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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAGCAGAAGATAATGTTCGCTCTTACCTCAATCAAAGGTATTGGGAGGCGATTTTCTAACATTTGCTGCAAGAAGGCTGATGTTGACATGAACAAAAGgtttgctttactttcattgccattattgttgttttcattgttagttaataatatttgtttattgttgcataagagtgttgtggttcaattggaatttgctgctgcttgctgtggatttggtttttcatgttttgtattgaaatgggctttggttatttttgttggcag

Basic information

species Glycine max
transcript GLYMA20G30730.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G30730.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os07g07719.1 (Oryza sativa), 5'ss of exon 1
GGAAGCAGAAGATAATGTTCGCTCTTACCTCAATCAAAGGTATTGGGAGGCGATTTTCTAACATTTGCTGCAAGAAGGCTGATGTTGACATGAACAAAAGgtttgc-----tttactttcattgccattattgttgttttcattgttagttaataatatttgtttattgttgcataagagtgttgtggttcaattggaatttgctgctgcttgctgtggatttggtttttcatgttttgtattgaaatgggctttggttatttttgttggcag
||||||||||||| |||||||| || ||||| ||||| ||||| ||  | || || || ||||||  |||||||||||| ||  | |||||||||||  |||  ||       | ||  | |  |  |            |      |     |  | |    |   ||||   |     |||||  | |    ||||||                                                                         
GGAAGCAGAAGATCATGTTCGCGCTCACCTCCATCAAGGGTATCGGCCGCCGCTTCTCCAACATTGCCTGCAAGAAGGCCGACATCGACATGAACAAGCGgtgagcaaaaaccttctcgcctcacgctccccaccccccccccccccaacccctcctctgatctgggtgttcgtttgtgctgttggtgatgttctggaat-------------------------------------------------------------------------

upper sequence: GLYMA20G30730.1 (Glycine max), 5'ss of exon 2
lower sequence: AT1G22780.1 (Arabidopsis thaliana), 5'ss of exon 2
GGAAGCAGAAGATAATGTTCGCTCTTACCTCAATCAAAGGTATTGGGAGGCGATTTTCTAACATTTGCTGCAAGAAGGCTGATGTTGACATGAACAAAAGgtttgctttactttcattgccattattgttgttttcattgttagttaataatatttgtttattgttgcataagagtgttgtggttcaattggaatttgctgctgcttgctgtggatttggtttttcatgttttgtattgaaatgggctttggttatttttgttggcag
||||||| || || ||||| ||| | ||||||||||| |||||||| ||||||||  ||||||||   ||||||||||||||||||||||||||||| ||||||| ||  |||   |||   || ||  |  |||||  |||| |||  |||     | |||    | |||||    || ||  ||    |   |||   | || | |  |   || |                                                  
GGAAGCAAAAAATTATGTTTGCTTTGACCTCAATCAAGGGTATTGGAAGGCGATTGGCTAACATTGTGTGCAAGAAGGCTGATGTTGACATGAACAAGAGgtttgttt--cttagcttg--gttcttaatactttca--gttacttaggaat-----tctat----ggataagga--ttatgaatcttgcgaggttt-tggatgttagtagaaaatgt--------------------------------------------------

upper sequence: GLYMA20G30730.1 (Glycine max), 5'ss of exon 2
lower sequence: AT4G09800.1 (Arabidopsis thaliana), 5'ss of exon 2
GGAAGCAGAAGATAATGTTCGCTCTTACCTCAATCAAAGGTATTGGGAGGCGATTTTCTAACATTTGCTGCAAGAAGGCTGATGTTGACATGAACAAAAGgtttgctttactttcattgccattattgttgttttcattgttagttaataatatttgtttattgttgcataagagtgttgtggttcaattggaatttgctgctgcttgctgtggatttggtttttcatgttttgtattgaaatgggctttggttatttttgttggcag
| ||||||||||| ||||| || |||||||| |||||||||||||| ||||||||  ||||||||  |||||||||||||||||| |||||||||||||||||||     ||||  ||||  ||  |    || || || ||   |   ||  |   |  |||||  |||  |||   | | |   | |   | |||   | |                                                                 
GTAAGCAGAAGATTATGTTTGCCCTTACCTCTATCAAAGGTATTGGTAGGCGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAGgtttg---agcttttgttgctctt-ctacgtttgtctttctttagtgtgaacttaaatcaattgtgacatttgagatatattgaagagtaatagttttgagata----------------------------------------------------------------

upper sequence: GLYMA20G30730.1 (Glycine max), 5'ss of exon 2
lower sequence: AT1G34030.1 (Arabidopsis thaliana), 5'ss of exon 2
GGAAGCAGAAGATAATGTTCGCTCTTACCTCAATCAAAGGTATTGGGAGGCGATTTTCTAACATTTGCTGCAAGAAGGCTGATGTTGACATGAACAAAAGgttt--gctttactttcattgccattattgtt--gttttcattgttagttaataatatttgtttattgttgcataagagtgttgtggttcaattggaatttgctgctgcttgctgtggatttggtttttcatgttttgtattgaaatgggctttggttatttttgttggcag
| ||||| ||||| ||||| || |||||||| |||||||||||||| ||| ||||  | ||||||  ||||||||| || ||||| ||||||||||| |||| |    || | |   | | | |   |||    |||   ||||  | |||  | | | |||||    ||| ||  || |  |||   |   |||    |||                                                                      
GTAAGCAAAAGATTATGTTTGCCCTTACCTCTATCAAAGGTATTGGAAGGAGATTGGCCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAGgtattgatttcaatcaaacttcaacctttggaaagttagaattga-aattagcagtctctgtttgcatttg-atttgatttgtgtatgtgttttgagtcttg----------------------------------------------------------------------

upper sequence: GLYMA20G30730.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv18s0072g00060.t01 (Vitis vinifera), 5'ss of exon 3
GGAAGCAGAAGATAATGTTCGCTCTTACCTCAATCAAAGGTATTGGGAGGCGATTTTCTAACATTTGCTGCAAGAAGGCTGATGTTGACATGAACAAAAGgtttgctttactttcattgccattattgttgttttcattgttagttaataatatttgtttattgttgcataagagtgttgtggttcaattggaatttgctgctgcttgctgtggatttggtttttcatgttttgtattgaaatgggctttggttatttttgttggcag
|||| |||||||||||||| || || || |||||||| |||||||||||||||||  |||| |||   ||||||||||| ||||||||||||||||||||||   || | | ||   |   ||| |      | |  ||| |       || || ||      |      |||  | | |   || | ||  |||   || ||   ||||                                                          
GGAAACAGAAGATAATGTTTGCCCTCACGTCAATCAAGGGTATTGGGAGGCGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgt---ctctgccttttcttttattctaagccctctgtttgatttcacggaaaatatg------ggaaaggaaggatttggaattttagtt--aatgcacttcttaatgcta---------------------------------------------------------

upper sequence: GLYMA20G30730.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ25542 (Selaginella moellendorffii), 5'ss of exon 2
GGAAGCAGAAGATAATGTTCGCTCTTACCTCAATCAAAGGTATTGGGAGGCGATTTTCTAACATTTGCTGCAAGAAGGCTGATGTTGACATGAACAAAAGgtttgctttactttcattgccattattgttgttttcattgttagttaataatatttgtttattgttgcataagagtgttgtggttcaattggaatttgctgctgcttgctgtggatttggtttttcatgttttgtattgaaatgggctttggttatttttgttggcag
||  ||||||||| |||||||| || || || ||||| || |||||| | |||||  | |||||   |||||||||||| ||||| ||||||||||| |||| |  ||| |  |   | |  ||  | ||| | |  | || || | | |    ||||||  |    | | |   | || | | ||  | ||  |  ||| ||  | | ||                                                         
GGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGGGAATTGGGCGCCGATTCGCCAACATCGTCTGCAAGAAGGCGGATGTGGACATGAACAAGAGgtattgtttgccct---ttcttttcctcttgctctgctggtgagctgaaagatcttgttttct----cgtca---ttttcttgatctttcgggttgggcttcta-tggatg---------------------------------------------------------

upper sequence: GLYMA20G30730.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ22352 (Selaginella moellendorffii), 5'ss of exon 2
GGAAGCAGAAGATAATGTTCGCTCTTACCTCAATCAAAGGTATTGGGAGGCGATTTTCTAACATTTGCTGCAAGAAGGCTGATGTTGACATGAACAAAAGgtttgctt-tactttcattgccattattgttgtt--ttcattgttagttaataatatttgtttattgttgcataagagtgttgtggttcaattggaatttgctgctgcttgctgtggatttggtttttcatgttttgtattgaaatgggctttggttatttttgttggcag--------------------
||  ||||||||| |||||||| || || || ||||| || |||||| | |||||  | |||||   |||||||||||| ||||| ||||||||||| |||| || ||   ||||| || ||  |     || |  |    ||  || |  |  | | |  | ||| |    || |  ||   |   |   |||   |||     || ||| | ||   ||  |  || || ||    |   ||||  |   |  | |||||| || |                       
GGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGGGAATTGGGCGCCGATTCGCCAACATCGTCTGCAAGAAGGCGGATGTGGACATGAACAAGAGgtatgtttgccctttcttttcctcttgctctgctggtgagctgaaagatcttgttttctcgtcattttcttctatggatgac-tatcttccttgatctttcggattgattgat-tgagcttcttcattgat-ttgaaaaaaaaaatctgtgcttatcatttttctttgtttctttctcttccatcgaacag

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|213595082|gb|DB971871.1|DB971871
EST:     CGATTTTCTAACATTTGCTGCAAGAAGGCTGATGTTGACATGAACAAAAG                         AGCTGGTGAACTGAGTGCTGCTGAGTTGGATAGTGTGATGACTGTGGTTGC
genomic: CGATTTTCTAACATTTGCTGCAAGAAGGCTGATGTTGACATGAACAAAAGgtttgcttta ... ttgttggcagAGCTGGTGAACTGAGTGCTGCTGAGTTGGATAGTGTGATGACTGTGGTTGC
EST: gi|298196088|gb|HO044479.1|HO044479
EST:     CGATTTTCTAACATTTGCTGCAAGAAGGCTGATGTTGACATGAACAAAAG                         AGCTGGTGAACTGAGTGCTGCTGAGTTGGATAGTGTGATGACTGTGGTTGC
genomic: CGATTTTCTAACATTTGCTGCAAGAAGGCTGATGTTGACATGAACAAAAGgtttgcttta ... ttgttggcagAGCTGGTGAACTGAGTGCTGCTGAGTTGGATAGTGTGATGACTGTGGTTGC
EST: gi|193484043|gb|FK452418.1|FK452418
EST:     CGATTTTCTAACATTTGCTGCAAGAAGGCTGATGTTGACATGAACAAAAG                         AGCTGGTGAACTGAGTGCTGCTGAGTTGGATAGTGTGATGACTGTGGTTGC
genomic: CGATTTTCTAACATTTGCTGCAAGAAGGCTGATGTTGACATGAACAAAAGgtttgcttta ... ttgttggcagAGCTGGTGAACTGAGTGCTGCTGAGTTGGATAGTGTGATGACTGTGGTTGC
EST: gi|298197095|gb|HO041838.1|HO041838
EST:     CGATTTTCTAACATTTGCTGCAAGAAGGCTGATGTTGACATGAACAAAAG                         AGCTGGTGAACTGAGTGCTGCTGAGTTGGATAGTGTGATGACTGTGGTTGC
genomic: CGATTTTCTAACATTTGCTGCAAGAAGGCTGATGTTGACATGAACAAAAGgtttgcttta ... ttgttggcagAGCTGGTGAACTGAGTGCTGCTGAGTTGGATAGTGTGATGACTGTGGTTGC
EST: gi|192324370|gb|FK015721.1|FK015721
EST:     CGATTTTCTAACATTTGCTGCAAGAAGGCTGATGTTGACATGAACAAAAG                         AGCTGGTGAACTGAGTGCTGCTGAGTTGGATAGTGTGATGACTGTGGTTGC
genomic: CGATTTTCTAACATTTGCTGCAAGAAGGCTGATGTTGACATGAACAAAAGgtttgcttta ... ttgttggcagAGCTGGTGAACTGAGTGCTGCTGAGTTGGATAGTGTGATGACTGTGGTTGC
EST: gi|6668027|gb|AW279478.1|AW279478
EST:     CGATTTTCTAACATTTGCTGCAAGAAGGCTGATGTTGACATGAACAAAAG                         AGCTGGTGAACTGAGTGCTGCTGAGTTGGATAGTGTGATGACTGTGGTTGC
genomic: CGATTTTCTAACATTTGCTGCAAGAAGGCTGATGTTGACATGAACAAAAGgtttgcttta ... ttgttggcagAGCTGGTGAACTGAGTGCTGCTGAGTTGGATAGTGTGATGACTGTGGTTGC
EST: gi|192300277|gb|FG988784.1|FG988784
EST:     CGATTTTCTAACATTTGCTGCAAGAAGGCTGATGTCGACATGAACAAAAG                         AGCTGGTGAACTGAGTGCTGCTGAGTTGGATAGTGTGATGACAGTGGTTGC
genomic: CGATTTTCTAACATTTGCTGCAAGAAGGCTGATGTTGACATGAACAAAAGgtttgcttta ... ttgttggcagAGCTGGTGAACTGAGTGCTGCTGAGTTGGATAGTGTGATGACTGTGGTTGC
EST: gi|193642238|gb|FK587198.1|FK587198
EST:     CGATTTTCTAACATTTGCTGCAAGAAGGCTGATGTTGACATGAACAAAAG                         AGCTGGTGAACTGAGTGCTGCTGAGTTGGATAGTGTGATGACTGTGGTTGC
genomic: CGATTTTCTAACATTTGCTGCAAGAAGGCTGATGTTGACATGAACAAAAGgtttgcttta ... ttgttggcagAGCTGGTGAACTGAGTGCTGCTGAGTTGGATAGTGTGATGACTGTGGTTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAGCAGAAGATAATGTTCGCTCTTACCTCAATCAAAGGTATTGGGAGGCGATTTTCTAACATTTGCTGCAAGAAGGCTGATGTTGACATGAACAAAAGgtttgctttactttcattgccattattgttgttttcattgttagttaataatatttgtttattgttgcataagagtgttgtggttcaattggaatttgctgctgcttgctgtggatttggtttttcatgttttgtattgaaatgggctttggttatttttgttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT