Sequence
atgc intronic sequence ATGC exonic sequencegttagtgaaatttcctttgaatgttttggttttgggcaattggaagcggctgccctctagggattggtttgccattttcttgataaactagttatatgatttttgtccagACTCCTTACAATTGCGGAGGAGACCCTGACAGAGTTCCTCTCCAAGGCTACAGGGACTGCTGTTGATTGGGTGCCAATGCCTGGGATGAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os10g33960.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g33960.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G469551_T02 (Zea mays), 3'ss of exon 4
gttagtgaaatttcctttgaa---tgttttggttttgggcaattggaagcggctgccctctagggattggtttgccattt-tcttgataaactagttatatgatttttgtccagACTCCTTACAATTGCGGAGGAGACCCTGACAGAGTTCCTCTCCAAGGCTACAGGGACTGCTGTTGATTGGGTGCCAATGCCTGGGATGAAG
|| ||| || | | | || | || | | | || | || || | | | || | | ||||| || | |||| | |||| |||||| ||||||| ||||||||| |||||||||||||||| |||||||||||||||||| |||||||||| | |||||||||||||||
gtaagtaaactgtaaaccagagcttgctgtgaaactctctcacttcaatag--tgtttaataagaacgtactgttgatacatgatactaaacc--ttttccacttttgggccagGCTCCTTGCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTACAGGGACTGCTATTGATTGGGTCCAGATGCCTGGGATGAAG
upper sequence: LOC_Os10g33960.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 3
gttagtgaaatttcctttgaatgttttggttttgggcaattggaagcggctgccctctagggattggtttgccattttcttgataaactagttatatgatttttgtccagACTCCTTACAATTGCGGAGGAGACCCTGACAGAGTTCCTCTCCAAGGCTACAGGGACTGCTGTTGATTGGGTGCCAATGCCTGGGATGAAG
| | | | | || | | | | || ||| | | | || |||| | ||| | | | | ||| ||| ||||||||| ||||||| ||||| || ||||||||||||| || ||||||||||| |||||||| |||||||| | |||||||||||||||
------------------gtaaatctgagcttcatgaagt--ggagttgct-tcttttgtggtgaagttttactcaaatttgtt---tttctgttgcgatccttg--cagACTCCTATCAATTGCAGAGGAAACTTTGACAGAGTTCCTTTCAAAGGCTACAGGAACTGCTGTAGATTGGGTCCAGATGCCTGGGATGAAG
upper sequence: LOC_Os10g33960.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA11G20520.1 (Glycine max), 3'ss of exon 3
gttagtgaaatttcctttgaatgttttggttttgggcaattggaagcggctgccctctagggattggtttgccattttcttgataaactagttatatgatttttgtccagACTCCTTACAATTGCGGAGGAGACCCTGACAGAGTTCCTCTCCAAGGCTACAGGGACTGCTGTTGATTGGGTGCCAATGCCTGGGATGAAG
| | | | || | | | |||| ||| | | || | ||||| | ||| | ||| |||| ||| ||||||||| ||||||| ||||| || ||||||||||||| || ||||||||||| |||||||| |||||||| | |||||||||||||||
------------------gtaattctgaacttcatgaagt--gaagttgcttcttttgtggtgaagttttgc--tcaaattggtttttctgttg--tgatccttg--cagACTCCTATCAATTGCAGAGGAAACTTTGACAGAGTTCCTTTCAAAGGCTACAGGAACTGCTGTAGATTGGGTCCAGATGCCTGGGATGAAG
upper sequence: LOC_Os10g33960.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 3
gttagtgaaatttcctttgaatgttttggttttgggcaattggaagcggctgccctctagggattggtttgccattttcttgataaactagttatatgatttttgtcc-agACTCCTTACAATTGCGGAGGAGACCCTGACAGAGTTCCTCTCCAAGGCTACAGGGACTGCTGTTGATTGGGTGCCAATGCCTGGGATGAAG
|| |||| |||||| || |||| | |||| | ||||||| ||| || || |||| ||| ||| | || |||| || |||||||| || |||||||||| |||||||||||||| ||||||||||||||||| | |||||||||||||||
-----------------gtaaagtttcatttttggt---tttgaagtaacctttttctaat----------cttttttctttgc---ctaattgcttggttttggtcttagATTGCTCTCAATCGCAGAGGAGACTTTGGCAGAGTTCCTATCCAAGGCTACAGGAACTGCTGTTGATTGGGTTCAGATGCCTGGGATGAAG
upper sequence: LOC_Os10g33960.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv06s0004g02800.t01 (Vitis vinifera), 3'ss of exon 3
gttagtgaaatttcctttgaatgttttggttttgggcaattggaagcggctgccctctagggattggtttgccattttcttgataaactagttatatgatttttgtccagACTCCTTACAATTGCGGAGGAGACCCTGACAGAGTTCCTCTCCAAGGCTACAGGGACTGCTGTTGATTGGGTGCCAATGCCTGGGATGAAG
|| | | | | ||||| | | ||| ||||| | | | | | | | | || | || |||||| ||||||||| | ||||| |||||||| || ||||||||||||| ||||||||||| |||||||| |||||||| | |||||||||||||||
----gtaatgtctaatacaaatgtcc----atcagttctctggctat-----ttctctacatgtggatccattgtaattcagtggtatgatttctttgctttttg--cagACTCCTCTCCATTGCAGAGGAGACTTTGGCAGAGTTCCTCTCAAAGGCTACAGGAACTGCTGTCGATTGGGTCCAGATGCCTGGGATGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctagggattggtttgccattttcttgataaactagttatatgatttttgtccagACTCCTTACAATTGCGGAGGAGACCCTGACAGAGTTCCTCTCCAAGGCTACAGGGACTGCTGTTGATTGGGTGCCAATGCCTGGGATGAAG
tcttgat putative branch site (score: 4)
tttttgtcc putative PPT
ataaactagttatatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtgaaatttcctttgaatgttttggttttgggcaattggaagcggctgccctctagggattggtttgccattttcttgataaactagttatatgatttttgtccagACTCCTTACAATTGCGGAGGAGACCCTGACAGAGTTCCTCTCCAAGGCTACAGGGACTGCTGTTGATTGGGTGCCAATGCCTGGGATGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT