Sequence
atgc intronic sequence ATGC exonic sequencegtaatattctgcttatgtggtttacgaagaactagctgctccattacctttttgaactcatgttggagtactttcgaagtttgaacttcataccttattgctgtgcctaatgtcagtcctgtccacttctgttagGACCATGTTGAAGGATACCTTGAATTGTCTGGCAAAACCAAGACATACTTTGCTACAGCTGTTTCTTTATGGGATGCTGACTTCTATGTGAAGGTTGACG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g46570.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g46570.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G007185_T01 (Zea mays), 3'ss of exon 6
gtaatattctgcttatgtggtttacgaagaactagctgctccattacctttttgaactcatgt-tgga--gtactttcgaagt-----ttgaacttcataccttattgctgtgcctaatgtcagtcctgtccacttctgtt--agGACCATGTTGAAGGATACCTTGAATTGTCTGGCAAAACCAAGACATACTTTGCTACAGCTGTTTCTTTATGGGATGCTGACTTCTATGTGAAGGTTGACG
||| | ||| | |||| ||| ||| | || || | | | || || | |||| | |||| ||| |||| || |||| |||||||||||||||||||| |||| || ||||||| |||||||||||| ||||||||| |||||||||||||| |||||||||||||||||||||
---------------------------------------------ttcttacaagatccatatatggactgtagttttggggtcattattactttctacatgttttttttcactctaactttagtcatgtgcactcggattgtagGATCATGTTGAAGGATACCTTGAGCTGTCAGGGAAAACCAGGACATACTTTGCAACAGCTGTTGCTTTATGGGATGCTAACTTCTATGTGAAGGTTGACG
upper sequence: LOC_Os06g46570.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA12G31980.1 (Glycine max), 3'ss of exon 6
-----------------------gtaatattctgc-ttatgtggtttacgaagaa---ctagctgctccattacctttttgaac-tcatgttggagtactttcgaagtttgaacttcataccttattgc---tgtgcctaatgtcagtcctgtccact--tctgttagGACCATGTTGAAGGATACCTTGAATTGTCTGGCAAAACCAAGACATACTTTGCTACAGCTGTTTCTTTATGGGATGCTGACTTCTATGTGAAGGTTGACG
| | ||| | || | | | || | ||| || || || | | | ||||| | | || |||| || | ||| | || | | | ||| ||| | | | | | |||| |||||||||||||||||||||||||| | || || |||||||||||||| || |||||| ||||||||||||||||||||| | || ||||| |
gtaatgatcctctttgtcttattgctgttttccccgttgtctcttctatcatttgtctctacttgaataatcacttgataagatatcatggtcacatttatttgaaggaaaaattaaataaaaaaaaagaaatgcaacaagtttcaaacctctgttttgatttttcagGATCATGTTGAAGGATACCTTGAATTGTCAGCAAAGACAAAGACATACTTTGCCACTGCTGTTAACTTATGGGATGCTGACTTCTATATCAAAGTTGATG
upper sequence: LOC_Os06g46570.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA12G10520.1 (Glycine max), 3'ss of exon 6
gtaatattctgcttatgtggtttacgaagaactagctgctccattacctttttgaactcatgttggagt--actttcgaagtttgaacttcataccttattgctgtgcctaatgtcagtcctgtccacttctgttagGACCATGTTGAAGGATACCTTGAATTGTCTGGCAAAACCAAGACATACTTTGCTACAGCTGTTTCTTTATGGGATGCTGACTTCTATGTGAAGGTTGACG
||||| || || | | || | | || ||||| | ||||| | | || |||| |||| | | | | | | | | ||| | || | ||| || | ||||| |||||||||||||||||||| | || || || || |||||||| || ||||| |||||||||||||| |||||||| || ||||| |
gtaatgtttccctcccacatgtcccttttcacattttttttcac--cctttctaaactcgcttcagtgtcagcttttgaagggaaagggaaaaatgtcacagattt--------tcacttctttatactatgtgcagAATCATGTGGAAGGATACCTTGAATTGTCAGCAAAGACAAAAACCTACTTTGCCACTGCTGTGAACTTATGGGATGCTGATTTCTATGTCAAAGTTGATG
upper sequence: LOC_Os06g46570.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G38500.1 (Glycine max), 3'ss of exon 6
gtaat-attctgcttatgtggtttacgaagaactagctgctccattacctttttgaactca-tgttggagta-----ctttcgaagtttgaacttcataccttattgctgtgc-------------ctaatgtcagtcctgtccacttctgtt----agGACCATGTTGAAGGATACCTTGAATTGTCTGGCAAAACCAAGACATACTTTGCTACAGCTGTTTCTTTATGGGATGCTGACTTCTATGTGAAGGTTGACG
||||| || || || | | || || || | | | | || ||| | | || || || || | || || ||| | | || ||| || | ||| || ||| || |||| |||||||| ||||| ||||||||||| | || || |||||||||||||| || |||||| ||||||||||||||||||||| | || || ||||
gtaatgatcctctttgtcttattgccgtttctgcccctatgtcccttctctcatgttgtcactacttgaataatcacctgtcaagattggatgatcacatttatttatagtggaaaaaaaacgcaactggtttcaaatcttagtgctttgattctgcagGATCATGTTGAGGGATATCTTGAATTGTCAGCAAAGACAAAGACATACTTTGCCACTGCTGTTAACTTATGGGATGCTGACTTCTATATTAAAGTCGACG
upper sequence: LOC_Os06g46570.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA06G46230.2 (Glycine max), 3'ss of exon 6
gtaatattctgcttatgtggtttacgaagaactagctgctccattacctttttgaactcatgttggagta-ctttcgaagtttgaacttcataccttattgctgtgcctaatgtcagtcctgtccacttctgt-tagGACCATGTTGAAGGATACCTTGAATTGTCTGGCAAAACCAAGACATACTTTGCTACAGCTGTTTCTTTATGGGATGCTGACTTCTATGTGAAGGTTGACG
||||| | |||| | | | | || || | | | ||| || || |||| |||| | | | | | | | | | || | | || | | || | ||||| |||||||||||||||||||| | || || || || |||||||| || ||||| |||||||||||||| |||||||| || ||||| |
gtaatgtgacatatatgatcccttttcacattttttcctaccgtttctataatcgcttcacagtgtcatagcttttgaag---ggaaagggaaaaatgtcacaggttttcacttc---tttatttgtttatatgcagAATCATGTGGAAGGATACCTTGAATTGTCAGCAAAGACAAAAACCTACTTTGCCACTGCTGTGAACTTATGGGATGCTGATTTCTATGTCAAAGTTGATG
upper sequence: LOC_Os06g46570.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G05170.2 (Arabidopsis thaliana), 3'ss of exon 6
gtaatattctgcttatgtggtttacgaagaactagctgctccattacctttttgaactcatgttggagtactttcgaagtttgaacttcataccttattgctgtgcctaatgtcagtcctgtccacttctgttagGACCATGTTGAAGGATACCTTGAATTGTCTGGCAAAACCAAGACATACTTTGCTACAGCTGTTTCTTTATGGGATGCTGACTTCTATGTGAAGGTTGACG
|| || |||| || | | | || |||| | | | | ||||| | | | | | || | ||||||||||||||||| ||||| || ||||| ||||| || || || |||||| ||||||| |||| | |||||||| || |||||||| || || || |
-------------------------------------------gtatagttctgaa--tatagttcactgtttaacaagtctaaggct-agctcttatcttcattctcatta-----ctcacttgttttttatagGACCATGTTGAAGGGTACCTAGAGTTGTCAGGCAAGACGAAAACTTACTTTTCTACAGCATTTTCGATGTGGGATGCAGATTTCTATGTCAAAGTAGATG
upper sequence: LOC_Os06g46570.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT2G32430.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaatattctgcttatgtggtttacgaagaactagctgctccattacctttttgaactcatgttggagtactttcgaagtttgaacttcataccttattgctgtgcctaatgtcagtcctgtccacttctgttagGACCATGTTGAAGGATACCTTGAATTGTCTGGCAAAACCAAGACATACTTTGCTACAGCTGTTTCTTTATGGGATGCTGACTTCTATGTGAAGGTTGACG
|| ||||| |||| ||| | | || || |||| | || | | | || | | ||| || | |||| ||||||||||||||||||||||||| || || |||||||| || ||||| ||| ||||||||||||| |||||||| || |||||||| || || || |
-------------------------------------------gtattttttttt-ctcaagtttaact-ctcgcgct-tttggtgtccaaatccttgaatattggtt--tctcattctctgctactttcaccagGACCATGTTGAAGGATACCTTGAGTTATCAGGCAAAACGAAAACATATTTTTCTACAGCTGTTTCGAAGTGGGATGCAGAGTTCTATGTCAAAGTAGATG
upper sequence: LOC_Os06g46570.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv12s0059g00640.t01 (Vitis vinifera), 3'ss of exon 6
gtaatattctgcttatgtggtttacgaagaactagctgc--tccattacctttttgaactcatgttggagtactttcgaagtttgaacttcataccttattgctgtgcctaatgtcagtcctgtccacttctgttagGACCATGTTGAAGGATACCTTGAATTGTCTGGCAAAACCAAGACATACTTTGCTACAGCTGTTTCTTTATGGGATGCTGACTTCTATGTGAAGGTTGACG
||||| | | | | | | || || ||| || | | |||| | ||| | ||| | | || | ||| | || || ||||| || | | |||| ||||||||||| ||||| ||| |||||| ||| || |||| ||| |||||||| |||||| |||| |||||||| || ||||| | || ||||| |
gtaatggttttgtatcttcttctgtgacttgctttctgtattcttctgtatgcttgatgcctccaaggaacatcttcattacctataattataaagttaat-ttgccccacatgtctgtgttactg--tgtgagcagGAACATGTTGAAGGTTACCTCGAACTGTCTGCCAAGACAAAGATATATTTTGCTACTGCTGTTGCTTTGTGGGATGCAGAGTTCTACATTAAAGTTGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgaacttcataccttattgctgtgcctaatgtcagtcctgtccacttctgttagGACCATGTTGAAGGATACCTTGAATTGTCTGGCAAAACCAAGACATACTTTGCTACAGCTGTTTCTTTATGGGATGCTGACTTCTATGTGAAGGTTGACG
gcctaat putative branch site (score: 3)
tcctgtccacttct putative PPT
ttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatattctgcttatgtggtttacgaagaactagctgctccattacctttttgaactcatgttggagtactttcgaagtttgaacttcataccttattgctgtgcctaatgtcagtcctgtccacttctgttagGACCATGTTGAAGGATACCTTGAATTGTCTGGCAAAACCAAGACATACTTTGCTACAGCTGTTTCTTTATGGGATGCTGACTTCTATGTGAAGGTTGACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG