Sequence
atgc intronic sequence ATGC exonic sequencegtgaggggactagttagattcttcaatatccagtccatttactggttgagtagtagtatctgttatatagtttggtggtgtgctaaaagcatctttgtttttttttccagGAAATAATGCAACATAAACTTGTCTTTATTGAGACTCAGGATGTGGTAGAGACTACATTGGCTCTTGATAACTACCGCAAGGCTTGTGATTGTGGAAGAG
Basic information
species | Glycine max |
transcript | GLYMA02G09080.1 |
intron # | 6 |
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 6
lower sequence: LOC_Os05g05260.1 (Oryza sativa), 3'ss of exon 5
gtgaggggactagttagattcttcaatatccagtccatttactggttgagtagtagtatctgttatatagtttggtggtgtgctaaaagcatctttgtttttttttccagGAAATAATGCAACATAAACTTGTCTTTATTGAGACTCAGGATGTGGTAGAGACTACATTGGCTCTTGATAACTACCGCAAGGCTTGTGATTGTGGAAGAG
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-------tgcttttactgttctcatgaatacagcattcttggcaaagccttgataacacgcaatgcattagcacctaatatg---aaaatcttatgacttcaatttgcagGACATCATGCAGCATAAGTTGGTATTCATTGAAACACCAGATGTTGTTGAGACAACATTGGCTCTTGATAATTACAGAAAGGCATGTGATTGTGGAAGAG
upper sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G097605_T01 (Zea mays), 3'ss of exon 5
gtgaggggactagttagattcttcaatatccagtccatttactggttgagtagt-agtatctgttatata---gtttggtggtgtgctaaaagcatctttgtttttttttccagGAAATAATGCAACATAAACTTGTCTTTATTGAGACTCAGGATGTGGTAGAGACTACATTGGCTCTTGATAACTACCGCAAGGCTTGTGATTGTGGAAGAG
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--------------ctgtgttatgaaaataaaatacctgtaaatgttatatagccaagataagatgtatatgcattagttccaataacgaaaacctggttttactgtttttcagGACATCATGCAACATAAATTAGTGTTTATCGAAACACCAGATGTCGTTGAGACAACATTGGCTCTTGATAACTACAGAAAGGCATGTGATTGTGGAAGAG
upper sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 6
--------------------------------------------gtgaggggactagttagattcttcaatatccagtccatttactggttgagtagtagtatctgtta-tatagtttggtggtgtgctaaaagcatctttgtttttttttccagGAAATAATGCAACATAAACTTGTCTTTATTGAGACTCAGGATGTGGTAGAGACTACATTGGCTCTTGATAACTACCGCAAGGCTTGTGATTGTGGAAGAG
| | | || || | || | || | || | || | || ||| | | ||| | || || || || || | || | | || | ||| |||||||||||||||| || ||||| || ||||| || || ||||| ||||| || |||||||| || ||||| || |||| |||||| ||||| |||||||
gtaaggtcttcttcatcgctttaccatgccagtaattttttcagagttttgcatgaattggaatttttatgatacc-tcaaaatatt--tttagttgcttcaggcattaatgtatatttgtttactgatattaccaattctcttaatgtttgtagGAAATAATGCAACAGAAGCTTGTTTTCATTGAAACACAAGATGTTGTAGAAACAACATTGGCACTGGATAATTATCGCAGGGCTTGCGATTGCGGAAGAG
upper sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 6
gtgaggggactagttagattcttcaatatccagtccatttactggttgagtagtagtatctgttatatagtttggtggtgt-gctaaaagcatctttgttttttt-ttccagGAAATAATGCAACATAAACTTGTCTTTATTGAGACTCAGGATGTGGTAGAGACTACATTGGCTCTTGATAACTACCGCAAGGCTTGTGATTGTGGAAGAG
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--------accgtctgtatagttctacacaca---ctttccctggg-aattatttttgctttatagaaaaactaattttcttgatagatacttaatgctatctttgttgcagGAAATAATGCAACATAAGCTTGTCTTTATTGAGACTCAGGATGTGGTGGAAACTACATTAGCTCTAGACAATTATCGCAGAGCTTGTGACTGTGGGAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtatctgttatatagtttggtggtgtgctaaaagcatctttgtttttttttccagGAAATAATGCAACATAAACTTGTCTTTATTGAGACTCAGGATGTGGTAGAGACTACATTGGCTCTTGATAACTACCGCAAGGCTTGTGATTGTGGAAGAG
tgctaaa putative branch site (score: 2)
catctttgtttttttt putative PPT
atctttgttttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaggggactagttagattcttcaatatccagtccatttactggttgagtagtagtatctgttatatagtttggtggtgtgctaaaagcatctttgtttttttttccagGAAATAATGCAACATAAACTTGTCTTTATTGAGACTCAGGATGTGGTAGAGACTACATTGGCTCTTGATAACTACCGCAAGGCTTGTGATTGTGGAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA