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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatggtttcatgacttttatctttaataatttgtggaatatgaacctttcttcctagagaaatcattgtggttctaattgtcgaatatttggtcatttcttccatgcttacagGAGAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGACCGCCTCGCAACTTAGTTATTCTTTCAGCTGTTGTTGGCACAG

Basic information

species Glycine max
transcript GLYMA08G13370.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os12g07670.1 (Oryza sativa), 3'ss of exon 7
gtgatggtttcatgacttttatctttaataatttgtggaatatgaacctttcttcctagagaaatcattg--tggttctaattg--tcgaatatttggtcatttcttccatgcttacagGAGAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGACCGCCTCGCAACTTAGTTATTCTTTCAGCTGTTGTTGGCACAG
      || |    || ||| | ||||||  | |    |     | | | |     | ||    |  |    | || | | | |  | | |  |   ||| |    | | |  |   ||||||||||||||| ||| |||||||| ||||| ||||| ||||||||||| ||||| || ||||| |  || |   ||||||| || ||||||||||  |
------gtatatctaccttt-tgtttaattgtattcttagctctagcatctaagt-tggatttgttttcacctagtgccactcgattgggacctcaagtcttgatattccttttgttagGAGAGAGATGTTAATGAGGAATCTGGATGGAAGCTTGTTCATGGTGATGTATTTCGCCCTCCTCGAAGTTTGGCCTTTCTTTCTGCAGTTGTTGGCATCG

upper sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g34690.1 (Oryza sativa), 3'ss of exon 7
gtgatggtttcatgacttttatctttaataatttgtggaatatgaacctttcttcctagagaaatcattgtggttctaattgtcgaatatttggtcatttcttccatgcttacagGAGAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGACCGCCTCGCAACTTAGTTATTCTTTCAGCTGTTGTTGGCACAG
            |||  || |   |  ||| ||     ||| |  |  ||   |  |        | |  |   ||   |||  ||  ||||      || ||| ||     ||||| |||||||| |||||||||||||| ||||| ||||| ||||| |||||||| || || |||||||  || | | ||||||||||  |||||||    |
-----------gtga--ttgactatctata-ttcaaataatgtacaaattctgttatgcg-----cttcatacatcctcttgctga-cattt------ttattcaatat---cagGAAAGAGATGTCAGTGAAGAATCTGGATGGAAGCTTGTCCATGGGGATGTTTTCCGGCCTCCTCGCAGTTTGGCTCTTCTTTCAGCCCTTGTTGGTGTTG

upper sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os11g07910.1 (Oryza sativa), 3'ss of exon 7
gtgatggtttcatgacttttatctttaataatttgtggaatatgaacctttcttcctagagaaatcattgtggttctaattgtcgaatatttggtcatttcttccatgcttacagGAGAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGACCGCCTCGCAACTTAGTTATTCTTTCAGCTGTTGTTGGCACAG
    ||  |  | || || | |   || | ||  |   |  ||    | || ||   |   ||    |||    | |  ||  |  ||||||      |||||  ||     ||||| |||||||||||||| |||||||| ||||| ||||| ||||| |||||||| || || ||||| | ||| ||  ||||||| ||| ||||||| |  |
---gtgactggacgaattatttgaatattcata-gcaaatcattttgcattattttcatctaatctcttgatagttttgttaacttatattt------ttcttttat-----cagGAAAGAGATGTTAGTGAGGAATCTGGTTGGAAGCTTGTCCATGGAGATGTTTTCCGGCCTCCTCGTAGCTTGGTGTTTCTTTCTGCTTTTGTTGGTATTG

upper sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G165631_T01 (Zea mays), 3'ss of exon 6
gtgatggtttcatgacttttatctt--taataattt-gtggaatatgaacctttcttcc--tagagaaatcattgtggttctaattgtcgaatatttggtcatttcttccatgcttacagGAGAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGACCGCCTCGCAACTTAGTTATTCTTTCAGCTGTTGTTGGCACAG
|||| | ||  ||   | | ||| |  |  || |   || |  | | ||  ||| | |   |   ||  | | |  | || || ||||    | |   |  ||   ||   |  |   ||||  ||||||| | |||||||||||| ||||| ||||| |||||||||||||| || || ||| ||||  ||||| ||||||||||| ||||||| |  |
gtga-gtttctatatatatgatcatggtgttattccagtagcgttttaatatttatgcaggttctgattttaattagtttatacttgtatcctttgctgatatacattagtttgtattagGAACGAGATGTCAATGAAGAATCTGGATGGAAGCTTGTACATGGTGATGTTTTCCGGCCTCCTTGCAATCTAGTTCTTCTTTCAGCTCTTGTTGGTATTG

upper sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G087212_T01 (Zea mays), 3'ss of exon 7
gtgatggtttcatgacttttatctttaataatttgtggaatatgaacctttcttcctagagaaatcattgtggttctaattgtcgaatatttggtcatttcttccatgcttacagGAGAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGACCGCCTCGCAACTTAGTTATTCTTTCAGCTGTTGTTGGCACAG
   ||    |  ||| |  ||    |   || |      |  | |    || ||| | ||    ||  ||        || ||  |  |||  |  |    || | |  || |||||| ||||||||| ||||||||| || ||||| ||||| ||||||||||| || || || |||||   |   ||  ||||||| ||  | ||||| |  |
--aataaaat--tgaatcatacaagttccaagtaacaacaagtaacaagtttttctttgac---tcgatg-------gatcgtttaggattaagatacagttttccttttt-cagGAGCGAGATGTTAATGAAGAATCCGGGTGGAAGCTTGTCCATGGTGATGTGTTCCGGCCTCCTCGTGGCCAGGTGTTTCTTTCTGCCCTAGTTGGTATTG

upper sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G026231_T01 (Zea mays), 3'ss of exon 7
------------gtgatggtttcatgacttttatctttaataatttgtggaatatgaacctttcttcctagagaaatcattgtggttctaattgtcgaatatttggtcatttcttccatgcttacagGAGAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGACCGCCTCGCAACTTAGTTATTCTTTCAGCTGTTGTTGGCACAG
             |  |||       ||| ||    |  ||  ||  | |     |||   || |  |||||     |    |    | | |       |  ||      |  |   |   ||  ||||||||||||||| ||| ||||| || ||||| ||||| |||||||| || ||||| || || || |  ||  |  ||||||| ||  ||||||| |  |
gtgaggagctgaattctggcgcgcctactgtttaactgtatgcttgatagctagagaaatgttttcactagattttgctggctccccccactccattgttgcttaagttatgatattacctttctagGAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGTGACGTATTTCGGCCTCCCCGAAGTTTGATGTTTCTTTCTGCACTTGTTGGTATCG

upper sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G420310_T01 (Zea mays), 3'ss of exon 7
gtgatggtttcatgacttttatctttaataatttgtggaatatgaacctttcttcctagagaaatcattgtggttc-taattgtcgaatatttggt-catttcttccatgcttacagGAGAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGACCGCCTCGCAACTTAGTTATTCTTTCAGCTGTTGTTGGCACAG
              |    |  ||| |||| || | | || ||   |  |   |  |   |   ||  ||   | | |  |||   ||  | || |  |||  |   |   ||  ||||||||||||||| ||| ||||| || ||||| ||||| ||||| ||||| ||||| || || |  |  ||  |  ||||||| ||  ||||||| |  |
--------------aaacatgcctt-aatagttagagaaacattttcactagattttgctggcttc--tgcactccattgttgcttaagttatgatatattgatattacctttttagGAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTATTTCGGCCTCCCCAAAGTTTGATGTTTCTTTCTGCACTTGTTGGTATCG

upper sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 7
gtgatggtttcatgacttttatctttaataatttgtggaata--------------tgaacctttct---------tcctagagaaatcattgtggttctaattgtcgaatatt-tggtcatttct----------tccatgcttacagGAGAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGACCGCCTCGCAACTTAGTTATTCTTTCAGCTGTTGTTGGCACAG
|||||| || |   |||||||| | | || | |||   |||               | |  || |||         ||| | |    |   | |  |||||| ||       |  | | |||||||          |  |||   ||||||  | ||||| |||||||||||||| ||||||||||||||||| ||||| ||  | ||  |  | |   ||||| | || ||||| || ||||| ||||
gtgatgtttcctcaacttttatttgtcattagttgcacaattgtttttttagctgttaatactctctagcagtctgtccaacacttctttctttacttctaaatgcaaggcttcatagccatttctgacgtgagtattgatgggcacagGAACGGGATGTAAGTGAAGAATCTGGTTGGAAACTTGTGCATGGAGATGTGTTCAGGCCAGCAAGTAGTCTAGTTCTGCTCTCAGCGGTAGTTGGTACAG

upper sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 7
gtgatggtttcatgacttttatctttaataatttgtggaatatgaacctttcttcctagagaaatcattgtggttctaattgtcgaatatttggtcatttcttccatgcttacagGAGAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGACCGCCTCGCAACTTAGTTATTCTTTCAGCTGTTGTTGGCACAG
||||   | |||  |||||| | | || |  |||      | | |   ||  ||  | |      ||||    || |||||||  |  ||||   ||| |         |  ||||| |||||||| |||||||| ||||||||||| ||||| ||||| |||||||| || || |||| ||| |||||| | ||||||||||||||||||||||
gtgacactctca--acttttgtttatattctttttc---ctttaa---ttggtttgtgggatttccatttc--ttttaattgt-aaccattttaacatgta------attctcagGAAAGAGATGTGAGTGAAGAGTCTGGCTGGAAGCTTGTTCATGGGGATGTTTTCCGGCCTCCTCCCAATTTAGTTCTACTTTCAGCTGTTGTTGGCACAG

upper sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 7
gtgatggtttcatgacttttatctttaataatttgtggaatatgaacctttcttcctagagaaatcattgtggttctaattgtcgaatatttggtcatttcttccatgcttacagGAGAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGACCGCCTCGCAACTTAGTTATTCTTTCAGCTGTTGTTGGCACAG
|| ||| | |  | | || |     | |   | | |    | |     ||| ||  || | | |    |   ||   |||| |    ||| |  |  |    |  ||  |  ||||| || ||||| |||||||| ||||||||||||||||| ||||| |||||||||||  | ||||||||  | ||| |  ||||||||||||||||||| |
gtaatgctattttaagttct-----tgactgtgtctatgtttttttttttttttaatatatatagtccttaagtgaaaattat---gtatcttattttccactatatattgtcagGAAAGGGATGTAAGTGAAGAGTCTGGCTGGAAACTTGTCCATGGGGATGTTTTTCGGTCTCCTCGCAATATGGTTTTATTTTCAGCTGTTGTTGGCACTG

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|7795427|gb|AW780752.1|AW780752
EST:     GAAATGACTATGCAAAGTATGCTCGGGAAGATGATGATTTGGAAAGTCTG                         GAGAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTT
genomic: GAAATGACTATGCAAAGTATGCTCGGGAAGATGATGATTTGGAAAGTCTGgtgatggttt ... atgcttacagGAGAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaatcattgtggttctaattgtcgaatatttggtcatttcttccatgcttacagGAGAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGACCGCCTCGCAACTTAGTTATTCTTTCAGCTGTTGTTGGCACAG
             ttctaat  putative branch site (score: 2)
                                     tttcttccatgctt  putative PPT
                         aatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatggtttcatgacttttatctttaataatttgtggaatatgaacctttcttcctagagaaatcattgtggttctaattgtcgaatatttggtcatttcttccatgcttacagGAGAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGACCGCCTCGCAACTTAGTTATTCTTTCAGCTGTTGTTGGCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT