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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgtactaatcattaatgtgtggacataaaacattgttatgtcatgattttatggggacccattccatataatcatttggtttgcgttgttgtttgtttagATCGGCATTGGAAGGGGATTGTGGATTCCTTGCTGCAAACCTTTATGCTAAGAGTGTTTTTGGGGAAGATGCTTTGGTGAATGTGAGCATTGAAAAGCAA

Basic information

species Glycine max
transcript GLYMA08G23780.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G23780.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g17430.1 (Oryza sativa), 3'ss of exon 3
cgtactaatcattaatgtgtggacataaaacattgt-tatgtcatgattttatggggacccattccatataatcatttggtt--tgcgttgttgtttgtttagATCGGCATTGGAAGGGGATTGTGGATTCCTTGCTGCAAACCTTTATGCTAAGAGTGTTTTTGGGGAAGATGCTTTGGTGAATGTGAGCATTGAAAAGCAA
     ||  ||   |  ||   |  |        ||  ||  ||  | ||           | |     |||||| |    |  | | |     ||     || || ||  | || || || || || || || || || ||||||||||| ||||||||||| || |||||||||||||| ||| | ||||| || ||||| 
---gttagccagataactggaaaactgttgtcccgtacattccactacttgtcatattaataatagggttaatcactcttctaattcataaaccttatgccagGTCTGCGCTTGACGGAGAATGCGGTTTTCTCGCCGCTAACCTTTATGCAAAGAGTGTTTTCGGTGAAGATGCTTTGGTAAATATCAGCATCGAGAAGCAG

upper sequence: GLYMA08G23780.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os11g07280.1 (Oryza sativa), 3'ss of exon 3
cgtactaatcattaatgtgtggacat--aaaacat-tgttatgtcatgattttatggggacccattccatataatc-atttggtttgcgttgttgtttgtttagATCGGCATTGGAAGGGGATTGTGGATTCCTTGCTGCAAACCTTTATGCTAAGAGTGTTTTTGGGGAAGATGCTTTGGTGAATGTGAGCATTGAAAAGCAA
  | | || ||| || |   ||   |  | | ||| | | ||| ||    |   |||   |  || ||    |  | |||    |||  |  |  |    | ||||| ||  | || || || ||||| ||  | ||||| || || ||||| |||||||||||||| || ||||| ||||||||  | ||| |||||||||||
--ttccaa-catcaaagctgggttcttcatagcatgtctaatgccactgctgcttggttgctaataccgctgaccctattatacttgtat-atgataacatcagATCTGCGCTTGATGGAGAATGTGGGTTTATCGCTGCTAATCTCTATGCCAAGAGTGTTTTTGGTGAGGATGCATTGGTGAACATCAGCGTTGAAAAGCAA

upper sequence: GLYMA08G23780.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G378906_T01 (Zea mays), 3'ss of exon 4
cgtactaatcattaatgtgtggacataaaacattg--ttatgtcatgattttatggggacccattccatataatcatttggtttgcgttgttgtttgtttagATCGGCATTGGAAGGGGATTGTGGATTCCTTGCTGCAAACCTTTATGCTAAGAGTGTTTTTGGGGAAGATGCTTTGGTGAATGTGAGCATTGAAAAGCAA
| | |||  | | |  |  |||||||     ||||  | |  |  ||     ||     |   | |  |  | |  |     || | |  ||  |     || || ||| |||| ||||| ||||| ||||||||||| ||||||||||| |||||||| ||||| || || |||||||||||  | |||||||| ||||||
ccttctagacttgaggggatggacatggtgtattgggtgaatttctgtcgaaatatttgcttgtcctctgaagttgtaaccctt-cttcattcgtcacc-agGTCTGCACTGGATGGGGAATGTGGTTTCCTTGCTGCTAACCTTTATGCAAAGAGTGTGTTTGGCGAGGACGCTTTGGTGAACATCAGCATTGAGAAGCAA

upper sequence: GLYMA08G23780.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G011101_T01 (Zea mays), 3'ss of exon 3
cgtactaatcattaatgtgtggacataaaacattgttatgtcatgattttatggggacccattc-catataatcatttgg---tttgcgttgttgtttgtt--tagATCGGCATTGGAAGGGGATTGTGGATTCCTTGCTGCAAACCTTTATGCTAAGAGTGTTTTTGGGGAAGATGCTTTGGTGAATGTGAGCATTGAAAAGCAA
     |     | |  |  ||    | | |   ||   ||   ||  ||| ||  |||  |||  | | |  || | ||    | | |    || |||| |   || || ||| | || || || ||||| ||||||||||| || |||||||| |||||||| ||||| || ||||||||||||||  | |||||||| ||||||
-----tcgctttgagcggatgtgtttgacatggtgaattgg-gtgtatttctgccgacatatttgcttgttctcttctgaacttgtccccctttatttgataccagGTCTGCACTAGACGGAGAATGTGGTTTCCTTGCTGCTAATCTTTATGCAAAGAGTGTGTTTGGTGAGGATGCTTTGGTGAACATCAGCATTGAGAAGCAA

upper sequence: GLYMA08G23780.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G094699_T01 (Zea mays), 3'ss of exon 3
cgtact---aatcattaatgtgtggacata-aaacattgttatgtcatgattttatggggacccattccatataatcatttggtttgcgttgttgtttgtttagATCGGCATTGGAAGGGGATTGTGGATTCCTTGCTGCAAACCTTTATGCTAAGAGTGTTTTTGGGGAAGATGCTTTGGTGAATGTGAGCATTGAAAAGCAA
  ||||   | | ||  | |  | ||||||  || |    |  |   ||  |||  |    |    |      |  ||||    |    || |  ||   | ||||| ||  | || || || ||||| |||||||||||||| || ||||| |||||||| ||||| || || ||| |||||||| | ||  |||| ||||| 
--tacttgaagttatataaggctagacatatgaaaaactctgcgctgtgcattt--gaatgctttgtttgctaaggcattgctctcattttctacttgcatcagATCTGCGCTCGATGGAGAATGTGGGTTCCTTGCTGCAAATCTCTATGCCAAGAGTGTGTTTGGCGAGGACGCTCTGGTGAATATCAGTGTTGAGAAGCAG

upper sequence: GLYMA08G23780.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0018g02080.t01 (Vitis vinifera), 3'ss of exon 3
cgtactaatcattaatgtgtggacataaaacattgttatgtcatgatttta-tggggacccattccatataatcatttggtttgcgttgttgtttg--tttagATCGGCATTGGAAGGGGATTGTGGATTCCTTGCTGCAAACCTTTATGCTAAGAGTGTTTTTGGGGAAGATGCTTTGGTGAATGTGAGCATTGAAAAGCAA
   || |||  || |  |     | ||   |         |  |  |   | ||   |  ||||  |  |      |     | | || ||| |||    ||| |||||||| || ||||| ||||| |||||||| |||||||| || || ||||| || ||||| || |||||||| || |||||||||||||| || |||
---accaatagtttaccttctatcttagttcccaagggccttgttttccaactgattaatcattttactttgcttgtcaccattctttcttggttggacatagCTCGGCATTAGATGGGGAGTGTGGGTTCCTTGCAGCAAACCTATACGCAAAGAGCGTATTTGGAGAGGATGCTTTAGTAAATGTGAGCATTGAGAAACAA

upper sequence: GLYMA08G23780.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S309_15V6.2 (Physcomitrella patens), 3'ss of exon 4
-----cgtactaatcattaatgtgtggacataaaacattgttatgtcatgattttatggggacccattccatataatcatttggtttgcgttgttgtttgtttagATCGGCATTGGAAGGGGATTGTGGATTCCTTGCTGCAAACCTTTATGCTAAGAGTGTTTTTGGGGAAGATGCTTTGGTGAATGTGAGCATTGAAAAGCAA
     |||  ||    || |||  |     | || ||   || || ||   ||| | | | |   || | |  |  | |      |||  |  ||||   |  ||||| || |||||||| |||||||| ||  | || ||||| |||||||| ||||| || ||||| || ||||| ||||||||||| ||  |||| ||||||
tgtaacgtgatagcttttgatgattt--tttcaatcaaacttttgccacagttt-aagtgaaatgatccgagtttgtaacaca-cttgaatc-ttgtacatgcagATCTGCTTTGGAAGGTGATTGTGGCTTTTTGGCGGCAAATCTTTATGCGAAGAGCGTGTTTGGAGAGGATGCGTTGGTGAATGTCAGTGTTGAGAAGCAA

upper sequence: GLYMA08G23780.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S42_100V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------cgta-ctaatcattaatgtgtggacataaaacattgttatgtcatgattttatggggacccattccata----taatcatttggtttgcgttgttgtt----tgtttagATCGGCATTGGAAGGGGATTGTGGATTCCTTGCTGCAAACCTTTATGCTAAGAGTGTTTTTGGGGAAGATGCTTTGGTGAATGTGAGCATTGAAAAGCAA
                                        || ||  ||     | | |    |||  |  || | |||  |    | |  || |||| | | |||     |||||   |  || || || ||||     ||   || || |||||||| || || ||||| || |||||||| || ||||||||||||||||||||||| || ||||||||||| ||||| |||||||| || |||
gtaagtctttgtttacacctgcaagtaatatctggtcttttatcttttcgcctttttttcataatatcatgttataatggaagatgtatcgggtgacctacttcattccgttaatctaatttttcgctttattgtcgtcatgagcagGTCTGCATTGGAGGGAGACTGTGGTTTTCTTGCTGCTAATCTTTATGCTAAGAGTGTTTTTGGAGAGGATGCTTTGGTCAATGTTAGCATTGAGAAACAA

upper sequence: GLYMA08G23780.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S168_28V6.1 (Physcomitrella patens), 3'ss of exon 4
cgtactaatc--attaatgtgtggacataaaacattgtta-tgtcatgattttatg--gggacccattccatataatcatttggtttgcgttgttgtttgtttagATCGGCATTGGAAGGGGATTGTGGATTCCTTGCTGCAAACCTTTATGCTAAGAGTGTTTTTGGGGAAGATGCTTTGGTGAATGTGAGCATTGAAAAGCAA
  |  |||||  | | |    ||    | |||| |  ||| ||   |||  | ||   |  ||   |   || | |||  | ||| || |    || | |   ||||| ||  ||||||| |||||||| ||| | |||||||| || ||||||||||| || |||||||| || || || || |||||||  ||||| ||||||
--tcataatctaagtgaaaattgccttttaaacttcattaatgcagtgacctgattttgtaacttgtctgat-tcatcgct-ggtgtgtgcacatgat-gcgcagATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAAGAGCGTATTTGGGGAGGACGCATTAGTTAATGTGAATATTGAGAAGCAA

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|254314865|gb|GR829858.1|GR829858
EST:     TT-CTGAACCACATTGTCAAGTCTACAAATATGAAGTGCCTGACTCCACC                         ATCGGCATTGGAAGGGGATTGTGGATTCCTTGCTGCAAACCTTTATGCTAA
genomic: TTCCTGAACCACATTGTCAAGTCTACAAATATGAAGTGCCTGACTCCACCgtaagttatc ... gtttgtttagATCGGCATTGGAAGGGGATTGTGGATTCCTTGCTGCAAACCTTTATGCTAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttatggggacccattccatataatcatttggtttgcgttgttgtttgtttagATCGGCATTGGAAGGGGATTGTGGATTCCTTGCTGCAAACCTTTATGCTAAGAGTGTTTTTGGGGAAGATGCTTTGGTGAATGTGAGCATTGAAAAGCAA
                                              tttgttt  CT-rich tract
                    atataatcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgtactaatcattaatgtgtggacataaaacattgttatgtcatgattttatggggacccattccatataatcatttggtttgcgttgttgtttgtttagATCGGCATTGGAAGGGGATTGTGGATTCCTTGCTGCAAACCTTTATGCTAAGAGTGTTTTTGGGGAAGATGCTTTGGTGAATGTGAGCATTGAAAAGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - -tgtgtgg
- - - - - - - - - - - - - aaaacatt
- - - - - - - - - - - - - - - - - - - tgtcatg
- - - - - - - - - - - - - - - - - - - - - - - - -tatgggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcgttg