Sequence
atgc intronic sequence ATGC exonic sequence...taaacaaaaggatttccctacatccttcttctcgtcctcctccgattcttgttgcgaaacaatagaaccttgaaacatgacctgttctagttgaatatagGTGTGCAGGATATTACAGTGATGCTGATGCTCCCAATCGAAGAATTGCCAAACCTCTGATCTTCTGTAGAACTGAAAGTGATAGCCCTATGGAGAATGGT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g38010.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g38010.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G38990.1 (Glycine max), 3'ss of exon 4
taaacaaaaggatttccctacatccttcttctcgtcctcctccgattcttgttgcgaaacaatagaaccttgaaacatgacctgttctagttgaa--tatagGTGTGCAGGATATTACAGTGATGCTGATGCTCCCAATCGAAGAATTGCCAAACCTCTGATCTTCTGTAGAACTGAAAGTGATAGCCCTATGGAGAATGGT
| | | | | | | | | | | | || || | | | | | | || ||| | | || | ||||||||| |||||| ||||||| ||||||||||| | || ||| |||| ||||| || ||||| ||||| ||||||||||| |||||||||| |||||
----gttagttactgcttcaagattatttgattggcatattatgagaatttatttcagctatgtcttgttctatctaatacttgtggtgttgaaacttgtagGTGTGCTGGATATCACAGTGAAGCTGATGCTCCTAGCCGGAGACTTGCTAAACCACTAATCTTTTGTAGGACTGAAAGTGACTGCCCTATGGAAAATGGC
upper sequence: LOC_Os02g38010.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G20800.1 (Glycine max), 3'ss of exon 4
taaacaaaaggatttccctacatccttcttctcgtcctcctccgattcttgttgcgaaacaatagaaccttgaaacatgacctgttctagttgaa---tatagGTGTGCAGGATATTACAGTGATGCTGATGCTCCCAATCGAAGAATTGCCAAACCTCTGATCTTCTGTAGAACTGAAAGTGATAGCCCTATGGAGAATGGT-
| | | | | | | | | | | | || || | || |||| | | | |||||| | ||||||||| |||||| ||||||| | ||||||||| | |||||| |||| ||||| || ||||| ||||| ||||||||||| |||| ||||| |||||
-----ttagttactgcttcaagatgatttgattgacatattatgagaatttattt----cagctatgtcttgttctgtctaatacttgtgttgaaacttgtaggTGTGCTGGATATCACAGTGAAGTTGATGCTCCTAGCCGAAGACTTGCTAAACCACTAATCTTTTGTAGGACTGAAAGTGACTGCCCCATGGAAAATGGCT
upper sequence: LOC_Os02g38010.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 4
------taaacaaaaggatttccctacatccttcttctcgtcctcc---tccgattcttgttgcgaaa--caatagaaccttgaaacatgacctgttctagttgaatatagGTGTGCAGGATATTACAGTGATGCTGATGCTCCCAATCGAAGAATTGCCAAACCTCTGATCTTCTGTAGAACTGAAAGTGATAGCCCTATGGAGAATGGT
|| | |||| |||| | | | || | | || ||| || || | | || ||| ||| || | | || ||||||| |||||| ||||||||||||||||||| | ||| ||| |||| ||||| || ||||| ||| |||| || |||||| | || ||||| ||||||
gttagttaccctgtcagattctttcacatgcatatcctgggagaaaaagctcaatatatgtggcaaactccttttacacattggtgtatgtgcttcttt-------tacagGTGTGTTGGATATCACAGTGATGCTGATGCTCCTAGTCGTAGACTTGCGAAACCACTTATCTTTTGTCGAACCGAGAGTGATTGTCCAATGGAAAATGGT
upper sequence: LOC_Os02g38010.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv17s0000g09100.t01 (Vitis vinifera), 3'ss of exon 4
--taaacaaaaggatttccctacatccttcttctcgtcctcctccgattcttgttgcgaaacaatagaac-cttgaaacatgacctg-ttctagttgaatata---gGTGTGCAGGATATTACAGTGATGCTGATGCTCCCAATCGAAGAATTGCCAAACCTCTGATCTTCTGTAGAACTGAAAGTGATAGCCCTATGGAGAATGGT
| ||| | | || | || |||| | | || | | || | || | || || || ||| | || | | | || || |||||| || || | |||| ||||||||||| | || ||| |||||||||| || || ||||||||||| || |||||| |||||||||| ||||||
gttggttaaatctacgttccaat-tctttctacagatacttattgtagatgaatttcaaatttaggcaatgttttaatcataagttggccccacatacatttactagGTGTGTTGGTTACCATGGTGAAGCTGATGCTCCTAGCCGTAGACTTGCCAAACCACTCATATTCTGTAGAACAGAGAGTGATTGCCCTATGGAAAATGGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttgttgcgaaacaatagaaccttgaaacatgacctgttctagttgaatatagGTGTGCAGGATATTACAGTGATGCTGATGCTCCCAATCGAAGAATTGCCAAACCTCTGATCTTCTGTAGAACTGAAAGTGATAGCCCTATGGAGAATGGT
ttgaatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taaacaaaaggatttccctacatccttcttctcgtcctcctccgattcttgttgcgaaacaatagaaccttgaaacatgacctgttctagttgaatatagGTGTGCAGGATATTACAGTGATGCTGATGCTCCCAATCGAAGAATTGCCAAACCTCTGATCTTCTGTAGAACTGAAAGTGATAGCCCTATGGAGAATGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
-aaacaaa
- - - - - - - -ccctaca
- - - - - - - - - - - - - - - - - - ctcctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgacc