCCATCCTTTGTGGGGTACAGCTCAGTTGTTCCATCATCCTCGCTATATGCATGGTGGTGCTACTAG

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|19053273|gb|BM731940.1|BM731940
EST:     ATGCAAACTTGGATGAAGTGGTTGCCCTTGCTCAAGAGCTCCAGACTAAG                         GCTNNNNNNNGAGTGTTATGGGGAACAGCTCAGTTGTTCATGCATCCTCGT
genomic: ATGCAAACTTGGATGAAGTGGTTGCCCTTGCTCAAGAGCTCCAGACTAAGgtaattttac ... taccatatagGCTAAAAAAAGAGTGTTATGGGGAACAGCTCAGTTGTTCATGCATCCTCGT
EST: gi|163926470|gb|EH039217.1|EH039217
EST:     ATGCAAACTTGGATGAAGTGGTTGCCCTTGCTCAAGAGCTCCAGACTAAG                         GCTNNNNNNNGAGTGTTATGGGGAACAGCTCAGTTGTTCATGCATCCTCGT
genomic: ATGCAAACTTGGATGAAGTGGTTGCCCTTGCTCAAGAGCTCCAGACTAAGgtaattttac ... taccatatagGCTAAAAAAAGAGTGTTATGGGGAACAGCTCAGTTGTTCATGCATCCTCGT
EST: gi|24136612|gb|BU927122.1|BU927122
EST:     ATGCAAACTTGGATGAAGTGGTTGCCCTTGCTCAAGAGCTCCAGACTAAG                         GCTNNNNNNNGAGTGTTATGGGGAACAGCTCAGTTGTTCATGCATCCTCGT
genomic: ATGCAAACTTGGATGAAGTGGTTGCCCTTGCTCAAGAGCTCCAGACTAAGgtaattttac ... taccatatagGCTAAAAAAAGAGTGTTATGGGGAACAGCTCAGTTGTTCATGCATCCTCGT
EST: gi|192294738|gb|FG986587.1|FG986587
EST:     ATGCAAACTTGGATGAAGTGGTTGCCCTTGCTCAAGAGCTCCAGACTAAA                         GCTNNNNNNNGAGTGTTATGGGGAACAGCTCAGTTGTTCATGCATCCTCGT
genomic: ATGCAAACTTGGATGAAGTGGTTGCCCTTGCTCAAGAGCTCCAGACTAAGgtaattttac ... taccatatagGCTAAAAAAAGAGTGTTATGGGGAACAGCTCAGTTGTTCATGCATCCTCGT
EST: gi|16276935|gb|BI942118.1|BI942118
EST:     GGTTGCCCTTGCTCAAGAGCTCCAGACTAAG                         GCTNNNNNNNGAGTGTTATGGGGAACAGCTCAGTTGTTCATGCATCCTCGT
genomic: GGTTGCCCTTGCTCAAGAGCTCCAGACTAAGgtaattttac ... taccatatagGCTAAAAAAAGAGTGTTATGGGGAACAGCTCAGTTGTTCATGCATCCTCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcttgaggtaaacaaccataatacatgtaataattttgttatgttaccatatagGCTAAAAAAAGAGTGTTATGGGGAACAGCTCAGTTGTTCATGCATCCTCGTTACATGCATGGTGCTGCTACTAG
                  ataatacatgtaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattttacatgaacgtttgatgtacagtcttctttttcttttcccctttgtctagttcatgaagtatttttgtgatttaaattccagtgttcctgtttatacaatattctgcctgaacactgttctaaatttatgtattttatgtcttgaggtaaacaaccataatacatgtaataattttgttatgttaccatatagGCTAAAAAAAGAGTGTTATGGGGAACAGCTCAGTTGTTCATGCATCCTCGTTACATGCATGGTGCTGCTACTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT