Sequence
atgc intronic sequence ATGC exonic sequence...atatttgatctgacatattaattctcatttgataaaatattagcatcatagatctgttagttttttgttcattttttttctgatgtgaatgatatggcagAGAGATGCAGGATAGGGTATGACGAGCAGAATGAGTGGTATTTCTTCAGCCACAAAGATAAAAAGTATCCAACAGGGACAAGAACTAATAGAGCCACCAT
Basic information
species | Glycine max |
transcript | GLYMA01G37310.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G37310.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g38834.1 (Oryza sativa), 3'ss of exon 2
---------atatttgatctgacatattaattctcatttgataaaatattagcatcatagatctgttagttttttgttcattttttttctgatgtgaat-gatatggcagAGAGA-----TGCAGGATAGGGTATGACGAGCAGAATGAGTGGTATTTCTTCAGCCACAAAGATAAAAAGTATCCAACAGGGACAAGAACTAATAGAGCCACCAT
|| || | | ||| | | | |||| || | ||| || || || | | | | || | | || || || | ||| |||| |||||||||||||| || ||||||| |||||||| ||||||||| |||| || | ||||| || || ||||| || || || || || || ||
gtttaattaatcttcatacatatatacttaatttcatgc-atgcatagctagatcaatcgagctagctatatatagatcgatgctgatcatgcatggattggggtgggtgagaagAGCATTGCAGGATAGGGTACGAGGAGCAGAGCGAGTGGTACTTCTTCAGCTACAAGGACAGGAAGTACCCGACGGGGACGAGGACGAACAGGGCGACGAT
upper sequence: GLYMA01G37310.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G18060.1 (Arabidopsis thaliana), 3'ss of exon 1
atatttgatctgacatattaattctcatttgataaaatattagcatcatagatctgttagttttttgttcattttttttctgatgtgaatgatatggcagAGAGATGCAGGATAGGGTATGACGAGCAGAATGAGTGGTATTTCTTCAGCCACAAAGATAAAAAGTATCCAACAGGGACAAGAACTAATAGAGCCACCAT
| || | | | | || || | |||| |||| || ||| | | | | | || | |||| ||| | || || ||||| || || ||||| |||||||| || || ||||| || || || |||||||| |||||||||||||||||||| |||||
-------------------gttacttaccgaacaccgtga-gatattttactttggttaaggttttattgattatcaccttaaatttta-aatgttacagAACAATGTCGAATCGGTTATGAGGAACAAAATGAATGGTATTTTTTTAGTCACAAGGACAAGAAATATCCAACGGGGACAAGAACTAATAGAGCGACCAT
upper sequence: GLYMA01G37310.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G66300.1 (Arabidopsis thaliana), 3'ss of exon 1
-atatttgatctgacatattaattctcatttgataaaatattagcatcatagatctgttagttttttgttcattttttttctgatgtgaatgatatg-gcagAGAGATGCAGGATAGGGTATGACGAGCAGAATGAGTGGTATTTCTTCAGCCACAAAGATAAAAAGTATCCAACAGGGACAAGAACTAATAGAGCCACCAT
|| | ||| | || | || | | || | |||| | | ||| | | | | | | | | || ||||| | | ||||||||| ||||||||||| || ||||| | |||||||||||||||||||| | ||| || |||||||| || ||||| || || || |||||||| |
aatttatgaattatgatttaaacgataccacctacacatgtaagcaactatactgtgtagctcgaaagagtaatatgtaacctaaatg--tgatacgtgtagAGAGATGTAGGATAGGGTACGAGGAGCAAACGGAGTGGTATTTCTTCAGCCATAGAGACAAGAAGTATCCGACTGGGACTAGGACAAACCGAGCCACCGT
upper sequence: GLYMA01G37310.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G36160.1 (Arabidopsis thaliana), 3'ss of exon 2
atatttgatctgacatatta---attctca-tttgataaaatattagcatcatagatctgttagttt---tttgttcattttttttctgatgtgaatg-atatggcagAGAGATGCAGGATAGGGTATGACGAGCAGAATGAGTGGTATTTCTTCAGCCACAAAGATAAAAAGTATCCAACAGGGACAAGAACTAATAGAGCCACCAT
||| | | | || | || || | ||| | | || | | ||||| | | | | | || | | | ||| |||| |||||| ||| | || || ||||| || ||||| |||||||||||||||||||||||||| || ||||||||||| |||||||| || ||||| |||||
-gttttcacaaaatacatgatgcatacttaatttaggatttttttcttcttcttaatctgacaatgtgaatacatagatctgatgagcattaattatgtatattatagAGAGCTGCCGAATCGGATATGAGGAAAGAAATGAATGGTATTTCTTCAGCCACAAAGATAAGAAATATCCAACAGGAACAAGAACAAACAGAGCGACCAT
upper sequence: GLYMA01G37310.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0023g03110.t01 (Vitis vinifera), 3'ss of exon 1
atatttgatctgacatattaattctcatttgataaaatattagcatcatagatctgtta-gtttt--ttgttcatttttttt--ctgatgtgaatgatat--ggcagAGAGATGCAGGATAGGGTATGACGAGCAGAATGAGTGGTATTTCTTCAGCCACAAAGATAAAAAGTATCCAACAGGGACAAGAACTAATAGAGCCACCAT
|| ||| || || | || || | | || ||| ||| ||||| ||||||| | |||| ||||| ||| | ||||||||||| |||| |||||||| |||||||||||||||||||||||||||||||| ||||| || |||||||| ||||| || || |||||||| |||||
-------ggctaacactttcataagctagccatcgcatttctgataagtaaatccgttgtgttttccttgttcaaagcgaataattgatctgaattataatggacagAGAGATGCCGGATCGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAGGATAAGAAATATCCAACGGGGACGAGGACCAATAGAGCGACCATMapped 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|192298382|gb|FG988428.1|FG988428EST: TGTTATCAGAGAGATCGATCTATATCGTATTGAACCATGGGATCTCCAAG AGAGATGCAGGATAGGGTATGACGAGCAGAATGAGTGGTATTTCTTCAGCC
genomic: TGTTATCAGAGAGATCGATCTATATCGTATTGAACCATGGGATCTCCAAGgtatatatac ... gatatggcagAGAGATGCAGGATAGGGTATGACGAGCAGAATGAGTGGTATTTCTTCAGCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatagatctgttagttttttgttcattttttttctgatgtgaatgatatggcagAGAGATGCAGGATAGGGTATGACGAGCAGAATGAGTGGTATTTCTTCAGCCACAAAGATAAAAAGTATCCAACAGGGACAAGAACTAATAGAGCCACCAT
ttctgat putative branch site (score: 3)
ttagttttttgttcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatttgatctgacatattaattctcatttgataaaatattagcatcatagatctgttagttttttgttcattttttttctgatgtgaatgatatggcagAGAGATGCAGGATAGGGTATGACGAGCAGAATGAGTGGTATTTCTTCAGCCACAAAGATAAAAAGTATCCAACAGGGACAAGAACTAATAGAGCCACCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - tctgaca
- - - - - - - - - - - - - - - -ataaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - -ctgttag