Sequence
atgc intronic sequence ATGC exonic sequence...tggatgaactaattttgaattccttttgcgcgtcgcaattcaactctttgattgcattattaccatccaatttagtctaagctatatgttcatgttgcagTAAGGGAAGAAATGGCCATATCCCCTACAGAGATTCAAAGCTGACTCGTATATTACAGTCTTCCTTGGGAGGCAATGCAAGAACTGCTATTATCTGCACA
Basic information
species | Oryza sativa |
transcript | LOC_Os08g43400.4 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g43400.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA01G37340.1 (Glycine max), 3'ss of exon 7
tggatgaactaattttgaattccttttgcgcgtcgcaattcaactctttgattgcattattaccatccaatttagtctaagctatatgttcatg-ttgcagTAAGGGAAGAAATGGCCATATCCCCTACAGAGATTCAAAGCTGACTCGTATATTACAGTCTTCCTTGGGAGGCAATGCAAGAACTGCTATTATCTGCACA
| || ||| |||| || | || | || | | | |||| | || || | ||| | || || |||||| ||||| |||||||| ||||| || | ||||||||||||||| || || ||||| ||||| || || || |||||||| ||||||||||| ||||||||
atattcgacatattgggaataatttatata-gttttattttggaaaggggggttgaatatttctttcactttcatcttaaaaaaaataaaattgcttgcagCAAGGGGAGAAATGGACATATTCCTTTCAGAGATTCAAAGCTAACCCGCATATTGCAGTCCTCATTAGGGGGCAATGCTAGAACTGCTATCATCTGCACC
upper sequence: LOC_Os08g43400.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA02G05650.1 (Glycine max), 3'ss of exon 8
tggatgaactaattttgaattccttttgcgcgtcgcaattcaac-tctttgattgcattattaccatccaatttagtctaagctatatgttcatgttgcagTAAGGGAAGAAATGGCCATATCCCCTACAGAGATTCAAAGCTGACTCGTATATTACAGTCTTCCTTGGGAGGCAATGCAAGAACTGCTATTATCTGCACA
||| || | | || ||| | | || | | || | | | |||| || || | | | |||| ||||| |||||||| ||| | || | ||||||||||||||| || || ||| | |||||||| || | ||||||||| | |||||| || ||||||||
-ggacacacgcgagacttggccgtaaaaattatcaatatttgatatacttttgggaaataatttttttgattttatctaaaaataattaatttgatggcagCAAGGGGAGAAATGGACATGTTCCTTTCAGAGATTCAAAGCTAACCCGCATACTGCAGTCTTCATTAGCAGGCAATGCTAAAACTGCAATCATCTGCACC
upper sequence: LOC_Os08g43400.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA11G07950.1 (Glycine max), 3'ss of exon 8
--tggatgaactaattt---tgaattccttttgcgcgtcgcaattcaactctttgattgcattattaccatccaatttagtctaagctatatgttcatgttgcagTAAGGGAAGAAATGGCCATATCCCCTACAGAGATTCAAAGCTGACTCGTATATTACAGTCTTCCTTGGGAGGCAATGCAAGAACTGCTATTATCTGCACA
| | | |||||| | || ||||| | || || || | || | | | | | || | || | | | |||||| ||||| |||||||| ||||| || | ||||||||||||||| || || ||||| ||||| || || ||||||||||| ||||||||||| ||||||||
catattgggaataatttatatagttttattttggaaaggggggttgaatatttc---ttcactttcatctttaaaaaaaaaaaaaa--aaaaactttgcttgcagCAAGGGGAGAAATGGACATATTCCTTTCAGAGATTCAAAGCTAACCCGCATATTGCAGTCCTCATTAGGAGGCAATGCTAGAACTGCTATCATCTGCACC
upper sequence: LOC_Os08g43400.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA16G24250.1 (Glycine max), 3'ss of exon 8
tggatgaactaattttgaattccttttgcgcgtcgcaattcaac-tctttgattgcattattaccatccaatttagtctaagc-tatatgttcatgttgcagTAAGGGAAGAAATGGCCATATCCCCTACAGAGATTCAAAGCTGACTCGTATATTACAGTCTTCCTTGGGAGGCAATGCAAGAACTGCTATTATCTGCACA
| || || | | ||||| | | || ||| | | || | | |||| | | |||| ||||| | | | | |||||||||| |||||||| ||||| || | ||||||||||||||| || || ||| | ||||| || || | ||||||||| | |||||| || ||||||||
ttcataaatttac--tgaatgcgtcgatataatcaatatttgatatagttttgggaaatattttttttcgattttatctaaaaatgattaatttgatggcagTAAGGGGAGAAATGGACATATTCCTTTCAGAGATTCAAAGCTAACCCGCATACTGCAGTCCTCATTAGCAGGCAATGCTAAAACTGCAATCATCTGCACC
upper sequence: LOC_Os08g43400.4 (Oryza sativa), 3'ss of exon 8
lower sequence: AT3G51150.1 (Arabidopsis thaliana), 3'ss of exon 10
tggatgaactaattttgaattccttttgcgcgtcgcaattcaactctttgattgcattattaccatccaatttagtctaagctatatgttca---tgttgcagTAAGGGAAGAAATGGCCATATCCCCTACAGAGATTCAAAGCTGACTCGTATATTACAGTCTTCCTTGGGAGGCAATGCAAGAACTGCTATTATCTGCACA
| | | ||| | || || | || || | | | || || | | | | ||| || | ||| || | | |||||||| |||| |||||| || || || | |||||||||||||||||| || ||| | ||| ||||||||||||| || || |||||| | || |||||||||
cagtaacgccagtttaccaagttattagcagattgctgttattaacatctaatgt-ttgcttctttttacatta--ctgaattatgtggctagcttaatgcagTAAAGGAAAAAATGGGCACATTCCATTCAGAGATTCAAAGCTGACACGCATACTTCAGACTTCCTTGGGAGGAAACGCCAGAACTTCCATAATCTGCACA
upper sequence: LOC_Os08g43400.4 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G66310.1 (Arabidopsis thaliana), 3'ss of exon 10
tggatgaactaattttgaattccttttgcgcgtcgcaattcaactctttgattgcattattaccatccaatttagt--ctaagctatatg-ttcatgt--tgcagTAAGGGAAGAAATGGCCATATCCCCTACAGAGATTCAAAGCTGACTCGTATATTACAGTCTTCCTTGGGAGGCAATGCAAGAACTGCTATTATCTGCACA
|| || |||| | | | | | | | || | ||| | || | ||||| || ||| || || | | |||||||| | || || ||| || || || | |||||||||||| ||||| || ||| | |||||||| |||||||| |||||||||||||| || || |||||
--attgttcttctttttacctttgatcagttcctatgaataaggctctcttttttacgatt-caat--agcttagtaacttgcttatgtggtttacttcatgcagTAAAGAAAAAACTGGGCACATTCCATTCAGAGATTCAAAACTGACACGCATACTTCAGTCTTCTTTGGGAGGAAATGCAAGAACTGCCATAATTTGCACT
upper sequence: LOC_Os08g43400.4 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv04s0023g03060.t01 (Vitis vinifera), 3'ss of exon 8
tggatgaactaattttgaattccttttgcgcgtcgcaattcaactctttgattgcatt-attaccatccaatttagtctaagctatatgttcatgt-------tgcagTAAGGGAAGAAATGGCCATATCCCCTACAGAGATTCAAAGCTGACTCGTATATTACAGTCTTCCTTGGGAGGCAATGCAAGAACTGCTATTATCTGCACA
||| | || ||| ||| | | || || ||| || | || | ||| ||| | | || ||||| | || ||||| || ||||||| ||| ||||| || || ||||||||||| | || || ||||| ||||| ||||| ||||||||||| | ||||||||| || || ||
-----gaatttccctttcatttcttagtggttgtatagttgaattctgcagctgaaaggataattatcaaatctgct---agttatataattgggtatttggatgcagCAAAGGAAGAAGTGGACATATTCCTTATAGAGATTCAAAATTAACCCGCATATTGCAGTCCTCCTTAGGAGGCAATGCCAAAACTGCTATCATATGTACT
upper sequence: LOC_Os08g43400.4 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S343_28V6.1 (Physcomitrella patens), 3'ss of exon 8
--------------------------------tggatgaactaattttgaattccttttgcgcgtcgca-----attcaactctttgattgcattat---taccatccaatttag--tctaagctatatgttcatgttgcagTAAGGGAAGAAATGGCCATATCCCCTACAGAGATTCAAAGCTGACTCGTATATTACAGTCTTCCTTGGGAGGCAATGCAAGAACTGCTATTATCTGCACA
||| || || | | || || || | ||| || |||| | ||| | || || || || | ||| | | ||| || | | | | || || ||||| || || ||||| ||||||||||| | || ||||| ||| |||||||| ||||||||||||||||||||
gtacacactatctagagctcttgcatctgaaacttgcgaattagttaaagaaccagcatgtgcatcctattttcatttaaatcttggtatgcctaatatttaatgctgaacttgaattttaatccgttgcttccagTGGAGGAAGTAAGATCAAAGGGCATATACCGTATAGAGACTCAAAGCTGACGAGGATTCTACAGCATTCGTTGGGAGGAAATGCAAGAACTGCTATTATT------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttgattgcattattaccatccaatttagtctaagctatatgttcatgttgcagTAAGGGAAGAAATGGCCATATCCCCTACAGAGATTCAAAGCTGACTCGTATATTACAGTCTTCCTTGGGAGGCAATGCAAGAACTGCTATTATCTGCACA
ctttgat putative branch site (score: 5)
attatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggatgaactaattttgaattccttttgcgcgtcgcaattcaactctttgattgcattattaccatccaatttagtctaagctatatgttcatgttgcagTAAGGGAAGAAATGGCCATATCCCCTACAGAGATTCAAAGCTGACTCGTATATTACAGTCTTCCTTGGGAGGCAATGCAAGAACTGCTATTATCTGCACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - -gaactaa
- - - - - - - - - - - cttttgc
- - - - - - - - - - - - - - - - - - - - - - - - - -ttgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatcca