Sequence
atgc intronic sequence ATGC exonic sequence...gcatgcatgctcacacacattaatagcttagtagatgtcatttgtcaaaaactggagtaatagtttctgtagtgccttttaattttgtatgcaatggaagTGAGATGTATGGGAGAGAACTGGTGGACCTGCGAAAGGAGAGTCGATGGGAGTTTCTCAATACACTGTTTTCTGTGTCTGAAGCTGTGGCCTACATGCAG
Basic information
species | Glycine max |
transcript | GLYMA17G04580.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G04580.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G044819_T02 (Zea mays), 3'ss of exon 4
gcatgcatgctcacacacattaatagcttagtagatgtcatttgtcaaaaactggagtaatagtttctgtagtgccttttaattttgtatgcaatggaagTGAGATGTATGGGAGAGAACTGGTGGACCTGCGAAAGGAGAGTCGATGGGAGTTTCTCAATACACTGTTTTCTGTGTCTGAAGCTGTGGCCTACATGCAG
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-------------------------gtagaggtaacacatttcgtcaaagtttctgggcttcattgatgagaa--ctctaattcatgtttttga--atagTGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGAGTTCCTTAATACCCTTTTCTCTGTTTCAGAAGCTGTCATGTTCATGCAG
upper sequence: GLYMA17G04580.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G48960.1 (Arabidopsis thaliana), 3'ss of exon 5
-----------------gcatgcatgctcacacacattaatagcttagtag--atgtcatttgtcaaaaactggagtaatagtttctgtagtgccttttaattttgtatgcaatggaagTGAGATGTATGGGAGAGAACTGGTGGACCTGCGAAAGGAGAGTCGATGGGAGTTTCTCAATACACTGTTTTCTGTGTCTGAAGCTGTGGCCTACATGCAG
|| || | | | || | ||| | | |||||| || || || || || || | | | || |||||||| ||| ||||||||| ||||| || || | || |||||||| || |||||||||||||||||||||||||| | ||||| || || || ||| |||| || |||
gtatatttgacttttcaacaccattggtaatgtgaagaaaaaagagagttgcaaagtcatt-gttctgttttgaaggaa--gtctcatt--ctcttattgtctttgtatg-gatgaaagTGAGATCTATGGAAGGGAGTTAGTTGACCTGCGGAACCAGAGTCGATGGGAGTTTCTCAATACATTTTTTTCAGTTTCAGAGGCTCTGGCTTATGCACAG
upper sequence: GLYMA17G04580.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv05s0020g00880.t01 (Vitis vinifera), 3'ss of exon 5
---gcatgcatgctcacacacattaatagcttagtagatgtcatttgtca-aaaactggagtaatagtttctgtagtgccttttaattttgtatgcaatggaagTGAGATGTATGGGAGAGAACTGGTGGACCTGCGAAAGGAGAGTCGATGGGAGTTTCTCAATACACTGTTTTCTGTGTCTGAAGCTGTGGCCTACATGCAG
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gtaccctagattttcccg-atgtttgtaatttgat--ttgctaattgtagcaagactagggtaatattttctagagtgcctgttaactttctatgca-tggcagTGAGATGTATGGGAGGGAACTGGTGGATCTGCGAAACGAAAGTCGATGGGTATTCCTCAATACACTATTCTCTGTTTCAGAAGCAGTGGCTTTTATGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaaaactggagtaatagtttctgtagtgccttttaattttgtatgcaatggaagTGAGATGTATGGGAGAGAACTGGTGGACCTGCGAAAGGAGAGTCGATGGGAGTTTCTCAATACACTGTTTTCTGTGTCTGAAGCTGTGGCCTACATGCAG
ttttaat putative branch site (score: 3)
ttttaattttgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcatgcatgctcacacacattaatagcttagtagatgtcatttgtcaaaaactggagtaatagtttctgtagtgccttttaattttgtatgcaatggaagTGAGATGTATGGGAGAGAACTGGTGGACCTGCGAAAGGAGAGTCGATGGGAGTTTCTCAATACACTGTTTTCTGTGTCTGAAGCTGTGGCCTACATGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - -catgctc
- - - - - - acacaca
- - - - - - - - - - - - - - - - - - - - - - -caaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtttctg