Sequence
atgc intronic sequence ATGC exonic sequence...ctttttgttttgaattaaaagagtactcatcatacattggtttatataaccaaagatatttatactgtctcacagtgactgataagatacattttccagtATTTTCTTTATCAGTTGCTACGAGGACTCAAATATGTACACTCAGCAAATGTTCTGCACCGTGATCTAAAGCCTAGCAACTTGCTACTGAATGCCAACTG
Basic information
species | Glycine max |
transcript | GLYMA18G47140.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G47140.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 3
-------------------------------------------------------------------------ctttttgttttgaattaaaagagtactcatcatacattggtttatataaccaaagat------atttatactgtctcacagtgactgataagatacatt---ttccagtATTTTCTTTATCAGTTGCTACGAGGACTCAAATATGTACACTCAGCAAATGTTCTGCACCGTGATCTAAAGCCTAGCAACTTGCTACTGAATGCCAACTG
||| || |||| | || || |||| | | | | | | || || ||||| || | | | | || | | || || || ||||| || || || |||||||||||||| || |||||||| ||||| |||||||| ||||||||||||| ||||| ||||| ||| | || ||||| || |
gtttgttgcttccagcttgtgctttgctgaaacattttgcttgcagaaaatctagacagagatttccatgcaccttgttcctttggtcgctatatgttttcttcatcctatccatatttcagcttaacattctcttgtttatctggtttaataatcacaagtgacatgttttgcattgcagTACTTCCTGTACCAGTTGCTACGAGGGCTAAAATATGTGCACTCGGCAAATGTCTTGCACCGTGATCTGAAGCCAAGCAATTTGTTCCTTAATGCAAATT-
upper sequence: GLYMA18G47140.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g06060.1 (Oryza sativa), 3'ss of exon 3
--------------ctttttgttt-tgaattaaaagagtact-catcatacattggtt------------tatataacca-aagatatttatactgtctcaca-gtgactgataagatacattttccagtATTTTCTTTATCAGTTGCTACGAGGACTCAAATATGTACACTCAGCAAATGTTCTGCACCGTGATCTAAAGCCTAGCAACTTGCTACTGAATGCCAACTG
| ||||||| || |||||| | || | | || ||| || || ||||| ||| | | | | | ||| ||| | | | |||| ||||||||||| |||||| | ||||||||| | || ||||| || ||||||||||| ||||| | || || | ||| || || ||||| |||||||| || |
gtctcactctattcttgtttgtttctgtattaaaccatctcttcgttatccatcaattcaattcaagcactaaataactgtaagttttctctccattctaacacatccccttcttttttttttttgcagTATTTTCTCTATCAGGTACTACGAGGATTGAAGTATGTGCATTCAGCAAATGTCTTGCACAGAGACCTCAGGCCAAGTAATTTGCTGCTGAATGCGAAAT-
upper sequence: GLYMA18G47140.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G127141_T01 (Zea mays), 3'ss of exon 3
-ctttttgttttgaattaaaagagtactcatcatacattggtttatataaccaaagatatttatactgtctcacagtgactgataagatacattttccagtATTTTCTTTATCAGTTGCTACGAGGACTCAAATATGTACACTCAGCAAATGTTCTGCACCGTGATCTAAAGCCTAGCAACTTGCTACTGAATGCCAACTG
| | | || | | | ||| |||| || | | | | | |||| | | | | | | || ||||| || | ||||||||| ||||||| || |||||||| |||||||||||| | ||||||| ||||| ||||| ||||| ||| | || ||||| || |
acaaagaactatattttggtacggagggagtaatatattgcttcacaacaatgatatattctataatctatatttctatgttccccctttttccttgcagTACTTCTTGTATCAGTTGTTACGAGGGCTAAAATATGTGCACTCAGCAAATATATTGCACCGCGATCTGAAGCCGAGCAATTTGTTCCTAAATGCAAATT-
upper sequence: GLYMA18G47140.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G01370.1 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------------------------------------------ctttttgttttgaatta---aaagagtact-catcatacattg---gtttatataaccaaagatat------ttatactgtctcacagtgactgataa---------gatacattttccagtATTTTCTTTATCAGTTGCTACGAGGACTCAAATATGTACACTCAGCAAATGTTCTGCACCGTGATCTAAAGCCTAGCAACTTGCTACTGAATGCCAACTG
|| |||| || | | | ||||| | | | |||| || || | || ||| | |||| || | ||| | ||| || |||| |||| |||||| ||||||||| | || || ||||||||||| || ||||| ||||| |||| || ||| | || |||||||| ||||| |||||||| || |
gtatgcatcaatctccatcttgcttatatctagcagctgaatcttctgtttctactttagaagcagctgttattgtgttagagcatctgatgagtattgcttgatactttataagtgagagctaataaggatttcgtttgttatgctttgaagttgtgtttagtaattagtttcgattatgttttgcagTTTTTTCTGTATCAGTTGTTGCGTGGGCTCAAATATGTTCATTCAGCTAATGTATTGCATCGAGATTTGAAACCTAGCAATTTGCTCCTGAATGCAAATT-
upper sequence: GLYMA18G47140.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 3
-ctttttgttttgaattaaaagagtactcatcatacattggtttatataac--caaagatatttatactgtctcacagtgactgataagatacattttc--cagtATTTTCTTTATCAGTTGCTACGAGGACTCAAATATGTACACTCAGCAAATGTTCTGCACCGTGATCTAAAGCCTAGCAACTTGCTACTGAATGCCAACTG
|| | | ||| || ||| | | || | | || | | ||| | | | |||| | | || |||| | | | | || ||||| || || |||||| || |||||||||| ||||||||||||||||||||||| |||| |||||| | ||||| || || ||||| |||||||| || |
actgtgggattt---ttgtaagtgcaaatataacatcttt-tctgtatgatttctatgataccgaactgagatgtcaatgacactccaattctactctctgcagTACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAATGTCTTGCATCGTGATTTGAAGCCGAGTAATTTGCTTCTGAATGCAAATT-Mapped 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|254335273|gb|GR846770.1|GR846770EST: ATTCGATCCAATCAACAATTGACTGATGATCATTGTCGGT ATTTTCTTTATCAGTTGCTACGAGGACTCAAATATGTACACTCAGCAAATG
genomic: ATTCGATCCAATCAACAATTGACTGATGATCATTGTCGGGttagcactat ... attttccagtATTTTCTTTATCAGTTGCTACGAGGACTCAAATATGTACACTCAGCAAATG
EST:
gi|151406082|gb|EV275897.1|EV275897EST: GCATCAAATAATTCGATCCAATCAACAATTGACTGATGATCATTGTCGGT ATTTTCTTTATCAGTTGCTACGAGGACTCAAATATGTACACTCAGCAAATG
genomic: GCATCAAATAATTCGATCCAATCAACAATTGACTGATGATCATTGTCGGGttagcactat ... attttccagtATTTTCTTTATCAGTTGCTACGAGGACTCAAATATGTACACTCAGCAAATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataaccaaagatatttatactgtctcacagtgactgataagatacattttccagtATTTTCTTTATCAGTTGCTACGAGGACTCAAATATGTACACTCAGCAAATGTTCTGCACCGTGATCTAAAGCCTAGCAACTTGCTACTGAATGCCAACTG
gactgat putative branch site (score: 3)
cattttcc putative PPT
aaagatatttatact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctttttgttttgaattaaaagagtactcatcatacattggtttatataaccaaagatatttatactgtctcacagtgactgataagatacattttccagtATTTTCTTTATCAGTTGCTACGAGGACTCAAATATGTACACTCAGCAAATGTTCTGCACCGTGATCTAAAGCCTAGCAACTTGCTACTGAATGCCAACTG
- - -tgttttg
- - - - - - - - - - - - - - - catacat
- - - - - - - - - - - - - - - - - - - - - - - -aaccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgactg