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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcattattattgccgcattctactagtttgagatgtatagaagtaaatgcatttgaaaaagatatttaacctagttgccactaatttcttttccccatagGTTCCAACAAAACATGGCTCAGTACCAAAATTTGATTACACAGTCAATGTATGACAAACAACTTGACAGTGGAAAGGGTACACTTCTTCATTTGTGTGAT

Basic information

species Glycine max
transcript GLYMA19G27800.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G27800.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os11g32490.1 (Oryza sativa), 3'ss of exon 11
----------------------gcattattattgcc---gcattctact-agtttgagatgtat-agaagtaaatgcatttga------aaaagatatttaacctagttgccactaatttctttt-ccccatagGTTCCAACAAAACATGGCTCAGTACCAAAATTTGATTACACAGTCAATGTATGACAAACAACTTGACAGTGGAAAGGGTACACTTCTTCATTTGTGTGAT
                      | |  |||||| |     ||||  | | |||| |  || ||| ||  ||| |   |  ||       | | ||| ||   | ||      | |  | ||| ||  |  | || || ||    || ||||     ||||| |||||||||||| | || |||||||| ||||| ||||||||||| || || |||||||| ||||||||||||
gtaagtggttaaacttatcatagtacaattatttcttaaacattagattcagttcggtatatatcagttgtataccgacatggtctattacacgatgttatgcttaccgagaatttttatctcttgtcaaacagATTTCAGGCCAATATGGTGTCTTACCAGAATTTGATTACAAAATCGATGTATGATAAACAGCTTGACAGTGGGAAAGGAACACTTCTGCATTTGTGTGAT

upper sequence: GLYMA19G27800.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os12g29550.1 (Oryza sativa), 3'ss of exon 11
-----------------gcattattattgccgcattctactagt-ttgagatgtatagaagtaaatgcatttgaaaaagatatttaacctagttgccactaatttcttttcc---ccatagGTTCCAACAAAACATGGCTCAGTACCAAAATTTGATTACACAGTCAATGTATGACAAACAACTTGACAGTGGAAAGGGTACACTTCTTCATTTGTGTGAT
                 | || ||||||  | ||||  |  | | | |   |  || |      | |  ||   |    | || ||    | | |  |   |||| | ||       | ||||| || ||||| ||| |    || ||||||||||| ||| | ||||||||||||||||| ||||| ||||| || || ||||| |||||  ||||||||
gtaagtgcttaggttttgtat-attattatc-catttgatcaatgtcgttctacatggtgaaggaagatttcctagggcaaatgtagtgcaat-gtgatagatttatcttttgtgatacagGTTTCAGCAAAATATGACAATATATCAAAATTTGATCACAAAATCAATGTATGACAAACAGCTTGATAGTGGGAAAGGAACACTGCTTCACCTGTGTGAT

upper sequence: GLYMA19G27800.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G011136_T01 (Zea mays), 3'ss of exon 11
gcattattattgccgcattctactagtttgagatgtatagaagtaaatgca-tttgaaaaagatatttaacctagttgc-cactaatttctt-ttccccatagGTTCCAACAAAACATGGCTCAGTACCAAAATTTGATTACACAGTCAATGTATGACAAACAACTTGACAGTGGAAAGGGTACACTTCTTCATTTGTGTGAT
   |  |||||    | | ||||   ||  | |  ||  | ||| | |  | | |      | ||| | ||    |  | || | || |||| ||    | || || |||||||| ||| |   ||| || |||||||||||| | ||||||||||||||||| ||||| ||||| || || || |||||||| || || |||
-tctccttattaat-cttgctaccttttccatac-tagtgcagtgattctagtcttttgctggtatatgacagtatgacacatttatgtcttgttatatacagATTTCAACAAAATATGACAATGTATCAGAATTTGATTACAAAATCAATGTATGACAAACAGCTTGATAGTGGGAAAGGAACTCTTCTTCACTTATGCGAT

upper sequence: GLYMA19G27800.1 (Glycine max), 3'ss of exon 11
lower sequence: AT3G19340.1 (Arabidopsis thaliana), 3'ss of exon 11
gcattattattgccgcattctactagtttgagatgtatagaagtaaatgcatttgaaaaagatatttaacctagttgccactaatttcttttccccatagGTTCCAACAAAACATGGCTCAGTACCAAAATTTGATTACACAGTCAATGTATGACAAACAACTTGACAGTGGAAAGGGTACACTTCTTCATTTGTGTGAT
           |     | ||  |  |||    | |       |  || | | |     |       | | |  |   |   ||||   || |  |  |||||||| || |||||||||  ||| || || ||||| || |||||||||||||| |||||||| ||||| || | ||| || || || ||||||||||||
-----------gttaagtgcttttctttttgcctttccttgttttcattcttctttgttaagcgaacagcttcttattcgaaaattgtattccttc--agGTTCCAGCAGAACATGGCTACGTATCAGAACTTGATAACTCAGTCAATGTATGATAAACAACTAGACAGCGGGAGGGGAACGCTACTACATTTGTGTGAT

upper sequence: GLYMA19G27800.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv14s0068g01000.t01 (Vitis vinifera), 3'ss of exon 11
-gcattattattgccgcattctactagtttgagatgtatagaagtaaatgcatttgaaaaagatatttaacctagttgccactaatttcttttcc-----ccatagGTTCCAACAAAACATGGCTCAGTACCAAAATTTGATTACACAGTCAATGTATGACAAACAACTTGACAGTGGAAAGGGTACACTTCTTCATTTGTGTGAT
  ||   || |   |  | |  |||| |   || ||  |      |  |    || ||||     | | ||| |  ||   ||||||| | |||      |  ||| || ||   ||||||||||   || || || || || ||||| || |||||||| || || || || |||||||||||||| |||||||| |||||||||
gacagctttgtctacataata-actaat---agctgggtgcctccatttctcatttaaaatttggtgttaccaa--tgtggctaatttttcttcaactgactgtagATTTCAGGCAAACATGGCTGCATATCAGAACTTAATCACACAATCCATGTATGATAAGCAGCTGGATAGTGGAAAGGGTACTCTTCTTCACTTGTGTGAT

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|13481712|gb|BG511055.1|BG511055
EST:     ATTGCTGTTCTCTCCACAGTAATTGGTTATATCGCTAAGACATACTTCAC                         GTTCCAACAAAACATGGCTCAGTACCAAAATTTGATTACACAGTCAATGTA
genomic: ATTGCTGTTCTCTCCACAGTAATTGGTTATATCGCTAAGACATACTTCACgtaagtatgt ... ttccccatagGTTCCAACAAAACATGGCTCAGTACCAAAATTTGATTACACAGTCAATGTA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgcatttgaaaaagatatttaacctagttgccactaatttcttttccccatagGTTCCAACAAAACATGGCTCAGTACCAAAATTTGATTACACAGTCAATGTATGACAAACAACTTGACAGTGGAAAGGGTACACTTCTTCATTTGTGTGAT
                                 cactaat  putative branch site (score: 2)
                                   ctaatttcttttcccc  CT-rich tract
     atttgaaaaagatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcattattattgccgcattctactagtttgagatgtatagaagtaaatgcatttgaaaaagatatttaacctagttgccactaatttcttttccccatagGTTCCAACAAAACATGGCTCAGTACCAAAATTTGATTACACAGTCAATGTATGACAAACAACTTGACAGTGGAAAGGGTACACTTCTTCATTTGTGTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - -tattgcc
- - - - - - - gcattct
- - - - - - - - - - - - - - - - - - - - - - - -tgcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgccact