Sequence
atgc intronic sequence ATGC exonic sequence...aaaactaaaaagcaaggactacaataggggttatatgcatctagttgcatagaatgaatttactaattctttactttttctcccccctttaccggactagATGTGTTATGCTGCTAAAACTTGGCATGGTGGCTTCTTGGGCATGATGATATTTGGTGCAAGTGAAGTGAGTAGAAATGTGGACTTGGGTGATGAGACTA
Basic information
species | Glycine max |
transcript | GLYMA19G24980.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G24980.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G060727_T02 (Zea mays), 3'ss of exon 2
----aaaactaaaaagc-aaggactacaataggggttatatgcat---ctagttgcatagaatgaatttactaattctttactttttctcccccctttaccggactagATGTGTTATGCTGCTAAAACTTGGCATGGTGGCTTCTTGGGCATGATGATATTTGGTGCAAGTGAAGTGAGTAGAAATGTGGACTTGGGTGATGAGACTA
| | | | || |||| | | ||| | || ||| | | | | || | | | | | ||| | | | | | | || | |||||||| || || || ||| |||||| || ||||||||||||||||||| ||||||||||| || | ||||| || |||||||||||||| |
gtaaaccgttgacatgctgtatactaaatggtgcagtatttttatttcctattcataactagtaaacattttgagtgatgactaacaa-ctcgcatctccta---cagTTATGTTATGCAGCAAAGACATGGTTTGGTGGGTTTGTGGGCATGATGATATTTGGGGCAAGTGAAGTCAGCCGGAATGTTGATTTGGGTGATGAGACCA
upper sequence: GLYMA19G24980.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G472770_T01 (Zea mays), 3'ss of exon 4
-aaaactaaaaagcaaggactac-aataggggttatatgcatctagt-tgcatag--aatgaatttactaattctttactttttctcccccctttaccggactagATGTGTTATGCTGCTAAAACTTGGCATGGTGGCTTCTTGGGCATGATGATATTTGGTGCAAGTGAAGTGAGTAGAAATGTGGACTTGGGTGATGAGACTA-------------
|| || | | ||| || || | ||| || | || | |||| | | || | | | | | ||| | || | || | || | |||||||| || || || ||| |||||| || ||||||||||||||||||| ||||||||||| || | ||||| || |||||||||||||| |
gtaatctttggtacgctgtatactaaatggtgcagtatttatttcgtattcataactagtaaacattttgagtgatgactataacttacatctcctac-----agttatgttatgcagCAAAGACATGGTTTGGTGGATTTGTGGGCATGATGATATTTGGGGCAAGTGAAGTCAGCCGGAATGTTGATTTGGGTGATGAGACCACCACAATGATCTG
upper sequence: GLYMA19G24980.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G472770_T02 (Zea mays), 3'ss of exon 4
-aaaactaaaaagcaaggactac-aataggggttatatgcatctagt-tgcatag--aatgaatttactaattctttactttttctcccccctttaccggactagATGTGTTATGCTGCTAAAACTTGGCATGGTGGCTTCTTGGGCATGATGATATTTGGTGCAAGTGAAGTGAGTAGAAATGTGGACTTGGGTGATGAGACTA
|| || | | ||| || || | ||| || | || | |||| | | || | | | | | ||| | || | || | || | |||||||| || || || ||| |||||| || ||||||||||||||||||| ||||||||||| || | ||||| || |||||||||||||| |
gtaatctttggtacgctgtatactaaatggtgcagtatttatttcgtattcataactagtaaacattttgagtgatgactataacttacatctcctac-----agTTATGTTATGCAGCAAAGACATGGTTTGGTGGATTTGTGGGCATGATGATATTTGGGGCAAGTGAAGTCAGCCGGAATGTTGATTTGGGTGATGAGACCA
upper sequence: GLYMA19G24980.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G01780.1 (Arabidopsis thaliana), 3'ss of exon 6
aaaactaaaaagcaaggactacaataggggttat-atgcatctagttgcatagaatgaatttactaattctttactttttctcccccctttaccggactagATGTGTTATGCTGCTAAAACTTGGCATGGTGGCTTCTTGGGCATGATGATATTTGGTGCAAGTGAAGTGAGTAGAAATGTGGACTTGGGTGATGAGACTA
| | | || | | || | ||| ||| | || | || ||| | | | | | | | || || | ||||| ||||| ||||| |||||||| || || |||| |||||||| ||||| || ||||||||||| || || |||| ||||||| |||||||
------------------gtgaacttggttctgttattcttcttgttcctta-actggattgatggtctgataaacccctaacttgatgtcacta---cagCTTTGTTACGCTGCAAAAACGTGGCATGGAGGTTTTGTGGGTATGATGATCTTTGGCGCTAGTGAAGTGAGCAGGAACATGGATCTGGGTGACGAGACTA
upper sequence: GLYMA19G24980.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0171g00280.t01 (Vitis vinifera), 3'ss of exon 6
-aaaactaaaaagcaaggactacaa--taggggttatatgcatctagttgcatagaatgaatttactaattctttactttttctcccccctttaccggactagATGTGTTATGCTGCTAAAACTTGGCATGGTGGCTTCTTGGGCATGATGATATTTGGTGCAAGTGAAGTGAGTAGAAATGTGGACTTGGGTGATGAGACTA
| || | | | | | || | ||||| | | | | | | | | ||||| || || ||| || | |||| ||| || ||||| ||| |||| ||||| | || |||||||| |||||||| |||||||| || |||||||||||| | ||||||||||| |
ttctgccttcttgctatgttggtgaacttaagtttttttgcatggcctctctttagactacccttcattaaggtaactttaattctccgttttgtta---cagCTTTGTTTTGCAGCAAAAACCTGGTATGGAGGCTTTGTAGGGATGATGATTTTTGGTGCTAGTGAAGTAAGCAGAAATGTGGACCTTGGTGATGAGACGAMapped 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|193570109|gb|FK525852.1|FK525852EST: CATTCCACATAGTTTGTTCACATATAATCCGCACGGTGGCAGGGTTTGAG ATGTGTTATGCTGCTAAAACTTGGCATGGTGGCTTCTTGGGCATGATGATA
genomic: CATTCCACATAGTTTGTTCACATATAATCCGCACGGTGGCAGGGTTTGAGgtgtgtattt ... accggactagATGTGTTATGCTGCTAAAACTTGGCATGGTGGCTTCTTGGGCATGATGATA
EST:
gi|254320632|gb|GR827081.1|GR827081EST: CAGGGTTTGAG ATGTGTTATGCTGCTAAAACTTGGCATGGTGGCTTCTTGGGCATGATGATA
genomic: CAGGGTTTGAGgtgtgtattt ... accggactagATGTGTTATGCTGCTAAAACTTGGCATGGTGGCTTCTTGGGCATGATGATA
EST:
gi|193430047|gb|FK395961.1|FK395961EST: CATTCCACATAGTTTGTTCACATATAATCCGCACGGTGGCAGGGTTTGAG ATGTGTTATGCTGCTAAAACTTGGCATGGTGGCTTCTTGGGCATGATGATA
genomic: CATTCCACATAGTTTGTTCACATATAATCCGCACGGTGGCAGGGTTTGAGgtgtgtattt ... accggactagATGTGTTATGCTGCTAAAACTTGGCATGGTGGCTTCTTGGGCATGATGATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcatagaatgaatttactaattctttactttttctcccccctttaccggactagATGTGTTATGCTGCTAAAACTTGGCATGGTGGCTTCTTGGGCATGATGATATTTGGTGCAAGTGAAGTGAGTAGAAATGTGGACTTGGGTGATGAGACTA
tactaat putative branch site (score: 1)
tttactaattctttac CT-rich tract
aatgaatttactaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaactaaaaagcaaggactacaataggggttatatgcatctagttgcatagaatgaatttactaattctttactttttctcccccctttaccggactagATGTGTTATGCTGCTAAAACTTGGCATGGTGGCTTCTTGGGCATGATGATATTTGGTGCAAGTGAAGTGAGTAGAAATGTGGACTTGGGTGATGAGACTA
- - - -aaaagcaa
- - - - - - - - gactaca
- - - - - - - - - - - - - - - - -tatgcat
- - - - - - - - - - - - - - - - - - - - - agttgca