Sequence
atgc intronic sequence ATGC exonic sequence...ttctcatttactaattgagctactagttgctgcggttgcttactactttacctatctattaagttcatctgagcctaagaatatgtctacttgtttgcagGGGAAAGGTTGCTGAAGGTATAGATTTTGATCGACATTATGGCCGACTAGTAATCATGTTTGGTGTTCCTTTTCAATACACATTAAGCAA
Basic information
species | Glycine max |
transcript | GLYMA02G09080.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os05g05260.1 (Oryza sativa), 3'ss of exon 6
ttctcat-ttactaattgagctact--agttgctgcggttgcttactactttacctatctattaagttcatctgagcctaagaatatgtctacttgtttgcagGGGAAAGGTTGCTGAAGGTATAGATTTTGATCGACATTATGGCCGACTAGTAATCATGTTTGGTGTTCCTTTTCAATACACATTAAGCAA
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-tcaagtgttattattataaatgtttaagtggtcttgactcatggctacataatatgatggacatatgactcatagctaactaccac-tatgctcaatc-cagGGGCAAAGTAGCCGAAGGTATTGATTTTGATCGACACTATGGCAGACTTGTGATCATGTTTGGTGTTCCTTTCCAGTACACACTCAGCAG
upper sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G097605_T02 (Zea mays), 3'ss of exon 1
------------------------------------------------------------ttctcatttactaattgagctactagttgc-tgcggttgcttactactttacctatctattaagtt-catctgagcctaagaatatgtctacttgtttgcagGGGAAAGGTTGCTGAAGGTATAGATTTTGATCGACATTATGGCCGACTAGTAATCATGTTTGGTGTTCCTTTTCAATACACATTAAGCAA
| | | | | | | ||| | || | | | | | || | | |||| | | | | | | | || | | ||||||| || |||||||||||||| ||||||||||| || |||||| || |||| |||||||||||||||||||| || |||||||| ||
gttggtccaccttattattttgcgttctgaaagcaaccttccaaaatttatatttgatcatgtcaaataatcagtaatgtgactgactatgtgatatagataaaaatgttgtcgccattgtaagctatagtttcacttttgctaacacttaactaat-gcagGGGCAAAGTTGCTGAAGGTATTGATTTTGATCGGCACTATGGCAGATTAGTTATCATGTTTGGTGTTCCTTTCCAGTACACATTGAGTCG
upper sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 7
-------------------------------------------------------------------------ttct-catt-tactaattgagcta-ctagttgctgcggttgcttactactttacc--tatctattaagtt---catctgag-----cctaagaatatgtcta---cttgt-------ttgcagGGGAAAGGTTGCTGAAGGTATAGATTTTGATCGACATTATGGCCGACTAGTAATCATGTTTGGTGTTCCTTTTCAATACACATTAAGCAA
|||| ||| || || | || | || | || | || | | || || ||| | | ||| | | |||| | ||||| || | |||| |||||||| || |||||||||||||| ||||||||||| |||||||| |||| || | |||| || || || || || || |||||||||||
gtaaaatttttatttttgaatggtagatggtttgggaattcattgcaatgcgtctttggttctgcttctttgtttctgtattataatactggaattgtctcttctctcctattcttggttggttaacaaatattaaagaggtttcacttttgagaaatttcaaagaaagtgatcaaattttgtatttgaactgcagGGGGAAAGTTGCTGAAGGTATCGATTTTGATCGTCATTATGGAAGACTGGTTGTAATGTACGGAGTACCATTCCAGTATACATTAAGCAA
upper sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 7
--------ttctcatttactaat-tgagctact--agttgctgcggttgcttactactttacctatctattaagttcatctgagcctaagaatatgtctacttgtttgcagGGGAAAGGTTGCTGAAGGTATAGATTTTGATCGACATTATGGCCGACTAGTAATCATGTTTGGTGTTCCTTTTCAATACACATTAAGCAA
|| || || | ||| || | | | || || || || || || ||| | | || ||| ||| ||| | ||||||||| || || ||||||||||| |||||||||||||||||||| || |||| |||||||||||||||||||| ||||||||||||||||
ggggaatcccctgatcccctggtatgaactgcataaagggatgggggtgattgagg--------gtccatcaagatga---gattaaaagtttatttctgcactgttgcagGGGGAAAGTAGCTGAAGGTATTGATTTTGATCGACATTATGGAAGATTAGTGATCATGTTTGGTGTTCCTTTCCAATACACATTAAGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttacctatctattaagttcatctgagcctaagaatatgtctacttgtttgcagGGGAAAGGTTGCTGAAGGTATAGATTTTGATCGACATTATGGCCGACTAGTAATCATGTTTGGTGTTCCTTTTCAATACACATTAAGCAA
tctactt CT-rich tract
tatctattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctcatttactaattgagctactagttgctgcggttgcttactactttacctatctattaagttcatctgagcctaagaatatgtctacttgtttgcagGGGAAAGGTTGCTGAAGGTATAGATTTTGATCGACATTATGGCCGACTAGTAATCATGTTTGGTGTTCCTTTTCAATACACATTAAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - gctacta
- - - - - - - - - - - - - ttgctgc
- - - - - - - - - - - - - - - - - - tgcttac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catctga