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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atattccaatgatgtttttgacactattgaataattatgagcatgctgttttttctagctttattccttattctgattcttattaggataaatgttttagGTCCCCAGGTCTTCTAAGAAGTTGTATGAGGATAATGAATATGCTCTTTATACTGTAACACTCTTCAGTCGTGTTGCGGATAATTTTAGAACTAGTGCAC

Basic information

species Glycine max
transcript GLYMA19G27360.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G27360.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G128995_T02 (Zea mays), 3'ss of exon 4
-------atattccaatgatgtttttgacactattgaataattatgagcatgctgttttttctagctttattccttattctgattcttattaggataaatgttttagGTCCCCAGGTCTTCTAAGAAGTTGTATGAGGATAATGAATATGCTCTTTATACTGTAACACTCTTCAGTCGTGTTGCGGATAATTTTAGAACTAGTGCAC
        | |   ||| ||||   ||||    ||| ||| ||||   ||| | |  |||    ||     | | |||       || | |     |||| || ||||| || ||||| ||||| ||| | ||||| || |||||||||||||| || ||||||||||| ||   |   ||||  || |||||||      |||| |
gtcaacgttgtctaaattatgtccctgacttccttgtatagttatattcataccggatttgactgcccccattcatat----gagctaactga---aaattttatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAATGAATATGCTCTCTACACTGTAACACTGTTTGCTAAGGTTGTTGACAATTTTAAGGTCCGTGCTC

upper sequence: GLYMA19G27360.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G12840.1 (Arabidopsis thaliana), 3'ss of exon 6
atattccaatgatgtttttgacactattgaataattatgagcatgctgttttttctagcttta--ttccttattctgattcttattaggataaat-gttttagGTCCCCAGGTCTTCTAAGAAGTTGTATGAGGATAATGAATATGCTCTTTATACTGTAACACTCTTCAGTCGTGTTGCGGATAATTTTAGAACTAGTGCAC
 ||      |    ||  |     |||||||||   |  ||  || |     | || | || |  | || |  | | | ||   |||   ||| | |||| |||| || ||||| || ||||| |||| |||||||||||| ||||| ||||| || || || ||||| | |||||| || |||||||| || | |  ||| |
gtaaatttgttgacttgctaggtttattgaatag--accag--tggtaacactactggtttgacgtaccgtgattttaatcaatttatcctaacttgtttcagGTTCCTAGGTCCTCGAAGAAATTGTTTGAGGATAATGAGTATGCCCTTTACACCGTCACTCTCTTTACTCGTGTCGCAGATAATTTCAGGATTGCTGCTC

upper sequence: GLYMA19G27360.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0068g01280.t01 (Vitis vinifera), 3'ss of exon 6
-------------------------------------------------------------------------------------atattccaatg--atgtttttgacactattgaataattatgagcatgctgttttttctagctttattccttattctgattcttattaggataaa--tgttttagGTCCCCAGGTCTTCTAAGAAGTTGTATGAGGATAATGAATATGCTCTTTATACTGTAACACTCTTCAGTCGTGTTGCGGATAATTTTAGAACTAGTGCAC
                                                                                      |  |   |||  ||   ||| | | |  || |  ||| |||  |   |||||    |    ||  |  | ||  |  |  ||| | |    ||  | ||| ||||||||||||| || |||||| || |||| || ||||| |||||||| || |||||||| || ||    |||||||| || ||||||||||| | |||||
gtaagaactattttttctggctatatattctaacttaagcgaattatggtcctgaagatatcatctgcagtaggttggtaactggctcgtgtgatgtcataccttttaaatttctggagtatt-tgaatacattgtttgactttttgttcattgtaatcttcctgattaattgagctaacctctttcagGTCCCCAGGTCATCCAAGAAGCTGCATGAAGACAATGAGTATGCTCTATACACTGTAACCCTGTTTCACCGTGTTGCTGACAATTTTAGAACAAATGCAC

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|10846063|gb|BF069052.1|BF069052
EST:     ATTCACAGAAGGATTGGCTCTCAAGCTACGAAACATTGACAAACTATGTG                         GTCCCCAGGTCTTCTAAGAAGTTGTATGAGGATAATGAATATGCTCTTTAT
genomic: ATTCACAGAAGGATTGGCTCTCAAGCTACGAAACATTGACAAACTATGTGgtaagtagta ... aatgttttagGTCCCCAGGTCTTCTAAGAAGTTGTATGAGGATAATGAATATGCTCTTTAT
EST: gi|192300408|gb|FG988825.1|FG988825
EST:     ATTCACAGAAGGATTGGCTCTCAAGCTACGAAACATTGACAAACTATGTG                         GTCCCCAGGTCTTCTAAGAAGTTGTATGAGGATAATGAATATGCTCCTTAT
genomic: ATTCACAGAAGGATTGGCTCTCAAGCTACGAAACATTGACAAACTATGTGgtaagtagta ... aatgttttagGTCCCCAGGTCTTCTAAGAAGTTGTATGAGGATAATGAATATGCTCTTTAT
EST: gi|7693148|gb|AW761245.1|AW761245
EST:     ATTCACAGAAGGATTGGCTCTCAAGCTACGAAACATTGACAAACTATGTG                         GTCCCCANGTCTTCTAAGAAGTTGTATGAGGATAATGAATATGCTCTTTAT
genomic: ATTCACAGAAGGATTGGCTCTCAAGCTACGAAACATTGACAAACTATGTGgtaagtagta ... aatgttttagGTCCCCAGGTCTTCTAAGAAGTTGTATGAGGATAATGAATATGCTCTTTAT
EST: gi|6502104|gb|AW203477.1|AW203477
EST:     ATTCACAGAAGGATTGGCTCTCAAGCTACGAAACATTGACAAACTATGTG                         GTCCCCAGGTCTTCTAAGAAGTTGTATGAGGATAATGAATATGCTCTTTAT
genomic: ATTCACAGAAGGATTGGCTCTCAAGCTACGAAACATTGACAAACTATGTGgtaagtagta ... aatgttttagGTCCCCAGGTCTTCTAAGAAGTTGTATGAGGATAATGAATATGCTCTTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttttttctagctttattccttattctgattcttattaggataaatgttttagGTCCCCAGGTCTTCTAAGAAGTTGTATGAGGATAATGAATATGCTCTTTATACTGTAACACTCTTCAGTCGTGTTGCGGATAATTTTAGAACTAGTGCAC
                         ttctgat  putative branch site (score: 3)
                                  ttattaggataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atattccaatgatgtttttgacactattgaataattatgagcatgctgttttttctagctttattccttattctgattcttattaggataaatgttttagGTCCCCAGGTCTTCTAAGAAGTTGTATGAGGATAATGAATATGCTCTTTATACTGTAACACTCTTCAGTCGTGTTGCGGATAATTTTAGAACTAGTGCAC

- - -ccaatga
- - - - - - - - - tgacact
- - - - - - - - - - - - - - - - - - - - gcatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgattc