Sequence
atgc intronic sequence ATGC exonic sequence...aagcatagattacctgtactgatgaacattttgagcttaatcttatttttttattttaactaacatcttaatggcttgatttgtacttgggcaaagaaagCCATGCTTATAGTAAGGGGAAGGTTCTCATTGTTAGCAAAGTTCCATTGCCTGATTATCGTGCAGATCTTGATGAGCGTCATGGATCAACACAGAAAGAG
Basic information
species | Glycine max |
transcript | GLYMA02G35240.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G35240.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g33275.2 (Oryza sativa), 3'ss of exon 2
aagcatagattacctgtactgatgaacattttg--agcttaatcttatttttttattttaactaa---catcttaat-ggcttgatttgtacttgggcaaagaaagCCATGCTTATAGTAAGGGGAAGGTTCTCATTGTTAGCAAAGTTCCATTGCCTGATTATCGTGCAGATCTTGATGAGCGTCATGGATCAACACAGAAAGAG
| ||| | || | ||||| ||| | || | |||| || | | || || ||| || || | || ||| || |||| |||| ||| ||| || | || |||||| | || | |||||||||||| | ||||||||||| ||||| ||||||||| | |||||||||||||| |
--gtatataatagatcatttgatgcctttttccgtatctctaacttacacttggaggctgacaaattccattttcattatcctgtttttaacctgggggaagATAGCAATGTGTACAACAAAGGGAAGACAATTGTTTTCAGCAAAGTTCCACTACCTGATTATCGAGCAGACCTTGATGAGAGACATGGATCAACACAACA----
upper sequence: GLYMA02G35240.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 2
aagcatagattacctgtactgatgaacattttgagcttaatcttatttttttattttaactaacatcttaatggcttgatt--tgtacttgggcaaagaaagCCATGCTTATAGTAAGGGGAAGGTTCTCATTGTTAGCAAAGTTCCATTGCCTGATTATCGTGCAGATCTTGATGAGCGTCATGGATCAACACAGAAAGAG
|| | | || | | | ||| | ||| | ||| | | | || | | ||| || || || || || | ||| ||||| || | ||| ||||||| ||| |||||||||||||||| || || |||||||| || ||||||||||| || |||||||| || |||||||||
---------gtaagtctctatatcttcttcgacaacttcgttttaagtccatatggtgag-agtatgtcatgaatttgcttatcgttttttgg-aatggaagTCATGCGTACAATAAAGGGAAGGCTCTTGTTGTTAGCAAAGTTCCTTTACCAGATTATCGAGCGGATCTTGATGAACGGCATGGATCCACTCAGAAAGAG
upper sequence: GLYMA02G35240.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0032g01230.t01 (Vitis vinifera), 3'ss of exon 2
-aagcatagattacctgtactgatgaacattttgagcttaatcttatttttttattttaactaacatcttaatggcttgattt-gtacttgggcaaagaaagCCATGCTTATAGTAAGGGGAAGGTTCTCATTGTTAGCAAAGTTCCATTGCCTGATTATCGTGCAGATCTTGATGAGCGTCATGGATCAACACAGAAAGAG
| | | ||| ||||| || || ||| || | | || ||| || |||||||| || |||| | |||||||||||||| |||| ||||||||| || |||| ||||||||||||||||| |||| || || ||||||||||| || |||||||| ||||| ||||||
catattcatgtctgttgttttgatggtacccctgtagttg--tctatggttagcctaaatcttacaaattctcttcttgattttgtgcttgtggaaagaaagCCATGCATATAACAAGGGGAAGACACTTGTTGTCAGCAAAGTTCCATTGCCAAATTACCGGGCTGATCTTGATGAACGCCATGGATCCACACAAAAAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttttattttaactaacatcttaatggcttgatttgtacttgggcaaagaaagCCATGCTTATAGTAAGGGGAAGGTTCTCATTGTTAGCAAAGTTCCATTGCCTGATTATCGTGCAGATCTTGATGAGCGTCATGGATCAACACAGAAAGAG
ttattttaactaacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagcatagattacctgtactgatgaacattttgagcttaatcttatttttttattttaactaacatcttaatggcttgatttgtacttgggcaaagaaagCCATGCTTATAGTAAGGGGAAGGTTCTCATTGTTAGCAAAGTTCCATTGCCTGATTATCGTGCAGATCTTGATGAGCGTCATGGATCAACACAGAAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - -acctgta
- - - - - - - - - ctgatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - actaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtacttg