Sequence
atgc intronic sequence ATGC exonic sequencegcatgtactagtttctcaaccttttactgcagtgcagagcactaatttgtaattttgtatcttggcatgcatctttatttaaacattcaccaatcgtcataacaaagtgttttttttcccctgtctttccagTACTATCTGAAGACAGGAACATGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGAATTGCTGGAAGAGTTGCCTTAAATATTT
Basic information
species | Glycine max |
transcript | GLYMA10G31370.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G31370.3 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os11g28270.1 (Oryza sativa), 3'ss of exon 3
gcatgtactagtttctcaaccttttactgcagtgcagagcactaatttgtaattttgtatcttggcatgcatctttatttaaacattcaccaatcgtcataacaaagtgttttttttcccctgtctttccagTACTATCTGAAGACAGGAACATGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGAATTGCTGGAAGAGTTGCCTTAAATATTT
| | || | | ||| | || || | |||||| | | ||| | |||| | || | | | || | ||| ||| | ||| ||||| ||| ||||||| |||||||||||||||||||| |||||||| ||||| || || ||| | |||| |||||| |||| | ||| ||
---------------------taatgtagctgcttaaagctgtctattagtatatcttatctttg---acgacttagc---agcatt-----gttttctgtattatttattgtgcttcaccttttttttcagTATTATTTGAAGACTGGAACATGCAAATTTGGAGCAACATGCAAGTTTCACCACCCCCGAGAAAAAGCTGCAATTGCAACCCGAGTACAGCTGAATGCTT
upper sequence: GLYMA10G31370.3 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g68860.3 (Oryza sativa), 3'ss of exon 3
gcatgtactagtttctcaaccttttactgcagtgcagagcactaatttgtaattttgtatcttggcatgcatctttatttaaacattcaccaatcgtcataacaaagtgttttttttcccctgtctttccagTACTATCTGAAGACAGGAACATGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGAATTGCTGGAAGAGTTGCCTTAAATATTT
| || || ||| | || || || ||||| | | || | | ||| |||| || || || || || | ||| | | ||| | ||||| ||||||||||| ||||||||||| ||||| | ||||||||||| |||||||| | ||| | ||||||||||| || || || |||| | |
---------------------tgtttctagagttga---catta---tgcaatttagagt---ggtgtagtttttttattaag--ttggacaggtgttgaaatgaaataatttctcaaaattttctgttcagTATTATCTGAAGACTGGAACATGCAAGTTTGGGCCTACATGCAAATTCCATCATCCCAGAGAAAAAGCTGGAATTGCAGGGAGGGTGCAGCTAAACACAT
upper sequence: GLYMA10G31370.3 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G100794_T01 (Zea mays), 3'ss of exon 3
gcatgtactagtttctcaaccttttactgcagtgcagagcactaatttgtaattttgtatcttggcatgcatctttatttaaacattcaccaatcgtcataacaaagtgttttttttcccctgtctttccagTACTATCTGAAGACAGGAACATGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGAATTGCTGGAAGAGTTGCCTTAAATATTT
||| |||| | || | |||| | | || || ||| || ||| | | | || ||| | | |||||| |||| |||| |||||||||||||||| || |||||||| |||||||| || ||||| ||||||||||| ||| |||||| ||| || ||||| | |||
--------------------------ttgct-tgcacattttctgcttttc-ttttctgtgttattat--atcgttttttggaaagtgtatggtca-cattatttattgttttcacatccct-cctttttagTACTATCTGAAGACTGGCACATGCAAGTTTGGAGCAACTTGCAAGTTTCATCATCCCCGAGAAAAGGCTGCAATGGCAACTCGAGTTCAGCTGAATGAAC
upper sequence: GLYMA10G31370.3 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G087032_T04 (Zea mays), 3'ss of exon 3
gcatgtactagtttctcaaccttttactgcagtgcagagcactaatttgtaattttgtatcttggcatgcatctttatttaaacattcaccaatcgtcataacaaagtgttttttttcccctgtctttccagTACTATCTGAAGACAGGAACATGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGAATTGCTGGAAGAGTTGCCTTAAATATTT
|| || || ||| | | ||| || || || | || | | || | | | | || | | |||||||| | |||| ||||||||||| ||||||||||| ||||| | |||||||||||||| ||||| | || ||||||||||||| || || || |||| | |
----------------------agatctacatctttgatcacacaatcc--attgagtgctttagcttatatgtcatgctgtgcaagtattgaagctgaaaattactgatcttttttcctgt--------agTATTATCTGAAGACTGGAACATGCAAGTTTGGCCCTACATGCAAATTTCACCATCCCAGGGAAAAGGCTGGAATTGCAGGGAGGGTGCAGCTAAACACAT
upper sequence: GLYMA10G31370.3 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G146514_T02 (Zea mays), 3'ss of exon 3
gcatgtactagtttctcaaccttttactgcagtgcagagcactaatttgtaattttgtatcttggcatgcatctttatttaaacattcaccaatcgtcataacaaagtgttttttttcccctgtctttccagTACTATCTGAAGACAGGAACATGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGAATTGCTGGAAGAGTTGCCTTAAATATTT
| | |||||| | || ||||| | |||||| | |||| | | | || || | ||| ||| ||| | |||||| | |||| || |||||||||||||||| || || ||||| |||||||| || ||||| ||||||||||| ||| |||||| ||| || ||||| || |||
------------attttgtcctttt----ctatgt-gagca------tataatttc---ttttggaaagtgt-ttggttacattattggtgaatttgcatttttat-tgttttcataccccc----ttttagTACTATCTGAAGACTGGCACGTGCAAGTTTGGAGCAACTTGCAAGTTTCATCATCCCCGAGAAAAGGCTGCAATGGCAACTCGAGTTCAGTTGAATGAAC
upper sequence: GLYMA10G31370.3 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G107491_T03 (Zea mays), 3'ss of exon 3
gcatgtactagtttctcaaccttttactgcagtgcagagcactaatttgtaattttgtatcttggcatgcatctttatttaaacat-tcaccaatcgtcataacaaagtgttttttttcccctgtctttcc---agTACTATCTGAAGACAGGAACATGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGAATTGCTGGAAGAGTTGCCTTAAATATTT
|||| | | || | || || | | ||| | || | || ||| ||| ||| || | | | ||||| |||| ||||||||||| ||||||||||| ||||| | |||||||||||||| ||||| | || |||| |||||||| || || || |||| | |
----------------------------------cagatctacatctt-tgatcacataatctattgagtg-cttgagctatatatgtcatgctgtaaaatactgaagctgaaaattactgatttttttcctatagTATTATCTGAAGACCGGAACATGCAAGTTTGGTCCTACATGCAAATTTCACCATCCCAGGGAAAAGGCCGGAATTGCAGGGAGGGTGCAGCTAAACACAT
upper sequence: GLYMA10G31370.3 (Glycine max), 3'ss of exon 3
lower sequence: AT3G02830.1 (Arabidopsis thaliana), 3'ss of exon 3
gcatgtactagtttctcaaccttttactgcagtgca-gagcactaatttgtaattttgtatcttggcatgcatctttatttaaacattcaccaatcgtcataacaaagtgttttttttcccctgtctttccagTACTATCTGAAGACAGGAACATGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGAATTGCTGGAAGAGTTGCCTTAAATATTT
|| ||| || | | | || | || || | | ||| ||| | | |||||| | | | | | || | | | | ||| | |||| | | ||||||||| ||||||||||||| ||||| ||||||| ||||| || ||||||||||| | | | ||||| |||||||||||||| | | ||||| |
------gtaagaatctttggtttgtccagttgtagatgaacattttgtcaaggtttggtaattgagt---catcttcttacacaaactaacttaacattttgtggtgttgtatgtttt-----ggttgcgcagTACTATTTGAAGACAGGAACCTGCAAGTTTGGAGTAACATGTAAGTTTCATCATCCAAGGAACAAAGCTGGGATTGCTGGAAGAGTCTCTCTCAATATGT
upper sequence: GLYMA10G31370.3 (Glycine max), 3'ss of exon 3
lower sequence: AT5G16540.2 (Arabidopsis thaliana), 3'ss of exon 3
gcatgtactagtttctcaaccttttactgcagtgcagagcactaatttgtaattttgtatcttggcatgcatctttatttaaacattcaccaatcgtcataacaaag-tgttttttttcccctgtctttccagTACTATCTGAAGACAGGAACATGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGAATTGCTGGAAGAGTTGCCTTAAATATTT
||| || || | | || |||| | | | | || ||| |||| || ||| || | ||||| || ||||| | |||| |||||||||||||| || |||||||| |||| || ||||| ||||||||||||| | | ||||| |||| |||||| || | | ||| | |
-----------------------------------gtagctctgtttcgaa--ttactatcatagtaatgtcttctagtta-----tcac--attgtctcaaagcttctatttttgttgttgtgtctgtgcagTTTTATCTGAAGACAGGGACCTGCAAATTCGGAGTGACTTGCAAGTTTCATCATCCTAGGAACAAAGCTGGTATTGATGGAAGTGTATCAGTTAATGTCT
upper sequence: GLYMA10G31370.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0023g00370.t01 (Vitis vinifera), 3'ss of exon 3
gcatgtactagtttctcaaccttttactgcagtgcagagcactaatttgtaattttgtatcttggcatgcatctttatttaaacattcaccaatcgtcataacaaagtgttttttttcccctgtctttccagTACTATCTGAAGACAGGAACATGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGAATTGCTGGAAGAGTTGCCTTAAATATTT
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--------------------------------tttaatgtcctcatatcatgtgtaagatctctattttctcatttttttaatatgttctgagttggaagagttgacaaatttgctttgaatggttctccagTACTACTTGAAGACAGGAACTTGCAAGTTTGGAGCCACATGCAAGTTTCATCATCCTAGAGACAAGGCTGGAATTGCTGGAAGAGTTTCTTTAAATATTTMapped 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|22522729|gb|BU081540.1|BU081540EST: CAAGGATGATAGGCGAGTTCCCAGAAAGAATAGGGCAACCAGAATGCCAG TACTATCTGAAGACAGGAACATGCAAATTTGGAGCCACATGCAAATTTCAT
genomic: CAAGGATGATAGGCGAGTTCCCAGAAAGAATAGGGCAACCAGAATGCCAGgcatgtacta ... gtctttccagTACTATCTGAAGACAGGAACATGCAAATTTGGAGCCACATGCAAATTTCAT
EST:
gi|23731682|gb|BU763980.1|BU763980EST: CAAGGATGATAGGCGAGTTCCCAGAAAGAATAGGGCAACCAGAATGCCAG TACTATCTGAAGACAGGAACATGCAAATTTGGAGCCACATGCAAATTTCAT
genomic: CAAGGATGATAGGCGAGTTCCCAGAAAGAATAGGGCAACCAGAATGCCAGgcatgtacta ... gtctttccagTACTATCTGAAGACAGGAACATGCAAATTTGGAGCCACATGCAAATTTCAT
EST:
gi|23053013|gb|BU577504.1|BU577504EST: CAAGGATGATAGGCGAGTTCCCAGAAAGAATAGGGCAACCAGAATGCCAG TACTATCTGAAGACAGGAACATGCAAATTTGGAGCCACATGCAAATTTCAT
genomic: CAAGGATGATAGGCGAGTTCCCAGAAAGAATAGGGCAACCAGAATGCCAGgcatgtacta ... gtctttccagTACTATCTGAAGACAGGAACATGCAAATTTGGAGCCACATGCAAATTTCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaaacattcaccaatcgtcataacaaagtgttttttttcccctgtctttccagTACTATCTGAAGACAGGAACATGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGAATTGCTGGAAGAGTTGCCTTAAATATTT
tcataac putative branch site (score: 2)
tgttttttttcccctg putative PPT
aaagtgtttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcatgtactagtttctcaaccttttactgcagtgcagagcactaatttgtaattttgtatcttggcatgcatctttatttaaacattcaccaatcgtcataacaaagtgttttttttcccctgtctttccagTACTATCTGAAGACAGGAACATGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGAATTGCTGGAAGAGTTGCCTTAAATATTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA