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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttccttgtttattctttcattcctaattttttggtaatttaaatatcttgttctgtcactgagttgtttttttttctttgatctctttttatgacttgacagTGTAGCATAGATGCACTTTTGGAACGGACCATTAAGCATATGCTTTTCTTACAAAGTGTGACAAAGCATGCTGACAAGCTGAAACAAACAGGGGAGTCTA

Basic information

species Glycine max
transcript GLYMA12G31460.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G31460.2 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os12g06330.1 (Oryza sativa), 3'ss of exon 6
gtatttccttgtttattctttcattcctaat----tttttggtaatttaaatatcttgttctgtc--actgagtt---------gtttttttttct-ttgatctct----ttttatgacttg---acagTGTAGCATAGATGCACTTTTGGAACGGACCATTAAGCATATGCTTTTCTTACAAAGTGTGACAAAGCATGCTGACAAGCTGAAACAAACAGGGGAGTCTA
||||   |||||| |  ||  || |   |||    ||| || | ||||| || |    | |  |   | | ||||          || | || | |  ||||  ||    |  | | | |||   |||||||||||| |||||| | ||||||  |||||||||||| ||| ||||||| ||||||||||| |||||||| ||||| || ||  |  |    || || |
gtatcctcttgttcaccctcacactttaaatgtcctttatgattatttagatcttgaatcccattgaatttagtttggatgtaaattctgttgtgtgctgatggctagcctcatgtcaattgccaacagTGTAGCATTGATGCATTATTGGAAAAGACCATTAAGCACATGGTTTTCTTGCAAAGTGTGACGAAGCATGCAGACAACCTCAAGGATTCTAACGAATCAA

upper sequence: GLYMA12G31460.2 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os11g06010.1 (Oryza sativa), 3'ss of exon 6
gtatttccttgtttattctttcattcctaa-----ttttttggtaatttaaatatcttgttctgtcactgagtt--------gtttttttttctttgatctcttt-ttatgac----------ttgacagTGTAGCATAGATGCACTTTTGGAACGGACCATTAAGCATATGCTTTTCTTACAAAGTGTGACAAAGCATGCTGACAAGCTGAAACAAACAGGGGAGTCTA
||||   ||  |  ||  ||    |  |||     |||  |||||||||  |  |  | |    |   |||  |         |||||      ||||  | ||  || |||           |  |||||||||||| |||||  |  ||||   |||  ||||||| ||||||||||| ||||||||||| |||||||| |||||||| ||  |  |    || || |
gtatcctctaatgaatctttctggttttaaataactttcatggtaatttgcactttatatagcatatttgaacttaagagcaatttttgcaatgttgacttgttaattgtgatcgcatttttttcaacagTGTAGCATCGATGCCTTGCTGGAGAAGACAGTTAAGCACATGCTTTTCTTGCAAAGTGTGACGAAGCATGCAGACAAGCTCAAGGATTCTACTGAATCCA

upper sequence: GLYMA12G31460.2 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g64560.2 (Oryza sativa), 3'ss of exon 6
gtatttccttgtttattctttcattcctaattttttggtaatttaaatatcttgttctgtcactgagttgtttttttttctttgatctctttttatgacttgacagTGTAGCATAGATGCACTTTTGGAACGGACCATTAAGCATATGCTTTTCTTACAAAGTGTGACAAAGCATGCTGACAAGCTGAAACAAACAGGGGAGTCTA
   |  |       |  | |  || ||   | | |||    || |||||        | |   | |  | |||||  | ||| ||| ||| |||  || |  |||||||||||| ||| || |  ||||   |||||||||||||||||||||||| |||| |||  ||||||||||||| ||| ||||   | | |||||| | |
--gtaacagcaccaacacatagatacccc-tatattgacctttaaaataaaacacattatttatca--tatttttggtacttagatttctgttt--gattaaacagTGTAGCATTGATACATTACTGGAGAAGACCATTAAGCATATGCTTTTCTTGCAAAATGTTGCAAAGCATGCTGATAAGTTGAAGGGATCTGGGGAGCCAA

upper sequence: GLYMA12G31460.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G069408_T01 (Zea mays), 3'ss of exon 6
gtatttccttgtt-tattctttcattcctaa--ttttttggtaattta---------aatat---------cttgttctg----tcactgagttgtttttttttctttgatctctttttatgacttg---acagTGTAGCATAGATGCACTTTTGGAACGGACCATTAAGCATATGCTTTTCTTACAAAGTGTGACAAAGCATGCTGACAAGCTGAAACAAACAGGGGAGTCTA
||||   ||| || || ||   |||| | ||  | |||| ||||||||         ||| |         ||||||       |||   | ||||    |     ||  ||||     ||   |||   ||||||||| || |||||| |  ||||   |||||||||||| ||||||||||| |||||||||||||||||||| || || || ||  |  ||    | ||| 
gtatcctcttcttctactcacgcatttcaaacgtgttttagtaatttagggttatttaatgttcaattgcacttgtttcaaacttcatacacttgtacgatgactgttagtctcacagcattttttgtcaacagTGTAGTATTGATGCATTACTGGAGAAGACCATTAAGCACATGCTTTTCTTGCAAAGTGTGACAAAGCATGCAGATAACCTCAAGGACTCAAACAAATCTG

upper sequence: GLYMA12G31460.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G031656_T01 (Zea mays), 3'ss of exon 6
gtatttccttgtt-tattctttcattcctaattttt--tggtaatttaaatatctt----gttc--tgtcactgagttg---tttttttttctt------tgatctct---ttttatgac--------ttgacagTGTAGCATAGATGCACTTTTGGAACGGACCATTAAGCATATGCTTTTCTTACAAAGTGTGACAAAGCATGCTGACAAGCTGAAACAAACAGGGGAGTCTA
||||   ||| || || |  | |||| | ||| | |  | | ||||||    | ||    ||||  || ||||   |||    ||  | | |||      |||    |     | || ||        |  |||||||||||| |||||  | |||||   |||||||||||| ||| ||||||| |||||||||||||||||||| || || || ||  |  ||   || ||||
gtatcctcttcttctacttgtgcatttcaaatgtgtgttaggaatttaggattatttaaggttcaatggcacttgtttgaaacttcatatgcttgtgcaatgactgttaagcctcataacattttttgtcaacagTGTAGCATTGATGCCTTGTTGGAGAAGACCATTAAGCACATGGTTTTCTTGCAAAGTGTGACAAAGCATGCAGATAACCTCAAGGACTCAAATGAATCTA

upper sequence: GLYMA12G31460.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G031656_T02 (Zea mays), 3'ss of exon 7
gtatttccttgtt-tattctttcattcctaattttt--tggtaatttaaatatctt----gttc--tgtcactgagttg---tttttttttctt------tgatctct---ttttatgac--------ttgacagTGTAGCATAGATGCACTTTTGGAACGGACCATTAAGCATATGCTTTTCTTACAAAGTGTGACAAAGCATGCTGACAAGCTGAAACAAACAGGGGAGTCTA--
||||   ||| || || |  | |||| | ||| | |  | | ||||||    | ||    ||||  || ||||   |||    ||  | | |||      |||    |     | || ||        |  |||||||||||| |||||  | |||||   |||||||||||| ||| ||||||| |||||||||||||||||||| || || || ||  |  ||   || ||||  
gtatcctcttcttctacttgtgcatttcaaatgtgtgttaggaatttaggattatttaaggttcaatggcacttgtttgaaacttcatatgcttgtgcaatgactgttaagcctcataacattttttgtcaacagtgtagCATTGATGCCTTGTTGGAGAAGACCATTAAGCACATGGTTTTCTTGCAAAGTGTGACAAAGCATGCAGATAACCTCAAGGACTCAAATGAATCTAAG

upper sequence: GLYMA12G31460.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G158281_T01 (Zea mays), 3'ss of exon 6
gtatttccttgtttattctttcattcctaattttttggtaatttaaatatcttgttctgtcactgagttgttttt-----ttttctttgatctctttttatgacttgacagTGTAGCATAGATGCACTTTTGGAACGGACCATTAAGCATATGCTTTTCTTACAAAGTGTGACAAAGCATGCTGACAAGCTGAAACAAACAGGGGAGTCTA
||||   ||||  |    | ||  |  | ||  ||||  | ||| |||    | |    ||    |  |   |       | | ||   |  |     | |   |  | |||||||||| ||||   | |||||   |||  ||||||| ||||||||||||||||||||||| ||| |||| |||||||| ||  |  |    |||||||
gtatgctcttgcatgaattctc--tgatgataatttgaaagtttgaatcatatatctgatctacaaactacctacagcagtgtactaacaattgcacatttatgtcaatagTGTAGCATTGATGGTTTGTTGGAGAAGACGGTTAAGCACATGCTTTTCTTACAAAGTGTGACGAAGAATGCAGACAAGCTCAAGGACTCTACCGAGTCTA

upper sequence: GLYMA12G31460.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G460472_T01 (Zea mays), 3'ss of exon 7
gtatttccttgtttattctttcattcctaatt-ttttggtaatttaaatatcttgttctgtcactgagttgtttt-----tttttctttgatctctttttatgac--ttgacagTGTAGCATAGATGCACTTTTGGAACGGACCATTAAGCATATGCTTTTCTTACAAAGTGTGACAAAGCATGCTGACAAGCTGAAACAAACAGGGGAGTCTA
||||   ||||  |    | ||  |  | ||  ||||   | ||| |||    | |    ||   ||    | |      |  |    | |    |    || |   |  | |||||||||| ||||   | |||||   |||  ||||||| ||||||||||||||||||||||| ||  |||| |||||||| ||  |  |    |||||||
gtatgcacttgaatgaattctctctaatgataattttcaaagtttgaatcgtatatctgatccacgaacaatctacacgatagtgtactaacaattgcacatcaatgtcaatagTGTAGCATTGATGGTTTGTTGGAGAAGACAGTTAAGCACATGCTTTTCTTACAAAGTGTGACGAAAAATGCAGACAAGCTCAAGGACTCTACTGAGTCTA

upper sequence: GLYMA12G31460.2 (Glycine max), 3'ss of exon 9
lower sequence: AT2G27230.2 (Arabidopsis thaliana), 3'ss of exon 5
gtatttccttgtttattctttcattcctaattttttggtaatttaaatatcttgttctgtcactgagttgtttttttttctttg-atctctttttatgacttgacagTGTAGCATAGATGCACTTTTGGAACGGACCATTAAGCATATGCTTTTCTTACAAAGTGTGACAAAGCATGCTGACAAGCTGAAACAAACAGGGGAGTCTA
            | | |     | |  |   || |||| || ||||| |     | |         ||| ||  |        | |  | |  || | | || |||||||||||| ||||||||  | ||||| || || ||||| ||||| ||||| |||| |||  | |||||| |||| |||||||| ||||| ||||| || |
-----------gtaagtgaaaaacttatctgttcttggcaaattaaaca----atccctaagaaaggttattactaacaaagagtacatgtggtttttatttaacagTGTAGCATTGATGCACTCCTTGAACGTACAATCAAGCACATGCTCTTCTTGCAAAATGTCTCCAAGCATTCTGATAAGCTGAAGCAAACCGGGGAATCCA

upper sequence: GLYMA12G31460.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv06s0009g00440.t01 (Vitis vinifera), 3'ss of exon 6
gtatttccttgtttattctttcattcctaattttttggtaatttaaatatcttgttctgtcactgagttgtttttttttctttgatctctttttatgacttgacagTGTAGCATAGATGCACTTTTGGAACGGACCATTAAGCATATGCTTTTCTTACAAAGTGTGACAAAGCATGCTGACAAGCTGAAACAAACAGGGGAGTCTA
|||  || |  ||  | ||||| | |  | |||||||         | || ||  | | |        || || | |  || | ||||  |  | ||  || |||||||||||| ||||||||  | ||||| ||||| ||||||||||||||||| |||||||| |  |||||||| |||||||| || ||||| || |||||||
gtaactcatctttcttcctttcttcctcacttttttga------ggacattttactatattgagatactgattatgtc-ctctaatctactgatgtggtttaacagTGTAGCATTGATGCACTGCTTGAACGCACCATCAAGCATATGCTTTTCTTGCAAAGTGTCATGAAGCATGCAGACAAGCTAAAGCAAACTGGAGAGTCTA

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|11411898|gb|BF423909.1|BF423909
EST:     TTCAAGATCGAGTGAAAGAGTTACGAGAAATTGTGCCAAACGGAGCAAAA                         TGTAGCATAGATGCACTTTTGGAACGGACCATTAAGCATATGCTTTTCTTA
genomic: TTCAAGATCGAGTGAAAGAGTTACGAGAAATTGTGCCAAACGGAGCAAAAgtatttcctt ... gacttgacagTGTAGCATAGATGCACTTTTGGAACGGACCATTAAGCATATGCTTTTCTTA
EST: gi|151403689|gb|EV273499.1|EV273499
EST:     TTCAAGATCGAGTGAAAGAGTTACGAGAAATTGTGCCAAACGGAGCAAAA                         TGTAGCATAGATGCACTTTTGGAACGGACCATTAAGCATATGCTTTTCTTA
genomic: TTCAAGATCGAGTGAAAGAGTTACGAGAAATTGTGCCAAACGGAGCAAAAgtatttcctt ... gacttgacagTGTAGCATAGATGCACTTTTGGAACGGACCATTAAGCATATGCTTTTCTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttctgtcactgagttgtttttttttctttgatctctttttatgacttgacagTGTAGCATAGATGCACTTTTGGAACGGACCATTAAGCATATGCTTTTCTTACAAAGTGTGACAAAGCATGCTGACAAGCTGAAACAAACAGGGGAGTCTA
                            ctttgat  putative branch site (score: 5)
                   tttttttttctttgat  CT-rich tract
                ttgtttttttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttccttgtttattctttcattcctaattttttggtaatttaaatatcttgttctgtcactgagttgtttttttttctttgatctctttttatgacttgacagTGTAGCATAGATGCACTTTTGGAACGGACCATTAAGCATATGCTTTTCTTACAAAGTGTGACAAAGCATGCTGACAAGCTGAAACAAACAGGGGAGTCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA