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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acgtcatgttggttcactcctgttgattatgaatttactaatggtattttaagcttaattttaacaaattgaatatgacttgccggtaactcttttgcagAGCAAATGCTCAGCAGCCTAAACTTTTTGTTGGAATGATTCTCATCCTCATTTTTGCTGAGGCATTGGCATTATATGGTCTCATCGTTGGCATCATCCTC

Basic information

species Glycine max
transcript GLYMA02G05630.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G05630.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g34510.1 (Oryza sativa), 3'ss of exon 1
acgtcatgttggttcactcctgttgattatgaatttactaatggta--ttttaagcttaatttta---acaaattgaatatgacttgccggtaactcttttgcagAGCAAATGCTCAGCAGCCTAAACTTTTTGTTGGAATGATTCTCATCCTCATTTTTGCTGAGGCATTGGCATTATATGGTCTCATCGTTGGCATCATCCTC
|  |||||    ||    |   ||||||   |    |  |||  |   ||||| ||||   ||      |   |  || || |  | |       |   |  ||| ||||||||||| ||||| ||||| ||||| || ||||| |||||||| || ||||| || ||  | ||| | ||||||||||| ||||| |||||| | 
atttcatgacactttgtgcagcttgattggaaccacaggaattttgatttttatgctttgcttggtgcgctgttctaacataatctact-----tttgctctcagGGCAAATGCTCAACAGCCAAAACTGTTTGTGGGTATGATCCTCATCCTTATCTTTGCGGAAGCGCTTGCACTCTATGGTCTCATTGTTGGTATCATCTTG

upper sequence: GLYMA02G05630.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G101020_T01 (Zea mays), 3'ss of exon 2
-acgtcatgttggttcactcctgttgattatga-atttactaatggtattttaagcttaattttaacaaattgaatatgacttgccggtaactctttt--gcagAGCAAATGCTCAGCAGCCTAAACTTTTTGTTGGAATGATTCTCATCCTCATTTTTGCTGAGGCATTGGCATTATATGGTCTCATCGTTGGCATCATCCTC
  |     ||||    | | | |   |||||   ||  |||        | ||  ||  |    ||||  |    |  | | |  |  |   ||||||  |||| || || ||||||||||| ||  | |||||||| ||||| |||||||| ||||||||||| ||| | ||  | |||||||||||||| ||||| ||||||
ttcaaagagttgtcctagttc-gaaaattatattatcaactggaacctgtctactctagaccgcaacatctc---tccgtcctaacacttgttcttttgtgcagGGCGAACGCTCAGCAGCCGAAGTTGTTTGTTGGCATGATCCTCATCCTTATTTTTGCTGAAGCACTTGCCCTCTATGGTCTCATCGTCGGCATTATCCTC

upper sequence: GLYMA02G05630.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G028432_T01 (Zea mays), 3'ss of exon 1
-acgtcatgttggttcactcctgttgattatgaatttactaatggtattttaagcttaattttaacaaattgaatatgacttgccggtaactcttttgc--agAGCAAATGCTCAGCAGCCTAAACTTTTTGTTGGAATGATTCTCATCCTCATTTTTGCTGAGGCATTGGCATTATATGGTCTCATCGTTGGCATCATCCTC
 || | |      |   || ||   ||  ||    ||   ||  |   |    || ||       | |  |        | || |  |   ||||||||  || || || ||||||||||| || || ||||| || ||||| ||||||||||| || ||||| ||  | ||  |||| ||||||||||| ||||||||||||
cac-ttaaacacttgtcctacttgggaaaatcggattgtcaaccgggctggctgcctagac--ggcgacatctcctcatcctgacacttgttcttttgcgcagGGCGAACGCTCAGCAGCCAAAGCTGTTTGTGGGCATGATCCTCATCCTCATCTTCGCTGAAGCGCTCGCCCTATACGGTCTCATCGTCGGCATCATCCTC

upper sequence: GLYMA02G05630.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G177005_T01 (Zea mays), 3'ss of exon 2
---acgtcatgt-tggttcactcctgttgattatgaatttactaatggtattttaagcttaattttaacaaattgaatatgacttgccggtaactcttttgcagAGCAAATGCTCAGCAGCCTAAACTTTTTGTTGGAATGATTCTCATCCTCATTTTTGCTGAGGCATTGGCATTATATGGTCTCATCGTTGGCATCATCCTC
   |  |||  |     |  ||||||  | || |   |||||  | |     |     || |  ||   |  |||| ||  | ||   ||  ||   ||| ||| |||||||| || ||||| || ||||| ||||| ||||| |||||||||||||| || || ||  | ||  | |||||||| || ||||| || ||||| 
agtagctcacatgcaactttctcctggcgtttcttcttttacagaggaggcatgggaattgaaattt-tagtttgacta--atttttgggccaccgattt-cagGGCAAATGCGCAACAGCCAAAGCTTTTCGTTGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTCTATGGTCTAATTGTTGGAATTATCCTT

upper sequence: GLYMA02G05630.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G75630.2 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------------------------------------------------------------acgtcatgttggttcactcctg-----ttgattatgaatttactaatggtatttta-agcttaattttaacaaattgaatatgacttgccggtaactcttttgcagAGCAAATGCTCAGCAGCCTAAACTTTTTGTTGGAATGATTCTCATCCTCATTTTTGCTGAGGCATTGGCATTATATGGTCTCATCGTTGGCATCATCCTC
                                                                                      |  |||    |  |  | ||||     ||| ||     |  |  ||   ||| | | ||| | |||   |    |    | | | |  |       | ||||||||||| ||||| || || || || || ||||| ||||||||||| || ||||| ||||| || ||  | ||| | ||||||||||| ||||| |||||||||
gtaacgttgtttgatattagatttggtgttggttaagaactgtctggattgaatctttgaagcagattaggataaattaccagtagaattcaacaggcgttgcacctgatgctttgttttcttttacatcaactatatgtgacagcatcattcagaactctgttttgttaatctcaatgtcttattttgcagAGCGAATGCGCAACAACCGAAGCTGTTTGTGGGAATGATTCTGATTCTCATCTTTGCGGAAGCGCTTGCACTGTATGGTCTCATTGTTGGTATCATCCTC

upper sequence: GLYMA02G05630.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G19910.1 (Arabidopsis thaliana), 3'ss of exon 2
acgtcatgttggttcactcctgttgattatgaatttactaatggtattttaagcttaattttaacaaattgaatatgact----tgccggtaactcttttgcagAGCAAATGCTCAGCAGCCTAAACTTTTTGTTGGAATGATTCTCATCCTCATTTTTGCTGAGGCATTGGCATTATATGGTCTCATCGTTGGCATCATCCTC
   |  |    | || ||  | ||| || | | |||    |||| | |  |   || |        |  ||  | | | |    ||   ||   | | ||||||||| ||||| || || |||||  | ||||| ||||||||||| || ||||| |||||||| ||| | ||  | || |||||||| ||||| |||||||||
--atagtcgcagctc-ctgatattg-ttgtaagtttttgtatggaactcgagttttgaaaggtgttatgtgtttgtaattctggtgtgtgtttttgtgttgcagAGCGAATGCACAACAACCTAAGTTGTTTGTGGGAATGATTCTGATTCTCATCTTTGCTGAAGCACTTGCCCTGTACGGTCTCATTGTTGGTATCATCCTC

upper sequence: GLYMA02G05630.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G75630.1 (Arabidopsis thaliana), 3'ss of exon 2
acgtcatgttggttcactcctgttgattatgaatttactaatggtatttta-agcttaattttaacaaattgaatatgacttgccggtaactcttttgcagAGCAAATGCTCAGCAGCCTAAACTTTTTGTTGGAATGATTCTCATCCTCATTTTTGCTGAGGCATTGGCATTATATGGTCTCATCGTTGGCATCATCCTC
||     ||||   |       ||| ||     |  |  ||   ||| | | ||| | |||   |    |    | | | |  |       | ||||||||||| ||||| || || || || || ||||| ||||||||||| || ||||| ||||| || ||  | ||| | ||||||||||| ||||| |||||||||
acag-gcgttgcacctgatgctttgttttcttttacatcaactatatgtgacagcatcattcagaactctgttttgttaatctcaatgtcttattttgcagAGCGAATGCGCAACAACCGAAGCTGTTTGTGGGAATGATTCTGATTCTCATCTTTGCGGAAGCGCTTGCACTGTATGGTCTCATTGTTGGTATCATCCTC

upper sequence: GLYMA02G05630.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S1_66V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------------------------------acgtcatgttggttcactcctgttgattatgaatttactaatggtattttaagct-taattttaacaaattga-atatgacttgcc--------ggtaactcttttgcagAGCAAATGCTCAGCAGCCTAAACTTTTTGTTGGAATGATTCTCATCCTCATTTTTGCTGAGGCATTGGCATTATATGGTCTCATCGTTGGCATCATCCTC
                                                                            |  || | ||| || | |  | ||   | ||||||  |     | ||  |  | |  ||||||    |  |||  |||   ||| |        ||| |  | | || ||||| ||||| |||||||| || || || ||||| |||||| | |||||||||||||| |||||  | || || ||||| || ||||| ||||||||| | 
gtagtaatcccgtctctacgtttttctgcatttagtatttttctttttttcttcttttttttttctgcttgatatgatttcctattgctttatt--tattttctgtgaattgccattatgcatcatgtgatgcaatttttgttacctgatgtattctttgaccggattatggttatacgtctgtagAGCGAATGCCCAGCAGCCCAAGCTCTTCGTTGGTATGATTTTGATCCTCATTTTTGCCGAGGCGCTTGCTTTGTATGGACTTATCGTCGGCATCATCTTG

upper sequence: GLYMA02G05630.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S45_100V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------------------------------------------------------------acgtcatgttggttcactcctgttgattatgaatttactaatg----gtattttaagcttaattttaacaaattgaatatg-acttgcc---------ggtaac-tcttttgcagAGCAAATGCTCAGCAGCCTAAACTTTTTGTTGGAATGATTCTCATCCTCATTTTTGCTGAGGCATTGGCATTATATGGTCTCATCGTTGGCATCATCCTC
                                                                                    |      |  |||||||     | ||       |||    |||    ||   ||| |      |||      |||   |||   |||           | |  | || ||||||| || |||||||||||||| || || || || || ||||| || ||||||||||| ||||||||  | || || ||||| || ||||| ||||| ||| | 
gtagcggacgaacccttgcaatgtggtgatgtatgggaatacgtagtgaagttggaaagagagatgtaatcgggattgaaatggattcgcagagggttcacggtgatggacatgaggtttgaggatgcagagtgagttatgggagggtttggtgtgttgtggatgtggttgttaacgtggaggatggcatcgtttgcagGGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCATTTTCGCTGAGGCGCTTGCCTTGTATGGACTGATCGTCGGCATTATCTTG

upper sequence: GLYMA02G05630.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S45_97V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------------------------------------------------------------acgtcatgttggttcactcctgttgattatgaatttactaatg----gtattttaagcttaattttaacaaattgaatatg-acttgcc---------ggtaac-tcttttgcagAGCAAATGCTCAGCAGCCTAAACTTTTTGTTGGAATGATTCTCATCCTCATTTTTGCTGAGGCATTGGCATTATATGGTCTCATCGTTGGCATCATCCTC
                                                                                    |      |  |||||||     | ||       |||    |||    ||   ||  |      |||      |||   |||   |||           | |  | || ||||||| || |||||||||||||| || || || || || ||||| || ||||||||||| ||||||||  | || || ||||| || ||||| ||||| ||| | 
gtagcggacgaacccttgcaatgtggtgatgtatgggaatacgtagtgaagttggaaagagagatgtaatcgggattgaaatggattcgcagagggttcacggtgatggacatgaggtttgaggatgcagagtgagttgtgggagggtttggtgtgttgtggatgtggttgttaacgtggaggatggcatcgtttgcagGGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCATTTTCGCTGAGGCGCTTGCCTTGTATGGACTGATCGTCGGCATTATCTTG

upper sequence: GLYMA02G05630.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
acgtcatgttggttcactcctgttgattatgaattt-actaatggtattttaagcttaattttaacaaattgaatatgacttgccggtaactcttttgcagAGCAAATGCTCAGCAGCCTAAACTTTTTGTTGGAATGATTCTCATCCTCATTTTTGCTGAGGCATTGGCATTATATGGTCTCATCGTTGGCATCATCCTC
                             | | ||  |   ||   |    |   ||   ||  | |  |  |   ||| | |   ||   ||||| |||| || ||||| ||||| || || ||||||||||||||||| ||||| ||||| ||||| ||||| |||||  |||| |||||||| || || |||||||| 
----------------------------gtaagttcgatcgatcaaaagccatctttttcttcgatatctccat--tgattggtttgtttttcttt-gcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG

upper sequence: GLYMA02G05630.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ26016 (Selaginella moellendorffii), 3'ss of exon 2
acgtcatgttggttcactcctgttgattatgaattt-actaatggtattttaagcttaattttaacaaattgaatatgacttgccggtaactcttttgcagAGCAAATGCTCAGCAGCCTAAACTTTTTGTTGGAATGATTCTCATCCTCATTTTTGCTGAGGCATTGGCATTATATGGTCTCATCGTTGGCATCATCCTC
                             | | ||  |   ||   |    |   ||   ||  | |  |  |   ||| | |   ||   ||||| |||| || ||||| ||||| || || ||||||||||||||||| || || ||||| ||||| ||||| |||||  |||| |||||||| || || |||||||| 
----------------------------gtaagttcgatcgatcaaaaaccatctttttcttcgatatctccat--tgattggtttgtttttcttt-gcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG

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|9203285|gb|BE329509.1|BE329509
EST:     GGCCTCTCCGCTGGCATGGCCATCGGCATCGTTGGCGATGCCGGTGTTAG                         AGCAAATGCTCAGCAGCCTAAACTTTTTGTTGGAATGATTCTCATCCTCAT
genomic: GGCCTCTCCGCTGGCATGGCCATCGGCATCGTTGGCGATGCCGGTGTTAGgtattcatca ... tcttttgcagAGCAAATGCTCAGCAGCCTAAACTTTTTGTTGGAATGATTCTCATCCTCAT
EST: gi|208144771|gb|GD943096.1|GD943096
EST:     GGCCTCTCCGCTGGCATGGCCATCGGCATCGTTGGCGATGCCGGTGTTAG                         AGCAAATGCTCAGCAGCCTAAACTTTTTGTTGGAATGATTCTCATCCTCAT
genomic: GGCCTCTCCGCTGGCATGGCCATCGGCATCGTTGGCGATGCCGGTGTTAGgtattcatca ... tcttttgcagAGCAAATGCTCAGCAGCCTAAACTTTTTGTTGGAATGATTCTCATCCTCAT
EST: gi|13181537|gb|BG352877.1|BG352877
EST:     GGCCTCTCCGCTGGCATGGCCATCGGCATCGTTGGCGATGCCGGTGTTAG                         AGCAAATGCTCAGCAGCCTAAACTTTTTGTTGGAATGATTCTCATCCTCAT
genomic: GGCCTCTCCGCTGGCATGGCCATCGGCATCGTTGGCGATGCCGGTGTTAGgtattcatca ... tcttttgcagAGCAAATGCTCAGCAGCCTAAACTTTTTGTTGGAATGATTCTCATCCTCAT
EST: gi|193347254|gb|FK313028.1|FK313028
EST:     CCTCTCCGCTGGCATGGCCATCGGCATCGTTGGCGATGCCGGTGTTAG                         AGCAAATGCTCAGCAGCCTAAACTTTTTGTTGGAATGATTCTCATCCTCAT
genomic: CCTCTCCGCTGGCATGGCCATCGGCATCGTTGGCGATGCCGGTGTTAGgtattcatca ... tcttttgcagAGCAAATGCTCAGCAGCCTAAACTTTTTGTTGGAATGATTCTCATCCTCAT
EST: gi|193438107|gb|FK402154.1|FK402154
EST:     GCCTCTCCGCTTGGCATGGCCATCGGCATCGTTGGCGATGCCGGTGTTAG                         AGCAAATGCTCAGCAGCCTAAACTTTTTGTTGGAATGATTCTCATCCTCAT
genomic: GCCTCTCCGC-TGGCATGGCCATCGGCATCGTTGGCGATGCCGGTGTTAGgtattcatca ... tcttttgcagAGCAAATGCTCAGCAGCCTAAACTTTTTGTTGGAATGATTCTCATCCTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttaagcttaattttaacaaattgaatatgacttgccggtaactcttttgcagAGCAAATGCTCAGCAGCCTAAACTTTTTGTTGGAATGATTCTCATCCTCATTTTTGCTGAGGCATTGGCATTATATGGTCTCATCGTTGGCATCATCCTC
                                            ctcttttgc  CT-rich tract
         ttaattttaacaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acgtcatgttggttcactcctgttgattatgaatttactaatggtattttaagcttaattttaacaaattgaatatgacttgccggtaactcttttgcagAGCAAATGCTCAGCAGCCTAAACTTTTTGTTGGAATGATTCTCATCCTCATTTTTGCTGAGGCATTGGCATTATATGGTCTCATCGTTGGCATCATCCTC

- -tcatgtt
- - - - - - - - ctcctgt
- - - - - - - - - - - - - - - - - - -ctaatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgccggt