Sequence
atgc intronic sequence ATGC exonic sequencegcacgtactagtttctcaaccttgtactgcagtgcagagcattaatttgtatcttggcatgcattctttatttaaacattcaccaatcatcataacagagttttttccccctgtttttctagTACTATCTGAAGACAGGAACGTGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGGATTGCTGGAAGAGTTGCCTTAAATATTT
Basic information
species | Glycine max |
transcript | GLYMA20G36140.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G36140.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os11g28270.1 (Oryza sativa), 3'ss of exon 3
gcacgtactagtttctcaaccttgtactgcagtgcagagcattaatttgtatcttggcatgcattctttatttaaacattcaccaatcatcataacagagttttttccccctgtttttctagTACTATCTGAAGACAGGAACGTGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGGATTGCTGGAAGAGTTGCCTTAAATATTT
|| | | | || | |||| | |||||| | | | ||| | |||| || || | | | | | | ||| ||||| |||| ||| ||||||| ||||| |||||||||||||| |||||||| ||||| || || ||| | |||| ||||| |||| | ||| ||
----------------taatgtagctgcttaaagctgtctattagt--atatcttatctttgacgacttagc--agcattgttt--tctgtattatttattgtgcttcaccttttttttcagTATTATTTGAAGACTGGAACATGCAAATTTGGAGCAACATGCAAGTTTCACCACCCCCGAGAAAAAGCTGCAATTGCAACCCGAGTACAGCTGAATGCTT
upper sequence: GLYMA20G36140.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g68860.3 (Oryza sativa), 3'ss of exon 3
gcacgtactagtttctcaaccttgtactgcagtgcagagcattaatttgtatcttggcatgcattctttatttaaacattcaccaatcatcataacagagttttttccccctgtttttctagTACTATCTGAAGACAGGAACGTGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGGATTGCTGGAAGAGTTGCCTTAAATATTT
| | || ||| | | || | || || ||| | || |||||| | || | || | | | ||| | | | | | |||| ||||||||||| ||||| ||||| ||||| | ||||||||||| |||||||| | ||| | ||||| ||||| || || || |||| | |
---------------------tgtttctagagttgacattatgcaatt-tagagtggtgtagtttttttattaagttggacaggtgttgaaatgaaataatttctcaaaattttctgttcagTATTATCTGAAGACTGGAACATGCAAGTTTGGGCCTACATGCAAATTCCATCATCCCAGAGAAAAAGCTGGAATTGCAGGGAGGGTGCAGCTAAACACAT
upper sequence: GLYMA20G36140.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G146514_T02 (Zea mays), 3'ss of exon 3
gcacgtactagtttctcaaccttgtactgcagtgca-gagcattaatttgtatcttggcatgcattctttatttaaacattcaccaatcatcataacagagttttttccccctgtttttctagTACTATCTGAAGACAGGAACGTGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGGATTGCTGGAAGAGTTGCCTTAAATATTT
| |||| || | |||||| | || | | |||| | | || | || | ||| ||| ||| || ||| | || ||||||||||||||||| || |||||||| |||||||| || ||||| ||||||||||| ||| |||||| || || ||||| || |||
------------------attttgtccttttctatgtgagcatataatt-tcttttggaaagtgtt--tggttacattattggtgaatttgcattttta--ttgttttcatacccccttttagTACTATCTGAAGACTGGCACGTGCAAGTTTGGAGCAACTTGCAAGTTTCATCATCCCCGAGAAAAGGCTGCAATGGCAACTCGAGTTCAGTTGAATGAAC
upper sequence: GLYMA20G36140.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G100794_T01 (Zea mays), 3'ss of exon 3
gcacgtactagtttctcaaccttgtactgcagtgcagagcattaatttgtatcttggcatgcattctttatttaaacattcaccaatcatcataacagagttttttccccctgtttttctagTACTATCTGAAGACAGGAACGTGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGGATTGCTGGAAGAGTTGCCTTAAATATTT
| | || | || ||| | | || || | ||| || | | ||| || | ||||| | || ||| ||||||||||||||||| || || ||||| |||||||| || ||||| ||||||||||| ||| |||||| || || ||||| | |||
--------------------ttgcttgcacattttctgcttttcttttctgtgttattatatcgttttttggaaagtgtatggtca-cattatt-tattgttttcacatccctcctttttagTACTATCTGAAGACTGGCACATGCAAGTTTGGAGCAACTTGCAAGTTTCATCATCCCCGAGAAAAGGCTGCAATGGCAACTCGAGTTCAGCTGAATGAAC
upper sequence: GLYMA20G36140.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G087032_T04 (Zea mays), 3'ss of exon 3
gcacgtactagtttctcaaccttgtactgcagtgcagagcattaatttgtatcttggcatgcattctttatttaaacattcaccaatcatcataacagagttttttccccctgtttttctagTACTATCTGAAGACAGGAACGTGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGGATTGCTGGAAGAGTTGCCTTAAATATTT
| ||| | | | | | | || || || || ||| || ||| | ||||| | | || ||| | | | || || || ||||| || | ||||| ||||||||||| ||||| ||||| ||||| | |||||||||||||| ||||| | || ||||||| ||||| || || || |||| | |
---agatctacatctttgatcacacaatccattg-agtgctttagcttatatgt---catgc------tgtgcaagtattgaa-gctgaaaattactgatcttttttcc--------tgtagTATTATCTGAAGACTGGAACATGCAAGTTTGGCCCTACATGCAAATTTCACCATCCCAGGGAAAAGGCTGGAATTGCAGGGAGGGTGCAGCTAAACACAT
upper sequence: GLYMA20G36140.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G107491_T03 (Zea mays), 3'ss of exon 3
gcacgtactagtttctcaaccttgtactgcagtgcagagcattaatttgtatcttggcatgcattctttatttaaacattcaccaatcatcataacagagttttttccccctgtttttctagTACTATCTGAAGACAGGAACGTGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGGATTGCTGGAAGAGTTGCCTTAAATATTT
|| | ||| | | | | || | | || || || || | | ||| | | ||||| | || ||| | | | | | || || || |||||||| | ||||| ||||||||||| ||||| ||||| ||||| | |||||||||||||| ||||| | || |||| || ||||| || || || |||| | |
-cagat-ctacatctttgatcacataatctattg-agtgc-ttgagctatatat-gtcatgc----tgta---aaatactgaa-gctgaaaattactgatttttttcc---------tatagTATTATCTGAAGACCGGAACATGCAAGTTTGGTCCTACATGCAAATTTCACCATCCCAGGGAAAAGGCCGGAATTGCAGGGAGGGTGCAGCTAAACACAT
upper sequence: GLYMA20G36140.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G02830.1 (Arabidopsis thaliana), 3'ss of exon 3
gcacgtactagtttctcaaccttgtactgcagtgca-gagcattaatttgtatcttggcatgcattctttatttaaacattcaccaa-tcatcataacagagttttttcc-ccctgtttttctagTACTATCTGAAGACAGGAACGTGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGGATTGCTGGAAGAGTTGCCTTAAATATTT
|| ||| |||| | | || | || |||| | |||| | | || ||| || || | | ||| || || | || || |||||||| ||||||||||||| ||||| ||||||| ||||| || ||||||||||| | | | |||||||||||||||||||| | | ||||| |
------gtaagaatctttggtttgtccagttgtagatgaacattttgtcaaggtttggtaattgagtcatcttcttacacaaactaacttaacattttgtggtgttgtatgttttggttgcgcagTACTATTTGAAGACAGGAACCTGCAAGTTTGGAGTAACATGTAAGTTTCATCATCCAAGGAACAAAGCTGGGATTGCTGGAAGAGTCTCTCTCAATATGT
upper sequence: GLYMA20G36140.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G16540.2 (Arabidopsis thaliana), 3'ss of exon 3
gcacgtactagtttctcaaccttgtactgcagtgcagagcattaatttgtatcttggcatgcattctttatttaa-acattcaccaatcatcataacagagttttttccccctgtttttctagTACTATCTGAAGACAGGAACGTGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGGATTGCTGGAAGAGTTGCCTTAAATATTT
| || | | |||| |||| | | | | | || ||| ||||| | | | |||| | ||| | | ||| |||||||||||||| || |||||||| |||| || ||||| ||||||||||||| | | ||||| |||| |||||| || | | ||| | |
----------------------------gtagctctgt-ttcgaattactatcatagta-atgtcttctagttatcacattgtctcaaagcttctat----ttttgttgttgtgtctgtgcagTTTTATCTGAAGACAGGGACCTGCAAATTCGGAGTGACTTGCAAGTTTCATCATCCTAGGAACAAAGCTGGTATTGATGGAAGTGTATCAGTTAATGTCT
upper sequence: GLYMA20G36140.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0023g00370.t01 (Vitis vinifera), 3'ss of exon 3
gcacgtactagtttctcaaccttgtactgcagtgcagagcattaatttgtatcttggcatgcattctttatttaaacattcaccaatcatcataacagagttttttccccctgtttttctagTACTATCTGAAGACAGGAACGTGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGGATTGCTGGAAGAGTTGCCTTAAATATTT
||| ||| || ||| | || | ||| || ||| || |||| | | | ||| | ||| | || || || ||||||| ||||||||||||| ||||| ||||||||||||||||| ||||||||||||| ||| ||||||| ||||||||||||||| | ||||||||||
-----------tttaatgtcctcatatcat-gtgtaag------atctctattttctcat---ttttttaatatgttctgagttggaagagttgaca-aatttgctttgaatggttctccagTACTACTTGAAGACAGGAACTTGCAAGTTTGGAGCCACATGCAAGTTTCATCATCCTAGAGACAAGGCTGGAATTGCTGGAAGAGTTTCTTTAAATATTTMapped 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|6726931|gb|AW311211.1|AW311211EST: CAAGGATGATAGGCGAGTTCCCAGAAAGAATAGGGCAACCAGAATGCCAG TACTATCTGAAGACAGGAACGTGCAAATTTGGAGCCACATGCAAATTTCAT
genomic: CAAGGATGATAGGCGAGTTCCCAGAAAGAATAGGGCAACCAGAATGCCAGgcacgtacta ... gtttttctagTACTATCTGAAGACAGGAACGTGCAAATTTGGAGCCACATGCAAATTTCAT
EST:
gi|8283911|gb|BE021470.1|BE021470EST: GCGAGTTCCCAGAAAGAATAGGGCAACCAGAATGCCAG TACTATCTGAAGACAGGAACGTGCAAATTTGGAGCCACATGCAAATTTCAT
genomic: GCGAGTTCCCAGAAAGAATAGGGCAACCAGAATGCCAGgcacgtacta ... gtttttctagTACTATCTGAAGACAGGAACGTGCAAATTTGGAGCCACATGCAAATTTCAT
EST:
gi|298164490|gb|HO014135.1|HO014135EST: CAAGGATGATAGGCGAGTTCCCAGAAAGAATAGGGCAACCAGAATGCCAG TACTATCTGAAGACAGGAACGTGCAAATTTGGAGCCACATGCAAATTTCAT
genomic: CAAGGATGATAGGCGAGTTCCCAGAAAGAATAGGGCAACCAGAATGCCAGgcacgtacta ... gtttttctagTACTATCTGAAGACAGGAACGTGCAAATTTGGAGCCACATGCAAATTTCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatttaaacattcaccaatcatcataacagagttttttccccctgtttttctagTACTATCTGAAGACAGGAACGTGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGGATTGCTGGAAGAGTTGCCTTAAATATTT
tcataac putative branch site (score: 2)
ttttttccccctgttt putative PPT
taaacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcacgtactagtttctcaaccttgtactgcagtgcagagcattaatttgtatcttggcatgcattctttatttaaacattcaccaatcatcataacagagttttttccccctgtttttctagTACTATCTGAAGACAGGAACGTGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGGATTGCTGGAAGAGTTGCCTTAAATATTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA