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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctgtgttaagaatgacatttccattgactgcacactatgaaatcaaagttagattgatttggaggtttttgcttaccaatcataatgtttaattgcagGGATCTAGACTTACTGCCTTTGAGTTGGTGCATGAAAAAATACCAGGAACTCTTATTGCCGATTCTGCTGACGGTTATTGGCCGGACATGTGGATGCTGT

Basic information

species Glycine max
transcript GLYMA09G08190.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G08190.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G139533_T01 (Zea mays), 3'ss of exon 6
---atctgtgttaagaatgacatttccattgactgcacactatgaaatcaaagttagattgatttggaggtttttgcttaccaatcataatgtttaattgcagGGATCTAGACTTACTGCCTTTGAGTTGGTGCATGAAAAAATACCAGGAACTCTTATTGCCGATTCTGCTGACGGT-TATTGGCCGGACATGTGGATGCTGT
   | |||  |  |   |   | ||| ||| | ||   |  |  | ||| |   | | ||     |  |     ||| | |  ||  || |||  | || |||||||| |||||||| || || ||||| || |||||||||||||| | ||| || || || ||||||||||  | |   |||     ||| | | ||| |  
gacaactgcttacaaccttgaacttcgatt-attgtg-ataaaaacatcgagtgttgtttatggagatgtaacatgcatgctgatt-tactgtcaatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACACTGATAGCAGATTCTGCTGCTGCTGCGTTGATGAAACAAGGGCATGTTC-

upper sequence: GLYMA09G08190.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G05830.3 (Arabidopsis thaliana), 3'ss of exon 6
atctgtgttaagaatgacatttccattgact-gcacactatgaaatcaaagttagattgatttggaggtttttgcttaccaatcat--aatgtttaattgcagGGATCTAGACTTACTGCCTTTGAGTTGGTGCATGAAAAAATACCAGGAACTCTTATTGCCGATTCTGCTGACGGT-TATTGGCCGGACATGTGGATGCTGT
   ||||  | |         |||||||  |   | | | |  |      |||  | || | | ||   | ||    |   || |   ||||   | |  |||||||| || ||||| || ||||||||||||||||| ||||| || | |||||| ||||| || || ||||  | |  | ||     | |||    || || 
--ttgtggca-gctccctgaatccattgctttatagagttttcatatcttgttgaactgttgttgaaagtcttttgaatttatgactaaatggcaattgacagGGATCGAGGCTTACAGCGTTTGAGTTGGTGCATGAGAAAATCCCTGCAACTCTCATTGCAGACTCAGCTGCAGCTGCACTGATGAAAGATGGTCGTGTTG-

upper sequence: GLYMA09G08190.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv11s0016g00830.t01 (Vitis vinifera), 3'ss of exon 7
---------atctgtgttaagaatgacatttccattgactgcacac-tatgaaatcaaagttagattgatttggaggtttttgcttaccaatcataatgtttaattgcagGGATCTAGACTTACTGCCTTTGAGTTGGTGCATGAAAAAATACCAGGAACTCTTATTGCCGATTCTGCTGACGGT-------TATTGGCCGGACATGTGGATGCTGT
          | | | |||  ||||         | |  |       ||| | ||   | ||| |||   ||     |||||| ||           |    || |||||||||| || ||||| || ||||||||||||||||| || ||||| |  |||||||| || || |||||||  | |       |   ||| ||||  ||||       
attgaagtggtttatattataaatggttaagttgtaggttatttttatataacatggtacttaaatttgcttttc--tttttgtttctt--------taaccaactgcagGGATCCAGGCTTACAGCTTTTGAGTTGGTGCATGATAATATACCTGCTACTCTTATAGCAGACTCTGCTGCAGCTGCATTAATGCAGGCTGGACGCGTGG-------

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|151411952|gb|EV281763.1|EV281763
EST:     CCGGAGTTCTAAAAAGGGCTTATTGCACAGAAACACGCCCATTTAATCAA                         AGATCTAGACTTACTGCCTTTGAGTTGGTGCATGAAAAAATACCAG-AACT
genomic: C-GGAGTTCTAAAAAGGGCTTATTGCACAGAAACACGCCCATTTAATCAAgtgagtgcac ... ttaattgcagGGATCTAGACTTACTGCCTTTGAGTTGGTGCATGAAAAAATACCAGGAACT
EST: gi|151406212|gb|EV276027.1|EV276027
EST:     CCGGAGTTCTAAAAAGGGCTTATTGCACAGAAACACGCCCATTTAATCAA                         GGATCTAGACTTACTGCCTTTGAGTTGGTGCATG
genomic: CCGGAGTTCTAAAAAGGGCTTATTGCACAGAAACACGCCCATTTAATCAAgtgagtgcac ... ttaattgcagGGATCTAGACTTACTGCCTTTGAGTTGGTGCATG
EST: gi|192321692|gb|FK014036.1|FK014036
EST:     CCGGAGTTCTAAAAAGGGCTTATTGCACAGAAACACGCCCATTTAATTAA                         GGATCTAGACTTACTGCCTTTGAGTTGGTGCATGAAAAAATACCAGGAACT
genomic: CCGGAGTTCTAAAAAGGGCTTATTGCACAGAAACACGCCCATTTAATCAAgtgagtgcac ... ttaattgcagGGATCTAGACTTACTGCCTTTGAGTTGGTGCATGAAAAAATACCAGGAACT
EST: gi|151409355|gb|EV279163.1|EV279163
EST:     CCGGAGTTCTAAAAAGGGCTTATTGCACAGAAACACGCCCATTTAATCAA                         GGATCTAGACTTACTGCCTTTGAGTTGGTGCATGAA
genomic: CCGGAGTTCTAAAAAGGGCTTATTGCACAGAAACACGCCCATTTAATCAAgtgagtgcac ... ttaattgcagGGATCTAGACTTACTGCCTTTGAGTTGGTGCATGAA
EST: gi|254341135|gb|GR854863.1|GR854863
EST:     CCGGAG-TCTAAAAAGGGCTTATTGCACAGAAACACGCCCATTTAATCAA                         GGATCTAGACTTACTGCCTTTGAGTTGGTGCATGAAAAAATACCAGGAACT
genomic: CCGGAGTTCTAAAAAGGGCTTATTGCACAGAAACACGCCCATTTAATCAAgtgagtgcac ... ttaattgcagGGATCTAGACTTACTGCCTTTGAGTTGGTGCATGAAAAAATACCAGGAACT
EST: gi|21600546|gb|BQ610877.1|BQ610877
EST:     CCGGAGTTCTAAAAAGGGCTTATTGCACAGAAACACGCCCATTTAATCAA                         GGATCTAGACTTACTGCCTTTGAGTTGGTGCATGAAAAAATACCAGGAACT
genomic: CCGGAGTTCTAAAAAGGGCTTATTGCACAGAAACACGCCCATTTAATCAAgtgagtgcac ... ttaattgcagGGATCTAGACTTACTGCCTTTGAGTTGGTGCATGAAAAAATACCAGGAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaagttagattgatttggaggtttttgcttaccaatcataatgtttaattgcagGGATCTAGACTTACTGCCTTTGAGTTGGTGCATGAAAAAATACCAGGAACTCTTATTGCCGATTCTGCTGACGGTTATTGGCCGGACATGTGGATGCTGT
                                  aatcataatgtttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctgtgttaagaatgacatttccattgactgcacactatgaaatcaaagttagattgatttggaggtttttgcttaccaatcataatgtttaattgcagGGATCTAGACTTACTGCCTTTGAGTTGGTGCATGAAAAAATACCAGGAACTCTTATTGCCGATTCTGCTGACGGTTATTGGCCGGACATGTGGATGCTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
atctgtg
- - - - - - - - - - - - -ttgactg
- - - - - - - - - - - - - - - - cacacta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttggagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaatca