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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaattggttgtctttagtcattgtgaacattgtttgatgttccattcattctttatgtaaacaggaaataaatcatatttttatgctaatgcattacagGAAGGATGTGGTGTCACTGCCGGATGGTCTATTTGCCGATGTCCTACTTATATGGCAAGAGGTTTGTTGGTCCAATCTCACCAACAGTATTATCTTTGAG

Basic information

species Glycine max
transcript GLYMA01G00430.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G00430.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g04710.2 (Oryza sativa), 3'ss of exon 5
---------------------------------taaattggttgtctttagtcattgtgaacattgtttgatgttccattcatt--ctttatgtaaacaggaaataaatcatat-ttttatgctaatgcattacagGAAGGATGTGGTGTCACTGCCGGATGGTCTATTTGCCGATGTCCTACTTATATGGCAAGAGGTTTGTTGGTCCAATCTCACCAACAGTATTATCTTTGAG
                                    ||||  ||| | |  | ||  |   ||||  ||    | |  |  |||   ||  ||  |  |     | | | |||   |||||  | |||   |  |||  | ||||||||||| ||||||||||| |||||||| ||||  ||| | ||||| ||||||||||| || ||| |  ||||||   ||||    || ||
gttgtgctccccctgtaggcatttatatcttctcctattgaatgtatatgataat-atattcattactttgcttgctgtagattacattagtgctagtaatttcttactgataaactttataattatg---tgaagGGCGAATGTGGTGTCATTGCCGGATGGTTTATTTGCCTATGTGTTACATTTATGGAAAGAGGTTTGTGGGCCCAGTTACACCAATTATATTGGAATTAAG

upper sequence: GLYMA01G00430.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G065494_T01 (Zea mays), 3'ss of exon 5
-taaattggttgtctttagtcattgtgaacattgtttgatgtt-ccat-tcattctttatgtaaacaggaaataaatcatatttttatgctaatgcattacagGAAGGATGTGGTGTCACTGCCGGATGGTCTATTTGCCGATGTCCTACTTATATGGCAAGAGGTTTGTTGGTCCAATCTCACCAACAGTATTATCTTTGAG
 ||  |||  |  |  ||||| ||  | |   || |    ||| | || |  ||  || ||   | | ||  || |  ||  |  | | | ||||  ||||||| |||||||||||||| || || ||||| |||||||| |||| |||| | ||||| |||||||||||||||| |||| |||||   || ||    || ||
ctatgttgcattaccatagtctttcggtagtctgctcttggttgctatgttgttacttttgctgatacga--tacactattatggtttac-aatgtcttacagGGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATCTATGGGAAGAGGTTTGTTGGTCGAATCACACCACTCGTGTTGGAATTAAG

upper sequence: GLYMA01G00430.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G023798_T02 (Zea mays), 3'ss of exon 3
-------taaattggttgtctttagtcattgtgaacattgtttgatgttccattcattctttatgtaaacaggaaataaatcatatttttatgctaatgcattacagGAAGGATGTGGTGTCACTGCCGGATGGTCTATTTGCCGATGTCCTACTTATATGGCAAGAGGTTTGTTGGTCCAATCTCACCAACAGTATTATCTTTGAG
       ||  |   | ||||||    | ||||  | | ||||     |   ||  ||| || |    | | || |    |      ||||    ||||  || |||| |||||||||||||| || || ||||| |||||||| |||| |||| | ||||| |||||||||||||| | |||| |||||    | ||    || ||
attaccataggtccatagtctttcagtagtgtgctcttggttt----ctttgttgtttcctttttctcatatgatacgcttttgtggtttac---aatgtcttgcagGGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATTTATGGGAAGAGGTTTGTTGGCCGAATCACACCACTTCTGTTGGAATTAAG

upper sequence: GLYMA01G00430.2 (Glycine max), 3'ss of exon 6
lower sequence: AT2G07050.1 (Arabidopsis thaliana), 3'ss of exon 5
taaattggttgtctttagtcattgtgaacattgtttgatgttccattcattctttatgtaaacaggaaataaatcatatt----tttatgctaatgcattacagGAAGGATGTGGTGTCACTGCCGGATGGTCTATTTGCCGATGTCCTACTTATATGGCAAGAGGTTTGTTGGTCCAATCTCACCAACAGTATTATCTTTGAG
  |  ||||| ||||| |  |       | || || | | ||      |||  |   ||  |||| |||   |||| | |    || ||  |       | |||||||||||||||| || || || ||||| || ||||||||||| || || ||||| || |||||||| ||||| ||  |  | || || |||||  ||||
--atatggttttcttttgctacaacttgc-tttttagttcttatgcatattgctatagtgcacagtaaa-gcatcagaataagattaattttctcttgctccagGAAGGATGTGGTGCCATTGTCGAATGGTGTACTTGCCGATGTCGTATTTGTATGGAAAAAGGTTTGTGGGTCCCATAACGTCCACTGTTTTATCACTGAG

upper sequence: GLYMA01G00430.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv11s0065g00640.t01 (Vitis vinifera), 3'ss of exon 6
-taaattggtt--gtctttagtcattgtgaacattgtttgatgttccattcattctttatgtaaacaggaaataaatcatatttttatgctaatgcattacagGAAGGATGTGGTGTCACTGCCGGATGGTCTATTTGCCGATGTCCTACTTATATGGCAAGAGGTTTGTTGGTCCAATCTCACCAACAGTATTATCTTTGAG
 | | ||  ||  ||    | | | |  |   | |  |  || ||| | |  ||| |  | |   || |||||  |  | | |||| | | |||   |  ||||||||||||||||||||||| ||||||| |||||||| ||||| ||||||||||| |||||||||||||||||  || |||| |||||||| ||||||||
gtgactttatttggttggaaattaattagtgaacttgtaaattttcaaatt-ttcctactctgtccaagaaatggagaagaatttt-ttccaatttgt-gcagGAAGGATGTGGTGTCACTGCAGGATGGTTTATTTGCCTATGTCATACTTATATGGGAAGAGGTTTGTTGGTCCTCTCACACCTACAGTATTGTCTTTGAG

upper sequence: GLYMA01G00430.2 (Glycine max), 3'ss of exon 6
lower sequence: PP1S33_211V6.1 (Physcomitrella patens), 3'ss of exon 5
taaattggttgtctttagtcattgtgaacattgtttgat-gttccattcattctttatgtaaacaggaaataaatc-atatttttatgctaatgcattacagGAAGGATGTGGTGTCACTGCCGGATGGTCTATTTGCCGATGTCCTACTTATATGGCAAGAGGTTTGTTGGTCCAATCTCACCAACAGTATTATCTTTGAG
| ||  | |    | | ||  |    ||  |    || |  || | ||   | |||  |   |||||    |  || | || || ||  |  ||  ||||||| ||||||||||| || ||||| ||||||||| | || |||  |||| ||||||||||| | ||   |||   |||| |   |   ||     |  | ||
tgaac-gctctaatctggttttgaaaaatctcagatggttattgctttagatatttggggttacaggtcggatgtccaaatgttgatattcgtg-gttacagGTAGGATGTGGTGCCATTGCCGCATGGTCTATCTCCCAATGAGCTACATATATGGCAAGCGATTCACTGGGAAAATCACTGAACTCGTGAAGGCAATTAG

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|120495719|gb|EH223886.1|EH223886
EST:     CCTGCCCCCTGAGATATGGCTCCTTCCATACATGCTTCCATTTCATCCAG                         GAAGGATGTGGTGTCACTGCCGGATGGTCTAT
genomic: CCTGCCCCCTGAGATATGGCTCCTTCCATACATGCTTCCATTTCATCCAGgttcttgctc ... tgcattacagGAAGGATGTGGTGTCACTGCCGGATGGTCTAT
EST: gi|15812322|gb|BI784597.1|BI784597
EST:     CTGAGATATGGCTCCTTCCATACATGCTTCCATTTCATCCAG                         GAAGGATGTGGTGTCACTGCCGGATGGTCTATTTGCCGATGTCCTACTTAT
genomic: CTGAGATATGGCTCCTTCCATACATGCTTCCATTTCATCCAGgttcttgctc ... tgcattacagGAAGGATGTGGTGTCACTGCCGGATGGTCTATTTGCCGATGTCCTACTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcattctttatgtaaacaggaaataaatcatatttttatgctaatgcattacagGAAGGATGTGGTGTCACTGCCGGATGGTCTATTTGCCGATGTCCTACTTATATGGCAAGAGGTTTGTTGGTCCAATCTCACCAACAGTATTATCTTTGAG
                                       tgctaat  putative branch site (score: 2)
             taaacaggaaataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaattggttgtctttagtcattgtgaacattgtttgatgttccattcattctttatgtaaacaggaaataaatcatatttttatgctaatgcattacagGAAGGATGTGGTGTCACTGCCGGATGGTCTATTTGCCGATGTCCTACTTATATGGCAAGAGGTTTGTTGGTCCAATCTCACCAACAGTATTATCTTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - tgtgaac
- - - - - - - - - - - - - - - ttgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttatgc