Sequence
atgc intronic sequence ATGC exonic sequence...acgctacaacatttaagttatacctgaactattttatttttgttcaccttgtagatgttaagagtcatgctgttaatgtttaaacattgtgttatttcagCTGGCCAGTATGTGACTGTTTGATTGCTTTCTATTCCTCGGGATATCCCCTTGAAAAGGCTGAGGCATATGCTGCTTTAAGAAA
Basic information
species | Glycine max |
transcript | GLYMA13G05060.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G15070.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------------------------------------------------------------------------acgctacaacatt-taagttatacctgaactattttatttttgttcacc-ttgtagatgttaagagtcatgctgttaatg--tttaaacattgtgttatttcagCTGGCCAGTATGTGACTGTTTGATTGCTTTCTATTCCTCGGGATATCCCCTTGAAAAGGCTGAGGCATATGCTGCTTTAAGAAA
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gtacgtctctaaacaaatttatgaatatcgtttttacttttggttttatcctatttaattcatggatttgtaccaattctctctattagattatatggagagagtgtagttaatgattatcaagtaccattatattcttggaccacaaattcaccagggactttactccctttactgtttcagTTGGCCGATTTGTGATTGTTTGATTGCTTTCTATTCCTCTGGATATCCTCTTGAGAAAGTTCAAGCATATTCTTCTTTAAGAAA
upper sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 4
----------------------------------------acgctacaacatttaagttatacctgaact--attttatttttgttcaccttgtag-atgttaagagt-catgctg---ttaatgttt----aaacattgtgttatttcagCTGGCCAGTATGTGACTGTTTGATTGCTTTCTATTCCTCGGGATATCCCCTTGAAAAGGCTGAGGCATATGCTGCTTTAAGAAA
| | || | | | ||| | || | | | | | | | | | || | || | ||| || ||| | || || | || | | | |||||| ||||| | ||||| || ||||||||||| ||||||| |||||||| ||||| |||||| ||||||||||||||||||||||
gtattctgtaccaaatagagctctcttttggctttaactcatgttatgaaagattcgttgttagtgtatttagacaaactgtagctgaatatatatcaagtacaaagtatatactggaatcaaaactttaccagactgtttactctttcagTTGGCCCATTTGTGATTGCTTGATTGCTTTTCATTCCTCTGGATATCCTCTTGAGAAGGCTCAGGCATATGCTGCTTTAAGAAA
upper sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 3
---acgctacaacatttaagttatacctgaact-attttatttttgttcaccttgtagatgttaagagtcatgctgttaatgtttaaacattgtgttatttcagCTGGCCAGTATGTGACTGTTTGATTGCTTTCTATTCCTCGGGATATCCCCTTGAAAAGGCTGAGGCATATGCTGCTTTAAGAAA
| | | | |||||| || || | || | | | ||| | | | | | || |||| | | ||| |||||||||||| ||||||| || ||| |||| |||||||| || || || || |||||||||||||| || ||||||||||| |||||
tgatttcagctatttataagttgagggtgtccttgtaacataatcatgcggtttg--gtctctgattgatgtctaatt--tgttgccatgctcgcttacttcagCTGGCCAATATGTGATTGCTTGGTTGCCTTCTATTCATCTGGCTACCCTCTTGAAAAGGCTGAAGCTTATGCTGCTTTGAGAAA
upper sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S70_284V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------------------------------------------------------------acgctacaacatttaagttatacctgaactattttatttttgttcaccttgtagatgt-taagagtcatgctgttaatgtttaaacattgtgttatttcagCTGGCCAGTATGTGACTGTTTGATTGCTTTCTATTCCTCGGGATATCCCCTTGAAAAGGCTGAGGCATATGCTGCTTTAAGAAA
|||| || | || |||| | | ||| || | | || | | || | || || | || | | ||| || | ||| ||||| | |||||||||||||| || |||||||| | || ||||||||||| || ||||| || ||||||||| | | ||
gtgagtgtttctgttctatcctgcaactgcttcgtcatcaagtgttactttgtaaaatagttggaactgtctgcagttgtgaatctttttctaagtataaacgtctcattgaactgatttctgatgtggtc-attgttctaccccatttctatttacgagtgtaccttcgatacgttctttgaattacatt-tcgcagGTGGCCGCTCTGTGACTGTTTGATAGCATTCTATTCTACTGGCTATCCCCTTGACAAAGCTGAAGCTTATGCTGCTCTTCGCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.accttgtagatgttaagagtcatgctgttaatgtttaaacattgtgttatttcagCTGGCCAGTATGTGACTGTTTGATTGCTTTCTATTCCTCGGGATATCCCCTTGAAAAGGCTGAGGCATATGCTGCTTTAAGAAA
tgttaat putative branch site (score: 3)
ttatttc putative PPT
ttaatgtttaaacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acgctacaacatttaagttatacctgaactattttatttttgttcaccttgtagatgttaagagtcatgctgttaatgtttaaacattgtgttatttcagCTGGCCAGTATGTGACTGTTTGATTGCTTTCTATTCCTCGGGATATCCCCTTGAAAAGGCTGAGGCATATGCTGCTTTAAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
-cgctaca
- - - - - - - - - - -acctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgct