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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgattgcgcatttcctagattcagattcttctctaggataatcattttagtcaaaaaatgacttttttgttgtttcttcttcctttttttgtgttatagGTGGTTATGACAAGGAGGATAAGGCAGCCAGAGCTTATGATCTCGCAGCTCTCAAGTACTGGGGTCCAACTACCACCACTAACTTTCCT

Basic information

species Glycine max
transcript GLYMA17G07010.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G07010.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G086573_T01 (Zea mays), 3'ss of exon 4
-------ttgattgcgcatttcctagattcagattcttctctagg-ataatcattttagtcaaaaa-atgacttttttgttgtttcttcttcctttttttgtgttatagGTGGTTATGACAAGGAGGATAAGGCAGCCAGAGCTTATGATCTCGCAGCTCTCAAGTACTGGGGTCCAACTACCACCACTAACTTTCCT
        |||||   ||      |  || |  |  || || | | || |||   | |  || ||  || || ||  || || | ||  ||  |||  |     |  |||||| ||||| |||||||| ||||| ||||| || |||||||| |||||| | |||||||||||| | |  |||||||| |||||||| 
gtaagaactgattaaacaagcttcatgtttatttcattatccatgcatcatctcgtcaagcagaagcatcacattgctgatggtactattttttttcatgaatctgaagGTGGCTATGATAAGGAGGAGAAGGCTGCCAGGGCGTATGATCTTGCAGCTTTGAAGTACTGGGGTTCTAGCACCACCACCAACTTTCCG

upper sequence: GLYMA17G07010.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G57390.1 (Arabidopsis thaliana), 3'ss of exon 4
---------------------------------------ttgattgcgcatttcctagat-tcagattcttctctaggata--atcattttagtcaaaaaatgactttt-ttgttgtttcttcttcctttttttgtgttatagGTGGTTATGACAAGGAGGATAAGGCAGCCAGAGCTTATGATCTCGCAGCTCTCAAGTACTGGGGTCCAACTACCACCACTAACTTTCCT
                                       |   || |   |||| |   | |   ||||   |||   |    |||||| |  | | |     | || | ||  | |    |      ||| || ||||  |||||||||||| ||||| ||||| ||||| |||||||| || || |||||||| ||||| |||||||| || || || ||||| || || 
gtgagttccaataaattctctattaaacaatttatttcatctctttcttctttcttgtgtatttaattcccttctgaaacgttatcattctctttatatttaaatttgtattaatatgaagtaaattgtttgttatgtt-cagGTGGTTATGATAAGGAAGATAAAGCAGCTAGAGCTTACGACCTTGCAGCTCTTAAGTATTGGGGTCCTACAACTACGACTAATTTCCCG

upper sequence: GLYMA17G07010.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0052g00840.t01 (Vitis vinifera), 3'ss of exon 4
------------------------------ttgattgcgcatttcctagattcagattcttctctaggataatcattttagtcaaaaaatgacttttttg--------ttgtttcttcttcctttttttgtgttatagGTGGTTATGACAAGGAGGATAAGGCAGCCAGAGCTTATGATCTCGCAGCTCTCAAGTACTGGGGTCCAACTACCACCACTAACTTTCCT
                               ||| |    ||||   |   |   ||       |  |||| || ||  |||   | | |  | |||| |        || ||| ||  |   |||||||| ||  |||||| ||||| ||||| || |||||||| ||||||||||||||||| ||||| |||||||||||||| || |||||||||||||| |||
gtgagtaggatctcatctcgtggtcttgtcctgaatcatgatttttcactgttgaataaaagattctgatattccttcaagttttagattctcattttggatcaatttttatttatttatttattttttgt-ttgcagGTGGGTATGATAAGGAAGAGAAGGCAGCTAGAGCTTATGATCTCGCCGCTCTTAAGTACTGGGGTCCGACCACCACCACTAACTTCCCT

upper sequence: GLYMA17G07010.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ17692 (Selaginella moellendorffii), 3'ss of exon 1
ttgattgcgcatttcctagattcagattcttctctaggataatcattttagtcaaaaaatgacttttttgttgtttcttcttcctttttt--tgtgtt----atagGTGGTTATGACAAGGAGGATAAGGCAGCCAGAGCTTATGATCTCGCAGCTCTCAAGTACTGGGGTCCAACTACCACCACTAACTTTCCT
     | |    | | ||| |   || |  ||| | | ||  |   |  | |    |  | |  |||| || ||||  | ||| ||||||  || |||     |||| || |||||   |||||| |||||||| |||||||| ||||| |||||||||||||||||||| || || || || || |||||||| 
--tcctccagtgtacttaggt---gagtaatctatcgaattttt-ctcgattgtggagctaaacttttggtggttttcttttctttttttcttgcgttttgcgtagGGGGGTATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG

upper sequence: GLYMA17G07010.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ16224 (Selaginella moellendorffii), 3'ss of exon 1
---------------------------------------------------------------------------ttgattgcgcattt--cctagattcagattc-ttctctaggataatcattttagtcaaaaaatgactttttt---gttgt----------ttcttcttcctttttttgtgtt----atagGTGGTTATGACAAGGAGGATAAGGCAGCCAGAGCTTATGATCTCGCAGCTCTCAAGTACTGGGGTCCAACTACCACCACTAACTTTCCT
                                                                           | ||| | |  |||    | |     ||| | | ||| ||  || | |  | ||| |   |  || |||||     ||||          || |  |   ||| |||| |||     |||| || |||||   |||||| |||||||| |||||||| ||||| |||||||||||||||||||| || || || || || |||||||| 
gtactgcttaaaagttttgagagttttttttcatggttttttttctctcttgggtgatttttccgtccttggatctggatggtgtttttggtgtggtacttgatccatcctccagtgtacttaggtgagtaatctatcgaatttttctcgattgtggagctaaacttttggtggttttctttgcgttttgcgtagGGGGATATGATGCGGAGGAGAAGGCAGCAAGAGCTTACGATCTGGCAGCTCTCAAGTACTGGGGGCCTACGACAACTACAAACTTTCCG

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|14259750|gb|BG882658.1|BG882658
EST:     GGAAAGGAAGGCAAGTTTACTTGG                         GTGGTTATGACAAGGAGGATAAGGCAGCCAGAGCTTATGATCTTC-CAGCTC
genomic: GGAAAGGAAGGCAAGTTTACTTGG
EST: gi|7685789|gb|AW756437.1|AW756437
EST:     GGAAAGGAAGGCAAGTTTACTTGG                         GTGGTTATGACAAGGAGGATAAGGCAGCCAGAGCTTATGATCTCGCAGCTCT
genomic: GGAAAGGAAGGCAAGTTTACTTGG
EST: gi|14259589|gb|BG882497.1|BG882497
EST:     AGTTTACTTGG                         GTGGTTATGACAAGGAGGATAAGGCAGCCAGAGCTTATGATCTCGCAGCTCT
genomic: AGTTTACTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttagtcaaaaaatgacttttttgttgtttcttcttcctttttttgtgttatagGTGGTTATGACAAGGAGGATAAGGCAGCCAGAGCTTATGATCTCGCAGCTCTCAAGTACTGGGGTCCAACTACCACCACTAACTTTCCT
                 cttttttgttgtttct  CT-rich tract
        aaaaaatgactttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgattgcgcatttcctagattcagattcttctctaggataatcattttagtcaaaaaatgacttttttgttgtttcttcttcctttttttgtgttatagGTGGTTATGACAAGGAGGATAAGGCAGCCAGAGCTTATGATCTCGCAGCTCTCAAGTACTGGGGTCCAACTACCACCACTAACTTTCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
-tgattgc
- - - - gcatttc
- - - - - - - - - - - - - - - - - - - - - - - - - - caaaaaa