Sequence
atgc intronic sequence ATGC exonic sequence...gtgcttatgattcacactgatgtgttgcagtttgtgttcataatcaactgaaaattgggtagaaattaatgtgtgcgattcatttgccactctctggaagGAGCAACTGGTTTTAGCATGGGTACCCTGCTCATCTCAAAGATCAGGGAGGAGTACCCAGACAGGATGATGCTGACATTCTCTGAGAAGTTTTCCCCTCA
Basic information
species | Oryza sativa |
transcript | LOC_Os06g07280.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g07280.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EDP03008 (Chlamydomonas reinhardtii), 3'ss of exon 3
----------------------------------------------gtgcttatgatt-cacactgatgtgt---tgcagtttgtgttcataatcaactgaaaattgggtagaaattaatgtgtgc---------gattc---atttgccactctctggaagGAGCAACTGGTTTTAGCATGGGTACCCTGCTCATCTCAAAGATCAGGGAGGAGTACCCAGACAGGATGATGCTGACATTCTCTGAGAAGTTTTCCCCTCA
| |||| || | ||| || || ||| | || || | | | || | | || ||| | | ||| ||||||||||||||| || | ||||| | ||||||| |||||||| ||||| |||||| | ||||||||||| ||| | ||||||||
gtgagcagttttgcacgggccgccgggtgtcggggtgtggaccgcagggcttggcatgacgggctgctgggtctgtgctcctcgtcgtcttcaacggttgctgacttctctcctcttgttgttcccttccctcagGCTTCCAGGTTTGCCACTCTCTGGGTGGTGGCACTGGCTCCGGCATGGGCACCCTGCTGATCTCCAAGATCCGTGAGGAGTACCCCGACCGCATGATGCT---------------------------
upper sequence: LOC_Os06g07280.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EDP02933 (Chlamydomonas reinhardtii), 3'ss of exon 3
----------------------------------------------------gtgcttatgattcacactga--tgtgttgcagtttgtgttcataatcaactgaaaattgg-------gtagaaattaatgtgtgcgattc---atttgccactctctggaagGAGCAACTGGTTTTAGCATGGGTACCCTGCTCATCTCAAAGATCAGGGAGGAGTACCCAGACAGGATGATGCTGACATTCTCTGAGAAGTTTTCCCCTCA
| | | | | || |||| | || || |||| | |||| | || | | ||| | ||||||||||||| || | || || | ||||||| |||||||| ||||| |||||| | ||||||||||| ||| | ||||||||
gtgagcagttctgcacgggccgtcgggtgtcagtgtatggaccgcagggctcggcatgacgggctgctttgggctgtgcgccccttcgtcttcacacgttgctgacttctctctcccctgttcttccctaccctcagGCTTCCAGGTCTGCCACTCTCTGGGTGGCGGCACCGGCTCCGGCATGGGCACCCTGCTGATCTCCAAGATCCGTGAGGAGTACCCCGACCGCATGATGCT--------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aactgaaaattgggtagaaattaatgtgtgcgattcatttgccactctctggaagGAGCAACTGGTTTTAGCATGGGTACCCTGCTCATCTCAAAGATCAGGGAGGAGTACCCAGACAGGATGATGCTGACATTCTCTGAGAAGTTTTCCCCTCA
aattaat putative branch site (score: 3)
ccactctct putative PPT
tagaaattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcttatgattcacactgatgtgttgcagtttgtgttcataatcaactgaaaattgggtagaaattaatgtgtgcgattcatttgccactctctggaagGAGCAACTGGTTTTAGCATGGGTACCCTGCTCATCTCAAAGATCAGGGAGGAGTACCCAGACAGGATGATGCTGACATTCTCTGAGAAGTTTTCCCCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
gtgctta
- - - -tgattca
- - - - - - - - ctgatgt
- - - - - - - - - - - -gttgcag
- - - - - - - - - - - - - - - -ttgtgtt
- - - - - - - - - - - - - - - - - - - - -aatcaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgtgc