Sequence
atgc intronic sequence ATGC exonic sequence...atggtacatgctctattctctctgtatggtttagctagtcatatatggatttcttcaatttagtcaatgacaataatattcaattggacataatctgcagGCCAATATCAGGAGCGTCCATGAACCCGGCCAGGACCATCGGACCGGCGATCATCCTCGGCCGGTATACCGGTATCTGGGTGTACATCGCCGGCCCGGTT
Basic information
species | Oryza sativa |
transcript | LOC_Os05g11560.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g11560.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G126582_T01 (Zea mays), 3'ss of exon 3
---------atggtacatgctctattctctctgtatggtttag--ctagtc--atatatggatttcttcaa----tttagtcaatgacaataatattcaattg-gacataatctgcagGCCAATATCAGGAGCGTCCATGAACCCGGCCAGGACCATCGGACCGGCGATCATCCTCGGCCGGTATACCGGTATCTGGGTGTACATCGCCGGCCCGGTT
| | | || | |||| || ||| | | | | || || || ||| || || | || || | ||||||| |||||||||||||||||||||||||| |||||| | || |||||| || || | ||||| || |||| |||||||||||| |||| || || |
gtgggtataaatacgtacagttcatataccttgtaaaaactaatactaattcagtgcactagctagttaaaaaaacgcagctcatg-tgatgggatgctgatgcgatgcgctgcgcagGCCTATATCAGGAGCGTCCATGAACCCGGCGAGGACCCTGGGCCCGGCGCTCGTCGTGGGCCGCTACGCCGGCATCTGGGTGTACTTCGCGGGGCCCATC
upper sequence: LOC_Os05g11560.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv11s0078g00490.t01 (Vitis vinifera), 3'ss of exon 2
atggtacatgctctattctctctgtatggtttagctagtcatatatggatttcttcaatttagtcaatgacaataatattcaattggacataatctgcagGCCAATATCAGGAGCGTCCATGAACCCGGCCAGGACCATCGGACCGGCGATCATCCTCGGCCGGTATACCGGTATCTGGGTGTACATCGCCGGCCCGGTT
||| ||| | || | || || | | | || ||| | | || || |||| | || ||| || |||||||||||||||| ||||||| ||||||||||| || |||| ||| || ||||| | || || | | | | ||| | ||||| | | || ||
---gta-atgaaat-ttttttccacatactaataaaaaccgaattcctctttatcataatttctctttgac--tcatgttc--ttcattgcaatctgcagGCCAATAACAGGAGCTTCCATGAACCCTGCTAGGAGCATAGGCCCGGCACTTGTCTCAATGGAGTTTGACTGCCTTTGGATCTACATTGTGGCTCCCATT
upper sequence: LOC_Os05g11560.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv07s0141g00160.t01 (Vitis vinifera), 3'ss of exon 2
------atggtacatgctctattctc-tctgtatggtttagctagtcatatatggatttcttcaatttagtcaatgacaataatattcaattggacataatctgcagGCCAATATCAGGAGCGTCCATGAACCCGGCCAGGACCATCGGACCGGCGATCATCCTCGGCCGGTATACCGGTATCTGGGTGTACATCGCCGGCCCGGTT
| | | | | || || | | || | || | || | |||| | || | |||| ||| || |||||||||||||||| ||||||| ||||||||||| || |||| ||| || ||||| | || || | | | | ||| | ||||| | | || ||
gtaatgaaaattctttccacatactaataaaaacggaattcctctttatcataatttctctttgacaagcacatcaatgctaatgttc--tttattgcaatctgcagGCCAATAACAGGAGCTTCCATGAACCCTGCTAGGAGCATAGGCCCGGCACTTGTCTCAATGGAGTTTGACTGCCTTTGGATCTACATTGTGGCTCCCATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggatttcttcaatttagtcaatgacaataatattcaattggacataatctgcagGCCAATATCAGGAGCGTCCATGAACCCGGCCAGGACCATCGGACCGGCGATCATCCTCGGCCGGTATACCGGTATCTGGGTGTACATCGCCGGCCCGGTT
acaataatattcaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atggtacatgctctattctctctgtatggtttagctagtcatatatggatttcttcaatttagtcaatgacaataatattcaattggacataatctgcagGCCAATATCAGGAGCGTCCATGAACCCGGCCAGGACCATCGGACCGGCGATCATCCTCGGCCGGTATACCGGTATCTGGGTGTACATCGCCGGCCCGGTT
- - tacatgc
- - - - - - - - - - -ctgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gacaataa