Sequence
atgc intronic sequence ATGC exonic sequencegtgctgatactttgcagcaagcagcatgctcatctgcagatggaaggcagCTCCTAGAGTCATCCAAAACTGCTTTAGACAAGGGAAAGCTTGAGGATGCAGTTACCTATGGCACAAAG
Basic information
species | Glycine max |
transcript | GLYMA07G06160.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G06160.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 14
-----------------------------------------------------------------------------------gtgctgatactttgcagcaagcagcatgctcatctgcagatggaaggcagCTCCTAGAGTCATCCAAAACTGCTTTAGACAAGGGAAAGCTTGAGGATGCAGTTACCTATGGCACAAAG
|| ||| | ||||||||| |||||||||||||| ||||||||||| || || || || || |||||||| | ||||||||||| ||||| ||||| || | ||||| || |
tcactagttttctgatattgattgaacttttgttaagacacagaatggagtaatttacaaatataactacacaactaacatgtttgtgcataatatgcagCAAGTTGCATGCTCATCTGCTGATGGAAGGCAACTGCTGGAATCCTCTAAAACTGCCCTTGACAAGGGAAAACTTGAAGATGCTGTCAATTATGGGACCA--
upper sequence: GLYMA07G06160.1 (Glycine max), 3'ss of exon 16
lower sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 16
----------------------------------------------------------------------------------------------gtgctgatactttgcagcaagcagcatgctcatctgcagatggaaggcagCTCCTAGAGTCATCCAAAACTGCTTTAGACAAGGGAAAGCTTGAGGATGCAGTTACCTATGGCACAAAG
| | | || |||||||||||||||| |||||||| ||||||||||| || || |||||||| ||||| ||||||||||| ||||||||||
gtaacggacaagacaatagatattaggaaaaatgttctatctgaatcaggattctttctaatatgttagtcagccatagttattcagACTTTCTATTTTAAATCTATGCAGCAAGCAGCATGTTCATCTGCTGATGGAAGGCAACTTCTGGAGTCATCTAAAACAGCTTTAGACAAAGGAAAGCTTG--------------------------
upper sequence: GLYMA07G06160.1 (Glycine max), 3'ss of exon 16
lower sequence: AT1G01320.2 (Arabidopsis thaliana), 3'ss of exon 16
----------------------------------------------------------------------------------------------gtgctgatactttgcagcaagcagcatgctcatctgcagatggaaggcagCTCCTAGAGTCATCCAAAACTGCTTTAGACAAGGGAAAGCTTGAGGATGCAGTTACCTATGGCACAAAG
| | | || |||||||||||||||| |||||||| ||||||||||| || || |||||||| ||||| ||||||||||| ||||||||||| ||||||||||| ||||| || |
gtaacggacaagacaatagatattaggaaaaatgttctatctgaatcaggattctttctaatatgttagtcagccatagttattcagactttctattttaaatctatgcagCAAGCAGCATGTTCATCTGCTGATGGAAGGCAACTTCTGGAGTCATCTAAAACAGCTTTAGACAAAGGAAAGCTTGAAGATGCAGTTACATATGGAACGA--
upper sequence: GLYMA07G06160.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv00s0388g00080.t01 (Vitis vinifera), 3'ss of exon 1
-----------------------------------------------------------------------------------------------------gtgctgatactttgcagcaagcagcatgctcatctgcagatggaaggcagCTCCTAGAGTCATCCAAAACTGCTTTAGACAAGGGAAAGCTTGAGGATGCAGTTACCTATGGCACAAAG
| || | |||| |||||||||||||||||||||||||||||| | || || ||||| ||||| ||||| || |||| |||||||| ||||| |||||||| | |||||| ||||
gtgatgaacaaactatgctatttgatagaagaatagaacacattgtttcttatcttgtcttacaaataattaaaccattcaataatctggatttaattgcatttctttttcttttcagCAAGCAGCATGCTCATCTGCAGATGGACGACAACTTCTAGAATCATCAAAAACAACTATAGATAAGGGAAAACTTGAAGATGCAGTCAGCTATGGGACAA--
upper sequence: GLYMA07G06160.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv15s0046g00740.t01 (Vitis vinifera), 3'ss of exon 16
-----------------------------------------------------------------------------------------------------gtgctgatactttgcagcaagcagcatgctcatctgcagatggaaggcagCTCCTAGAGTCATCCAAAACTGCTTTAGACAAGGGAAAGCTTGAGGATGCAGTTACCTATGGCACAAAG
| || | |||| |||||||||||||||||||||||||||||| | || || ||||| ||||| ||||| ||| |||| |||||||| ||||| |||||||| | |||||| ||||
gtgatgaacaaactatgctatttgatagaataatagaacacattgtttcttatcttgtcttacaaataattaaaccattcaataatctggatttaattgcatttctttttcttttcagCAAGCAGCATGCTCATCTGCAGATGGACGACAACTTCTAGAATCATCAAAAACAGCTCTAGATAAGGGAAAACTTGAAGATGCAGTCAGCTATGGGACAA-- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgctgatactttgcagcaagcagcatgctcatctgcagatggaaggcagCTCCTAGAGTCATCCAAAACTGCTTTAGACAAGGGAAAGCTTGAGGATGCAGTTACCTATGGCACAAAG
tgctgat putative branch site (score: 3)
atacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgctgatactttgcagcaagcagcatgctcatctgcagatggaaggcagCTCCTAGAGTCATCCAAAACTGCTTTAGACAAGGGAAAGCTTGAGGATGCAGTTACCTATGGCACAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG