Sequence
atgc intronic sequence ATGC exonic sequence...actaaaataataggaacctaagggattgtattgtttgtttaatgaaacttctcatctgtgttataacacttacatcttcttggatgtttttcctctgcagACAGCTGCAAGTTATCATGCAATAGCAATAGCACTTTCATTGATGGAAGCATATCCATTGAGTGTCCAGCATGAGCAAACAACTTTGCAAATTCTGCGGG
Basic information
species | Glycine max |
transcript | GLYMA07G06160.1 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G06160.1 (Glycine max), 3'ss of exon 20
lower sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 18
-------actaaaataataggaacctaagggattgtattgtttgtttaatgaaacttctcatctgtgttataacacttacatcttcttggatgtttttcctctgcagACAGCTGCAAGTTATCATGCAATAGCAATAGCACTTTCATTGATGGAAGCATATCCATTGAGTGTCCAGCATGAGCAAACAACTTTGCAAATTCTGCGGG
| | | | || | | | || || | |||||||| | | || | | | | ||| |||| |||| |||| || |||| ||||| || || ||||| ||||| || || || |||||||||||||| ||| | |||||||| ||||||||||||||||| ||||||||||| || |
agtacaggtttcactgttgactacttcacttaatgctttcatcatttaatgatattgcttgattatctgtttcaactaacata--cttgtctgttatttt-----agACTGCTGCGAGCTACCATGCCATAGCCATTGCTCTCTCATTGATGGAAGCTTATTCCTTGAGTGTTCAGCATGAGCAAACAACCTTGCAAATTCTTCGTG
upper sequence: GLYMA07G06160.1 (Glycine max), 3'ss of exon 20
lower sequence: AT1G01320.2 (Arabidopsis thaliana), 3'ss of exon 20
actaaaataataggaacctaagggattgtattgtttgtttaatgaaacttctcatctgtgttataacacttacatcttcttggatgtttttcctctgcagACAGCTGCAAGTTATCATGCAATAGCAATAGCACTTTCATTGATGGAAGCATATCCATTGAGTGTCCAGCATGAGCAAACAACTTTGCAAATTCTGCGGG
| | | | || || |||||| ||| | || | | | | || || || | | | | | | ||||| |||||||| || ||||| |||||||| || || || |||||||| ||||| | || ||||| ||||||||||||||||| || ||| || || |
---------gttcttttcccgatgctcgtttt--ttgttttgggaacataaatatgtaagaaacttgatttg-attttgctaattatgtcaaattt-cagACTGCTGCAAGCTACCATGCCATAGCAATTGCGCTCTCCTTGATGGAGGCATACCATTTAAGTGTTCAGCATGAGCAAACAACCTTAAGAATCCTTCGAG
upper sequence: GLYMA07G06160.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv15s0046g00740.t01 (Vitis vinifera), 3'ss of exon 20
actaaaataataggaacctaagggattgtattgtttgtttaatgaaacttctcatctgtgttataacacttacatcttcttggatgtttttc----ctctgcagACAGCTGCAAGTTATCATGCAATAGCAATAGCACTTTCATTGATGGAAGCATATCCATTGAGTGTCCAGCATGAGCAAACAACTTTGCAAATTCTGCGGG
| | || ||| || | | | || ||| | || || | | | | || | | || || | ||| |||| |||||||| |||||||| |||||||||||||| || || ||||||||||||||||| || ||||| || ||||||||||||||||| ||||||||||| || |
gaggatttcatctgaatttagaag---ggaaaaattattttgggccaca-cttgtgtatatcattcctttggagctaatttccatctcttttaatgctctccagACAGCAGCAAGTTACCATGCAATAGCAATTGCTCTATCATTGATGGAAGCATACCCTTTGAGCGTTCAGCATGAGCAAACAACCTTGCAAATTCTCCGAG
upper sequence: GLYMA07G06160.1 (Glycine max), 3'ss of exon 20
lower sequence: EFJ08067 (Selaginella moellendorffii), 3'ss of exon 19
actaaaataataggaacctaagggattgtattgtttgtttaatgaaact-tctcatctgtgttataacacttacatcttcttggatgtttttcctctgcagACAGCTGCAAGTTATCATGCAATAGCAATAGCACTTTCATTGATGGAAGCATATCCATTGAGTGTCCAGCATGAGCAAACAACTTTGCAAATTCTGCGGG
||| ||| ||||| | | || || || ||| | | ||| ||||| || ||||| || |||||||| || |||||||| ||| |||||||||||||| || | |||||||| || || ||||| || | ||||| ||| |
-----------------------------------------gtgatactatctcaaacaaaacaaatcagtt--ttcatctggagtacttt------acagACTGCAGCAAGCTACCATGCAATTGCTATAGCACTCTCACTGATGGAAGCATATACACTCAGTGTCCATCACGAACAAACTACGTATCAAATCTTGCAAG
upper sequence: GLYMA07G06160.1 (Glycine max), 3'ss of exon 20
lower sequence: EFJ24726 (Selaginella moellendorffii), 3'ss of exon 19
actaaaataataggaacctaagggattgtattgtttgtttaatgaaact-tctcatctgtgttataacacttacatcttcttggatgtttttcctctgcagACAGCTGCAAGTTATCATGCAATAGCAATAGCACTTTCATTGATGGAAGCATATCCATTGAGTGTCCAGCATGAGCAAACAACTTTGCAAATTCTGCGGG
||| ||| ||||| | | || || || ||| | | ||| ||||| || ||||| || |||||||| || |||||||| ||| |||||||||||||| || | |||||||| || || ||||| || | |||||| ||| |
-----------------------------------------gtgatactatctcaaacaaaacaaatcagtt--ttcatctggagtacttt------acagACTGCAGCAAGCTACCATGCAATTGCTATAGCACTCTCACTGATGGAAGCATATACACTCAGTGTCCATCACGAACAAACTACGTATCAAATTTTGCAAGMapped 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|9987721|gb|BE661829.1|BE661829EST: ACAAAGCTTTAAAGTGCAACCAAAGATTACTTGGTGCAGATCATATTCAG ACAGCTGCAAGTTATCATGCAATAGCAATAGCACTTTCATTGATGGAAGCA
genomic: ACAAAGCTTTAAAGTGCAACCAAAGATTACTTGGTGCAGATCATATTCAGgttttatttt ... tcctctgcagACAGCTGCAAGTTATCATGCAATAGCAATAGCACTTTCATTGATGGAAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacttctcatctgtgttataacacttacatcttcttggatgtttttcctctgcagACAGCTGCAAGTTATCATGCAATAGCAATAGCACTTTCATTGATGGAAGCATATCCATTGAGTGTCCAGCATGAGCAAACAACTTTGCAAATTCTGCGGG
cacttac putative branch site (score: 2)
tgtttttcctctgc putative PPT
tgttataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actaaaataataggaacctaagggattgtattgtttgtttaatgaaacttctcatctgtgttataacacttacatcttcttggatgtttttcctctgcagACAGCTGCAAGTTATCATGCAATAGCAATAGCACTTTCATTGATGGAAGCATATCCATTGAGTGTCCAGCATGAGCAAACAACTTTGCAAATTCTGCGGG
- -aaaataa
- - - - - - - - - - -gggattg
- - - - - - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacttac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggatgt