Sequence
atgc intronic sequence ATGC exonic sequence...accttggtgttattaaaatgttttatgctaacttgcacattcttttattttaattgaatccgtaacaaacgttttatttttgaattttgcaatacctcagGTAAAAGAGATCCTTATTGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCAGTGACTGTTTGTGGTGATATTCATGGTCAATTCCATGATCTAATGAAAC
Basic information
species | Glycine max |
transcript | GLYMA10G43470.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G43470.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G50370.1 (Arabidopsis thaliana), 3'ss of exon 1
accttggtgttattaaaatgttttatgctaacttgcacattcttttattttaat--tgaatccgtaacaaacgtt--ttatttttga---attttg-caatacctcagGTAAAAGAGATCCTTATTGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCAGTGACTGTTTGTGGTGATATTCATGGTCAATTCCATGATCTAATGAAAC
| || ||| | | | | | | ||||||| | | | ||| | ||| | || | | ||| | |||||| | || |||| ||||| || ||||||||||| || ||||| || |||||||| ||||| || || || ||||||||||| ||||| || || |||||||| |||||||
--------agtgttgaaacttgtagtagcagccgtcttcttcttttttcatgacaatgatttgctaagatactctggtaattcacaagatattttgactattatatagGTGAAAGAAATTCTTATTGAGGAATCAAATGTACAACCTGTCAACAGTCCTGTCACCGTCTGTGGTGATATCCATGGCCAGTTTCATGATCTTATGAAAC
upper sequence: GLYMA10G43470.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G19980.1 (Arabidopsis thaliana), 3'ss of exon 1
----accttggtgttattaaaatgttttatg-ctaacttgcacattcttttattttaattgaatccgtaac-aaacgttttatttttgaattttgcaatacctcagGTAAAAGAGATCCTTATTGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCAGTGACTGTTTGTGGTGATATTCATGGTCAATTCCATGATCTAATGAAAC
||| | | | | | | | | | || | ||| | | ||| |||| | | | | | | | ||| || | ||||| |||||||| || ||||||||||| || || |||||||| || |||||||| || || ||||||||||| ||||| || || |||||||| ||||| |
agataccattttatggtctcctttctcagcgattgatttatagatttgcgaagatgaatcatggtgttaaccagaagatgtttatcataatgttata------cagGTGAAAGAGATTCTGATTGAGGAGTCAAACGTACAGCCTGTAAACAGTCCAGTCACCGTATGTGGTGATATCCATGGCCAGTTTCATGATCTTATGAAGC
upper sequence: GLYMA10G43470.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv10s0071g00950.t01 (Vitis vinifera), 3'ss of exon 1
------accttggtgttattaaaatgttttatgctaacttgcacattcttttattttaattgaatccgtaacaaacgttttatttttgaattttgcaatacctcagGTAAAAGAGATCCTTATTGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCAGTGACTGTTTGTGGTGATATTCATGGTCAATTCCATGATCTAATGAAAC
| ||| ||||||| | | || | | ||| | | || | || | | | | || | || || | | | |||||||||||||||| ||||| ||||| ||||| |||||||||||||||||||| ||||||||||||||||||||||| || |||||||||||||||||||
ttctaggcaaaaaacacatttgggtgttttaaacaacactgaataagttttatagctgcctccatgcttatctgatgactgatatatg--ttctata----tttagGTAAAAGAGATCCTCATTGAAGAGTCTAATGTTCAGCCTGTCAATAGTCCAGTCACTGTTTGTGGTGATATTCATGGCCAGTTCCATGATCTAATGAAAC
upper sequence: GLYMA10G43470.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S207_36V6.1 (Physcomitrella patens), 3'ss of exon 1
----accttggtgttattaaaatgt-tttatgctaacttgcacattcttttattttaattgaatccgtaacaaacgttttatttttgaattttgcaatacctcagGTAAAAGAGATCCTTATTGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCAGTGACTGTTTGTGGTGATATTCATGGTCAATTCCATGATCTAATGAAAC
| || | | |||| | |||||| | | | | ||| | | | | | | || | | | ||| ||||| | | ||||| ||||| || | | ||||| |||||||| ||||||||||| ||||| || ||||||||||| ||||| ||||| || || ||||| | ||||| |
ctctgcgtttgagaaattagtccttctttatggttatacgaatggtctcgc-tggcatcggtgttcatgactttcatcaaacttt---gttttgtt-catcgcagGTGAAAGAAATATTGGTGGAGGAATCCAATGTTCAGCCTGTCAACAGTCCCGTTACTGTTTGTGGCGATATCCATGGCCAGTTTCATGACTTGATGAAGC
upper sequence: GLYMA10G43470.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S31_220V6.1 (Physcomitrella patens), 3'ss of exon 1
--accttggtgttattaaaatgttttatgc-taacttgcacattcttttattttaattgaatccgtaacaaacgttttatttttgaattttgcaatacctcagGTAAAAGAGATCCTTATTGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCAGTGACTGTTTGTGGTGATATTCATGGTCAATTCCATGATCTAATGAAAC
| | | |||| ||| | | | | || || | | | | | | | | | ||||| | || ||||| ||||| || | || |||||||||||||| ||||||||||| ||||| || ||||||||||| ||||||||||| ||||| ||||| ||||||| |
tgccgtcagctctatttggttgtgcgaggggttatcagcgcagatggcctctctggcattgtttttcattgctcaataaactctc--ttttgtc-tcccgcagGTGAAAGAAATATTGATGGAGGAGTCCAATGTTCAGCCTGTCAACAGTCCTGTTACTGTTTGTGGCGATATTCATGGACAATTTCATGACTTAATGAAGCMapped 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|298177211|gb|HO023458.1|HO023458EST: AAGATGGCCAGCATCTTCTCGAAGACGAGCTTCAACTTCTCTGCGAATAT GTAAAAGAGATCCTTATTGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCA
genomic: AAGATGGCCAGCATCTTCTCGAAGACGAGCTTCAACTTCTCTGCGAATATgtactcttct ... aatacctcagGTAAAAGAGATCCTTATTGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCA
EST:
gi|15286281|gb|BI470172.1|BI470172EST: AAGATGGCCAGCATCTTCTCGAAGACGAGCTTCAACTTCTCTGCGAATAT GTAAAAGAGATCCTTATTGAGGAGTCCAATGTGCATCCTGTCAATAGTCCA
genomic: AAGATGGCCAGCATCTTCTCGAAGACGAGCTTCAACTTCTCTGCGAATATgtactcttct ... aatacctcagGTAAAAGAGATCCTTATTGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattttaattgaatccgtaacaaacgttttatttttgaattttgcaatacctcagGTAAAAGAGATCCTTATTGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCAGTGACTGTTTGTGGTGATATTCATGGTCAATTCCATGATCTAATGAAAC
ccgtaac putative branch site (score: 3)
ttttatttttgaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
accttggtgttattaaaatgttttatgctaacttgcacattcttttattttaattgaatccgtaacaaacgttttatttttgaattttgcaatacctcagGTAAAAGAGATCCTTATTGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCAGTGACTGTTTGTGGTGATATTCATGGTCAATTCCATGATCTAATGAAAC
- cttggtg
- - - - - - - - - - -tttatgc
- - - - - - - - - - - - - - - -cttgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtaacaaa