Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtagcctttcttgtgctttcctatatctcagtcctgaacatatatttcacattgggatactgactttattttctttaatctcttattacaattcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTGCAAAGTGTAACAAAGCATGCTGACAAGCTGAAACAGACAGGGGAATCTA

Basic information

species Glycine max
transcript GLYMA12G09990.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G09990.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g64560.2 (Oryza sativa), 3'ss of exon 6
gtatgtagcctttcttgtgctttcctatatctcagtcctgaacatatatttcacattgggatactgactttattttctttaatctcttattacaattcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTGCAAAGTGTAACAAAGCATGCTGACAAGCTGAAACAGACAGGGGAATCTA
|||      |   |   |   | ||  ||| |    | | || ||| |   ||||||      |  | |||   | |||  || |||  ||   ||| ||||||||||||| ||| || | ||||| |||||||| ||||||||||||||| |||||| |||  ||||||||||||| ||| ||||     | |||||  | |
gtaacagcaccaacacatagatacccctatattgacctttaaaataaaa--cacattatttatcatatttttggtacttagatttctgtttg--attaaacagTGTAGCATTGATACATTACTGGAGAAGACCATTAAGCATATGCTTTTCTTGCAAAATGTTGCAAAGCATGCTGATAAGTTGAAGGGATCTGGGGAGCCAA

upper sequence: GLYMA12G09990.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os12g06330.1 (Oryza sativa), 3'ss of exon 6
----------------------gtatgtagcctttcttgtgctttcctatatctcagtcctgaac--atatatttcacattgggatactgactttattttct--ttaatctcttattacaattcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTGCAAAGTGTAACAAAGCATGCTGACAAGCTGAAACAGACAGGGGAATCTA
                         |  |   |   || || ||   || ||||     |  |    || || ||   ||    || |||   |    |  |   ||  ||| | | |     |||||||||||||| |||||| |  ||||||||||||| ||||| ||| ||||| |||||||||| || |||||||| ||||| || ||  |  |    ||||| |
gtatcctcttgttcaccctcacactttaaatgtcctttatgattatttagatcttgaatcccattgaatttagtttggatgtaaattctgttgtgtgctgatggctagcctcatgtcaattgccaacagTGTAGCATTGATGCATTATTGGAAAAGACCATTAAGCACATGGTTTTCTTGCAAAGTGTGACGAAGCATGCAGACAACCTCAAGGATTCTAACGAATCAA

upper sequence: GLYMA12G09990.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os11g06010.1 (Oryza sativa), 3'ss of exon 6
--------------------------gtatgtagcctttcttgtgcttt----cctatatctcagtcctgaacatatatttcacattgg-gatactgactttattttctttaatctcttattacaattcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTGCAAAGTGTAACAAAGCATGCTGACAAGCTGAAACAGACAGGGGAATCTA
                           ||  || | ||  | ||  |||      |||||  ||    ||||| ||      |  || |  ||  ||||||  ||   | | ||| | | ||    |||||||||||||||| |||||  | ||||| |||||  | ||||| ||||||||| |||||||||| || |||||||| |||||||| ||  |  |    ||||| |
gtatcctctaatgaatctttctggttttaaataactttcatggtaatttgcactttatatagcatatttgaacttaagagcaatttttgcaatgttgactt-gttaattgtgatcgcattttt---ttcaacagTGTAGCATCGATGCCTTGCTGGAGAAGACAGTTAAGCACATGCTTTTCTTGCAAAGTGTGACGAAGCATGCAGACAAGCTCAAGGATTCTACTGAATCCA

upper sequence: GLYMA12G09990.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G069408_T01 (Zea mays), 3'ss of exon 6
-----------------------gtatgtagcct-ttcttgtgctttcctatatctcagtcctgaa---catatatttcaca-ttgggatactgactttattttctttaatctcttattacaat---tcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTGCAAAGTGTAACAAAGCATGCTGACAAGCTGAAACAGACAGGGGAATCTA
                        | |  | | | || | ||  |||    |   | | |  | ||   ||  | ||||| | ||   | |||      ||     ||| ||||  |  |   |   |||||||||||| || |||||| | ||||| |||||||| ||||| ||||||||| |||||||||| ||||||||||| || || || ||  |  ||    ||||| 
gtatcctcttcttctactcacgcatttcaaacgtgttttagtaatttagggttatttaatgttcaattgcacttgtttcaaacttcatacacttgtacgatgactgttagtctcacagcattttttgtcaacagTGTAGTATTGATGCATTACTGGAGAAGACCATTAAGCACATGCTTTTCTTGCAAAGTGTGACAAAGCATGCAGATAACCTCAAGGACTCAAACAAATCTG

upper sequence: GLYMA12G09990.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G031656_T01 (Zea mays), 3'ss of exon 6
-----------------------gtatgtagcctttcttgtgctttccta--tatctcagtcctga--acatatatttcaca-ttgggatactgactttattttctttaatctcttattacaatt-----caacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTGCAAAGTGTAACAAAGCATGCTGACAAGCTGAAACAGACAGGGGAATCTA
                        | |  |   | | ||  |  ||      ||| | ||     |   ||  | ||| | | ||   || ||      ||     |||| | || || ||| ||     |||||||||||||| |||||  |  |||| |||||||| ||||| ||| ||||| |||||||||| ||||||||||| || || || ||  |  ||   |||||||
gtatcctcttcttctacttgtgcatttcaaatgtgtgttaggaatttaggattatttaaggttcaatggcacttgtttgaaacttcatatgcttgtgcaatgactgttaagc-ctcataacattttttgtcaacagTGTAGCATTGATGCCTTGTTGGAGAAGACCATTAAGCACATGGTTTTCTTGCAAAGTGTGACAAAGCATGCAGATAACCTCAAGGACTCAAATGAATCTA

upper sequence: GLYMA12G09990.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G031656_T02 (Zea mays), 3'ss of exon 7
-----------------------gtatgtagcctttcttgtgctttccta--tatctcagtcctga--acatatatttcaca-ttgggatactgactttattttctttaatctcttattacaatt-----caacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTGCAAAGTGTAACAAAGCATGCTGACAAGCTGAAACAGACAGGGGAATCTA--
                        | |  |   | | ||  |  ||      ||| | ||     |   ||  | ||| | | ||   || ||      ||     |||| | || || ||| ||     |||||||||||||| |||||  |  |||| |||||||| ||||| ||| ||||| |||||||||| ||||||||||| || || || ||  |  ||   |||||||  
gtatcctcttcttctacttgtgcatttcaaatgtgtgttaggaatttaggattatttaaggttcaatggcacttgtttgaaacttcatatgcttgtgcaatgactgttaagc-ctcataacattttttgtcaacagtgtagCATTGATGCCTTGTTGGAGAAGACCATTAAGCACATGGTTTTCTTGCAAAGTGTGACAAAGCATGCAGATAACCTCAAGGACTCAAATGAATCTAAG

upper sequence: GLYMA12G09990.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G27230.2 (Arabidopsis thaliana), 3'ss of exon 5
gtatgtagcctttcttgtgctttcctatatctcagtcctgaacatatatttcacattgggatactgactttattttctttaatctcttattacaattcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTGCAAAGTGTAACAAAGCATGCTGACAAGCTGAAACAGACAGGGGAATCTA
       |    |      |||  || | |||  |  |  |  | | | | |  |  |  |   |     ||         |  | |  ||   ||| ||||||||||||| |||||||| || |||   || |||||||| ||||| ||| |||||| |||  | |||||| |||| |||||||| || || |||||||| |
-------gtaagtgaaaaacttatctgt-tcttgg--caaattaaacaatccctaa-gaaaggttattactaacaaagagtacatgtggtttttatttaacagTGTAGCATTGATGCACTCCTTGAACGTACAATCAAGCACATGCTCTTCTTGCAAAATGTCTCCAAGCATTCTGATAAGCTGAAGCAAACCGGGGAATCCA

upper sequence: GLYMA12G09990.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0009g00440.t01 (Vitis vinifera), 3'ss of exon 6
gtatgtagcctttcttgtgctttcctatatctcagtcctgaacatatatttc-acattgggatactgactttattttctttaatctcttattacaattcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTGCAAAGTGTAACAAAGCATGCTGACAAGCTGAAACAGACAGGGGAATCTA
|||  |   |||||||   | || ||   || |  |  |||  | || || | | |||| ||||||||  |||| | || ||||||  |  |    || ||||||||||||| |||||||| || |||   ||||||||||||||||||||| |||||||||| |  |||||||| |||||||| || || || || || ||||
gtaactcatctttctt---cctttcttcctcacttttttgaggacattttactatattgagatactga--ttatgtcctctaatctactgatgtggtttaacagTGTAGCATTGATGCACTGCTTGAACGCACCATCAAGCATATGCTTTTCTTGCAAAGTGTCATGAAGCATGCAGACAAGCTAAAGCAAACTGGAGAGTCTA

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|254315695|gb|GR825504.1|GR825504
EST:     TTCAAGATCGTGTGAAAGAGTTGCGGGAAATTGTGCCAAATGGAGCAAAA                         TGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTG
genomic: TTCAAGATCGTGTGAAAGAGTTGCGGGAAATTGTGCCAAATGGAGCAAAAgtatgtagcc ... aattcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTG
EST: gi|19935121|gb|BQ080151.1|BQ080151
EST:     TTCAAGATCGTGTGAAAGAGTTGCGGGAAATTGTGCCAAATGGAGCAAAA                         TGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTG
genomic: TTCAAGATCGTGTGAAAGAGTTGCGGGAAATTGTGCCAAATGGAGCAAAAgtatgtagcc ... aattcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTG
EST: gi|15661769|gb|BI699140.1|BI699140
EST:     TTCAAGATCGTGTGAAAGAGTTGCGGGAAATTGTGCCAAATGGAGCAAAA                         TGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTG
genomic: TTCAAGATCGTGTGAAAGAGTTGCGGGAAATTGTGCCAAATGGAGCAAAAgtatgtagcc ... aattcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTG
EST: gi|193482644|gb|FK443991.1|FK443991
EST:     TTCAAGATCGTGTGAAAGAGTTGCGGGAAATTGTGCCAAATGGAGCAAAA                         TGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTG
genomic: TTCAAGATCGTGTGAAAGAGTTGCGGGAAATTGTGCCAAATGGAGCAAAAgtatgtagcc ... aattcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTG
EST: gi|21677028|gb|BQ629379.1|BQ629379
EST:     GTTGCGGGAAATTGTGCCAAATGGAGCAAAA                         TGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTG
genomic: GTTGCGGGAAATTGTGCCAAATGGAGCAAAAgtatgtagcc ... aattcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcacattgggatactgactttattttctttaatctcttattacaattcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTGCAAAGTGTAACAAAGCATGCTGACAAGCTGAAACAGACAGGGGAATCTA
                    tttattttctttaatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtagcctttcttgtgctttcctatatctcagtcctgaacatatatttcacattgggatactgactttattttctttaatctcttattacaattcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTGCAAAGTGTAACAAAGCATGCTGACAAGCTGAAACAGACAGGGGAATCTA

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