Sequence
atgc intronic sequence ATGC exonic sequence...tcactagttttctgatattgattgaacttttgttaagacacagaatggagtaatttacaaatataactacacaactaacatgtttgtgcataatatgcagCAAGTTGCATGCTCATCTGCTGATGGAAGGCAACTGCTGGAATCCTCTAAAACTGCCCTTGACAAGGGAAAACTTGAAGATGCTGTCAATTATGGGACCA
Basic information
species | Oryza sativa |
transcript | LOC_Os07g23990.2 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 16
tcactagttttctgatattgattgaacttttgttaagacacagaat-ggagtaatttacaaatat---aactacacaactaacatgtttgtgcataatatgcagCAAGTTGCATGCTCATCTGCTGATGGAAGGCAACTGCTGGAATCCTCTAAAACTGCCCTTGACAAGGGAAAACTTGAAGATGCTGTCAATTATGGGACCA
| | || ||||| | ||| | | | | | ||| || | | || |||| | | ||| || ||| ||||||||| |||||||||||||| ||||||||||| || || || || || |||||||| | ||||||||||| ||||| ||||| || | ||||| || |
gtaacaaacaagacatgttgatcataggttttcttgcatatttctttgaagttgattgaataaatccaaactttatacataatgctcatgctgatacgttgcagCAAGCAGCATGCTCATCTGCAGATGGAAGGCAGCTCCTAGAGTCATCCAAAACTGCTTTAGACAAGGGAAAGCTTGAGGATGCAGTTACCTATGGCACAA
upper sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA07G06160.1 (Glycine max), 3'ss of exon 16
tcactagttttctgatattgattgaacttttgttaagacacagaatggagtaatttacaaatataactacacaactaacatgtttgtgcataatatgcagCAAGTTGCATGCTCATCTGCTGATGGAAGGCAACTGCTGGAATCCTCTAAAACTGCCCTTGACAAGGGAAAACTTGAAGATGCTGTCAATTATGGGACCA--
|| ||| | ||||||||| |||||||||||||| ||||||||||| || || || || || |||||||| | ||||||||||| ||||| ||||| || | ||||| || |
-----------------------------------------------------------------------------------gtgctgatactttgcagcaagcagcatgctcatctgcagatggaaggcagCTCCTAGAGTCATCCAAAACTGCTTTAGACAAGGGAAAGCTTGAGGATGCAGTTACCTATGGCACAAAG
upper sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 14
lower sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 16
------------tcactagtt-ttctgatattgattgaacttttgttaagacacagaatggagtaatttacaaatataactacacaactaacatgtttgtgcataatatgcagCAAGTTGCATGCTCATCTGCTGATGGAAGGCAACTGCTGGAATCCTCTAAAACTGCCCTTGACAAGGGAAAACTTGAAGATGCTGTCAATTATGGGACCA
|| ||| | || || | || | | | | || | | | | || ||| || || | ||| | || ||||||||||| ||||| ||||||||||||||||||||||| ||||| || |||||||| || | ||||| ||||| ||||
gtaacggacaagacaatagatattaggaaaaatgttctatctgaatcaggattctttctaatatgttagtcagccatagttattcagACTTTCTATTT-TAAATC-TATGCAGCAAGCAGCATGTTCATCTGCTGATGGAAGGCAACTTCTGGAGTCATCTAAAACAGCTTTAGACAAAGGAAAGCTTG------------------------
upper sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 14
lower sequence: AT1G01320.2 (Arabidopsis thaliana), 3'ss of exon 16
------------tcactagtt-ttctgatattgattgaacttttgttaagacacagaatggagtaatttacaaatataactacacaactaacatgtttgtgcataatatgcagCAAGTTGCATGCTCATCTGCTGATGGAAGGCAACTGCTGGAATCCTCTAAAACTGCCCTTGACAAGGGAAAACTTGAAGATGCTGTCAATTATGGGACCA
|| ||| | || || | || | | | | || | | | | || ||| || || | ||| | || ||||||||||| ||||| ||||||||||||||||||||||| ||||| || |||||||| || | ||||| ||||| ||||||||||| || | ||||| || |
gtaacggacaagacaatagatattaggaaaaatgttctatctgaatcaggattctttctaatatgttagtcagccatagttattcagactttctattt-taaatc-tatgcagCAAGCAGCATGTTCATCTGCTGATGGAAGGCAACTTCTGGAGTCATCTAAAACAGCTTTAGACAAAGGAAAGCTTGAAGATGCAGTTACATATGGAACGA
upper sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv00s0388g00080.t01 (Vitis vinifera), 3'ss of exon 1
---------------------tcactagttttctgatattgattgaacttttgttaagacacagaatggagtaatttacaaatataactacacaactaacatgtttgtgcataatatgcagCAAGTTGCATGCTCATCTGCTGATGGAAGGCAACTGCTGGAATCCTCTAAAACTGCCCTTGACAAGGGAAAACTTGAAGATGCTGTCAATTATGGGACCA
| ||| | | |||| | || | | | | || | ||| | | |||| | ||| || | | | ||||||| |||||||||||||| |||||| | ||||| || ||||| || ||||| | | || |||||||||||||||||||| |||| |||||||| |
gtgatgaacaaactatgctatttgatagaagaatagaacacattgt-ttcttatcttgtcttacaaataattaaaccattca-ataatc-tggatttaattgcatttctttttcttttcagCAAGCAGCATGCTCATCTGCAGATGGACGACAACTTCTAGAATCATCAAAAACAACTATAGATAAGGGAAAACTTGAAGATGCAGTCAGCTATGGGACAA
upper sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv15s0046g00740.t01 (Vitis vinifera), 3'ss of exon 16
---------------------tcactagttttctgatattgattgaacttttgttaagacacagaatggagtaatttacaaatataactacacaactaacatgtttgtgcataatatgcagCAAGTTGCATGCTCATCTGCTGATGGAAGGCAACTGCTGGAATCCTCTAAAACTGCCCTTGACAAGGGAAAACTTGAAGATGCTGTCAATTATGGGACCA
| ||| | | | |||| | || | | | | || | ||| | | |||| | ||| || | | | ||||||| |||||||||||||| |||||| | ||||| || ||||| || ||||| || || || |||||||||||||||||||| |||| |||||||| |
gtgatgaacaaactatgctatttgatagaataatagaacacattgt-ttcttatcttgtcttacaaataattaaaccattca-ataatc-tggatttaattgcatttctttttcttttcagCAAGCAGCATGCTCATCTGCAGATGGACGACAACTTCTAGAATCATCAAAAACAGCTCTAGATAAGGGAAAACTTGAAGATGCAGTCAGCTATGGGACAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggagtaatttacaaatataactacacaactaacatgtttgtgcataatatgcagCAAGTTGCATGCTCATCTGCTGATGGAAGGCAACTGCTGGAATCCTCTAAAACTGCCCTTGACAAGGGAAAACTTGAAGATGCTGTCAATTATGGGACCA
aactaac putative branch site (score: 1)
taatttacaaatataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcactagttttctgatattgattgaacttttgttaagacacagaatggagtaatttacaaatataactacacaactaacatgtttgtgcataatatgcagCAAGTTGCATGCTCATCTGCTGATGGAAGGCAACTGCTGGAATCCTCTAAAACTGCCCTTGACAAGGGAAAACTTGAAGATGCTGTCAATTATGGGACCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG