Sequence
atgc intronic sequence ATGC exonic sequence...gtatgatgttttggacagtagagtaaagagacttcttcattttttaaagttgtgattctcaattaagttatctttgtttactgtaaatgattgctctcagGTTACTACAGTGGATAAGTTTCAAGGTCAGCAAAATGATTTTATATTGCTATCTATTGTGCGTACTCGATTTGTTGGTCACCTACGTGATGTAAGAAGAT
Basic information
species | Glycine max |
transcript | GLYMA0048S00340.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA0048S00340.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os03g26960.1 (Oryza sativa), 3'ss of exon 13
--gtatgatgttttggacagtagagtaaagagacttcttcattttttaaagttgtgattctcaattaagttatctttgtttactgtaaatgattgctctcagGTTACTACAGTGGATAAGTTTCAAGGTCAGCAAAATGATTTTATATTGCTATCTATTGTGCGTACTCGATTTGTTGGTCACCTACGTGATGTAAGAAGAT
| | || || | | | ||| | | || || || || | | | | | | ||| || | || || ||||||| |||||||| ||||| || ||||| ||||||||||| || || ||||| |||| || || || ||||| || || || |||||||| ||||||
gtatttattgcttgagctatgttttttaagctagtattttatcattc----tttctgctttgtgctgacatgtaccctttt-ctatgcatcatg-----tagGTTACCACAGTGGACAAGTTCCAGGGTCAACAAAATGATTTCATTTTATTATCTCTTGTCCGCACCCGTTTTGTGGGGCATCTTCGTGATGTCAGAAGAC
upper sequence: GLYMA0048S00340.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G410479_T01 (Zea mays), 3'ss of exon 14
gtatgatgttttggacagtagagtaaagagacttcttcattttttaaagttgtgattctcaattaagttatctttgt-ttactgtaaatgattgctctcagGTTACTACAGTGGATAAGTTTCAAGGTCAGCAAAATGATTTTATATTGCTATCTATTGTGCGTACTCGATTTGTTGGTCACCTACGTGATGTAAGAAGAT
||| | | | | ||| ||| | || || || | || | | || | | ||| | ||||||| || ||||| ||||| || || |||||||||||||| || || || ||| |||| ||||| || ||||| ||||| || |||||||| ||||||
-----------------gtaatttccaataagtatggtgtttgctaacagtttg---ctggctttatttttttgggtactgacatccatg-tcatatctagGTTACCACTGTGGACAAGTTCCAGGGCCAGCAAAATGATTTCATTTTACTTTCTCTTGTCCGTACCCGTTTTGTGGGTCATCTTCGTGATGTCAGAAGAC
upper sequence: GLYMA0048S00340.1 (Glycine max), 3'ss of exon 12
lower sequence: AT2G38770.1 (Arabidopsis thaliana), 3'ss of exon 12
gtatgatgttttggacagtagagtaaagagacttcttcattttttaaagttgtgattctcaattaagttatctttgtttactgt---aaatgattgctctcagGTTACTACAGTGGATAAGTTTCAAGGTCAGCAAAATGATTTTATATTGCTATCTATTGTGCGTACTCGATTTGTTGGTCACCTACGTGATGTAAGAAGAT
| | ||| || | | | | | | ||| || || | | |||| | | | || ||||| || | | ||||||| ||||||||||| ||||| ||||| || || |||||||| |||||||| ||| |||| || || || || || ||||| ||||||||||||||||| |
---tttaggtttcgattttggttttttggtatgcaatacccccctaagaaagttatcacagagttagttttgtgttttgactgttctaattttatttcctcagGTGACTACAGTGGACAAGTTCCAAGGACAACAGAATGATTTCATATTGCTCTCTCTTGTACGGACACGCTTCGTAGGTCATCTACGTGATGTAAGAAGGT
upper sequence: GLYMA0048S00340.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv13s0019g00880.t01 (Vitis vinifera), 3'ss of exon 12
gtatgatgttttggacagtagagtaaagagacttcttcattttttaaagttgtgattctcaattaagttatctttgtttactgtaaatgattgctct--------cagGTTACTACAGTGGATAAGTTTCAAGGTCAGCAAAATGATTTTATATTGCTATCTATTGTGCGTACTCGATTTGTTGGTCACCTACGTGATGTAAGAAGAT
| | ||| || | | | ||| ||||| | | | | ||| | ||| | | ||| || |||||| | | |||||||||||||| |||||||||||||||||||||||||||||||| || || ||| |||| |||||||| || || |||||||| |||||||| ||||||
------tctgctgg-caccatttcctgtgcattcctttattttcaataagggcatgtgtcatggctataatcacagatcact-tatttgattgtttttttctttacagGTTACTACAGTAGATAAGTTTCAAGGTCAGCAAAATGATTTTATCTTACTGTCTCTTGTTCGTACTCGCTTCGTGGGTCACCTTCGTGATGTTAGAAGAC
upper sequence: GLYMA0048S00340.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv08s0056g01110.t01 (Vitis vinifera), 3'ss of exon 12
gtatgatgttttggacagtagagtaaagagacttcttcattttt--taaagttgtgattctcaattaagttatctttgtttact--gtaaatgattgctct-cagGTTACTACAGTGGATAAGTTTCAAGGTCAGCAAAATGATTTTATATTGCTATCTATTGTGCGTACTCGATTTGTTGGTCACCTACGTGATGTAAGAAGAT
|| | ||| | | | | | ||| ||||| ||||| || || || | | | ||| | | || || || | |||||||||||||| |||||||||||||||||||||||||||||||| || || ||| |||| |||||||| || || |||||||| |||||||| ||||||
----aatctgcagga-accatttcctgtacattcctttattttcaataaaggcatgtgtcatggctataatcacatcacttagttgattgattttttctttacagGTTACTACAGTTGATAAGTTTCAAGGTCAGCAAAATGATTTTATCTTACTGTCTCTTGTTCGTACTCGCTTCGTGGGTCACCTTCGTGATGTTAGAAGACMapped 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|254341154|gb|GR854882.1|GR854882EST: TTGTAAATAGGAGATGCGTTCCATACGATTTCATTGGTCCTCCAAGCAAG GTTACTACAGTGGATAAGTTTCAAGGTCAGCAAAATGATTTTATATTGCTA
genomic: TTGTAAATAGGAGATGCGTTCCATACGATTTCATTGGTCCTCCAAGCAAGgtatgcttct ... ttgctctcagGTTACTACAGTGGATAAGTTTCAAGGTCAGCAAAATGATTTTATATTGCTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagttgtgattctcaattaagttatctttgtttactgtaaatgattgctctcagGTTACTACAGTGGATAAGTTTCAAGGTCAGCAAAATGATTTTATATTGCTATCTATTGTGCGTACTCGATTTGTTGGTCACCTACGTGATGTAAGAAGAT
ttgctctc CT-rich tract
aattaagttatcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgatgttttggacagtagagtaaagagacttcttcattttttaaagttgtgattctcaattaagttatctttgtttactgtaaatgattgctctcagGTTACTACAGTGGATAAGTTTCAAGGTCAGCAAAATGATTTTATATTGCTATCTATTGTGCGTACTCGATTTGTTGGTCACCTACGTGATGTAAGAAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - tgttttg
- - - - - - - - - - - - - - - -cttcttc
- - - - - - - - - - - - - - - - - - - - - - - -agttgtg