Sequence
atgc intronic sequence ATGC exonic sequencegttcgttcttctatcaattcttgtttgtattctttgccaatcttgaacttctatttatttcttctgaccaccagGAGGCCAAAAACACTGCAACTTTGAAGGCTCAGATTGACAAGCTGCAACAGGAACGCGATGAGTTCCAAAAAATGGTTATTGGCAATCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os08g14460.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g14460.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G147500_T04 (Zea mays), 3'ss of exon 5
gttcgttcttctatcaattcttgtttgtattctttgccaatcttgaacttctatttatttcttctgaccaccagGAGGCCAAAAACACTGCAACTTTGAAGGCTCAGATTGACAAGCTGCAACAGGAACGCGATGAGTTCCAAAAAATGGTTATTGGCAATCAG
||| || ||| |||||| |||| || ||||| ||| | || ||||| ||| || | |||||||||||||||||||||| || ||||| |||||||||| ||||||||||| ||||| ||||| || || ||||||||||| || ||||||
gtttgtccttgtatcaactctt---tggtttcttcaccattttttggattctaa--attcttttcaattaccagGAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAAGAACGTGATGAATTTCAGAAAATGGTTATAGGAAATCAG
upper sequence: LOC_Os08g14460.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA17G07040.2 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------------------------gttcgttcttc------tatcaattcttgtttgtattctttgccaatcttgaacttctatttattt--------cttctgaccaccagGAGGCCAAAAACACTGCAACTTTGAAGGCTCAGATTGACAAGCTGCAACAGGAACGCGATGAGTTCCAAAAAATGGTTATTGGCAATCAG
|| | || | | | ||||| ||| || | || | | | || || | | | ||| |||| || |||||||||||| || ||||||| || ||||| |||||||||||||| | ||||| ||||| | |||||||||||| ||||||
gtaaggagatgcttggaaatctggttttggcaaacgtaaagcatgctattgtcttgcttagatgaaaagatcagaagtgtgtccattatgcaagatgcaacaatttccttttttacgcagtgatgctgctagattttgtttaactggggttgaattcctgttatttagGAAGCTAAAAACACTGCAGCTCTGAAGGCCCAAATTGAGAAGCTGCAACAGGAGAGGGATGAATTCCAGAGAATGGTTATTGGTAATCAG
upper sequence: LOC_Os08g14460.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G00980.1 (Glycine max), 3'ss of exon 5
-------------------------------------------------------------------------------gttcgttcttc------tatcaattcttgtttgtattctttgccaatcttgaacttctatttatttc--------ttctgaccac-cagGAGGCCAAAAACACTGCAACTTTGAAGGCTCAGATTGACAAGCTGCAACAGGAACGCGATGAGTTCCAAAAAATGGTTATTGGCAATCAG
|| ||| || || | ||| | | ||| | || | | | || | |||| || ||| | ||||||| |||||||||||| || |||||||||| ||||| |||||||||||||| | ||||| || || | |||||||||||| ||||||
gtaaggagtgcttgtatttctggttttggcaaacctaaagcatgttattgtcttgcttagatgaaaagattagaagtgtgtctgttagtcaagatgtaacgatttccttatttatgcagtgatgctactagatttttgtttaatttgggtagaattccttttatatagGAGGCTAAAAACACTGCAGCTCTGAAGGCTCAAATTGAGAAGCTGCAACAGGAGAGGGATGAATTTCAGAGAATGGTTATTGGTAATCAG
upper sequence: LOC_Os08g14460.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G57410.3 (Arabidopsis thaliana), 3'ss of exon 5
gttcgttcttcta---tcaattcttgtttgtattctttgccaatcttgaacttctatttatttcttctgaccaccagGAGGCCAAAAACACTGCAACTTTGAAGGCTCAGATTGACAAGCTGCAACAGGAACGCGATGAGTTCCAAAAAATGGTTATTGGCAATCAG
|| || || | | | |||| ||| | ||||| ||| ||| | || || |||| ||||||||||||||| |||||||| |||||||||| ||| | || ||||| | ||||| ||||||| ||||| ||||| || |||
gtgagtcctataaagtttcagctgaaattgttttcgcttaggctcttgtttgattatgaattcactgtgttgac-agGAAGCCAAAAACACTGCAGCTTTGAAGTCTCAGATTGAAAAGTTACAGCAGGAGAGGGATGAATTCCAAAGGATGGTGATTGGTAACCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgtttgtattctttgccaatcttgaacttctatttatttcttctgaccaccagGAGGCCAAAAACACTGCAACTTTGAAGGCTCAGATTGACAAGCTGCAACAGGAACGCGATGAGTTCCAAAAAATGGTTATTGGCAATCAG
ttctgac putative branch site (score: 2)
cttctatttatttctt CT-rich tract
aacttctatttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcgttcttctatcaattcttgtttgtattctttgccaatcttgaacttctatttatttcttctgaccaccagGAGGCCAAAAACACTGCAACTTTGAAGGCTCAGATTGACAAGCTGCAACAGGAACGCGATGAGTTCCAAAAAATGGTTATTGGCAATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC