Sequence
atgc intronic sequence ATGC exonic sequencegtactttatcctttagatttgtatagctgtccttacatacatttttttaaatggagccctttattaattgtaatagcactaagttgctaatgcttttatgcagATAGAGGGTAACCTTGCACAGGCTGAGGATGCCATCATGCTAGATAAAGATGGTTTTGTATCAGAAACAAATGCAACAAACATT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g24460.3 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g24460.3 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G108416_T01 (Zea mays), 3'ss of exon 14
gtactttatcctttagatttgtatagctgtccttacatacatttttttaaatggagcc-ctttattaa---ttgtaatagcactaagttgctaatgcttttatgcagATAGAGGGTAACCTTGCACAGGCTGAGGATGCCATCATGCTAGATAAAGATGGTTTTGTATCAGAAACAAATGCAACAAACATT
|| | | |||||| |||||| | || |||| || | || || || | || || | || | | ||| || || || |||||||||| ||||| ||||| ||||||||||||||||| ||||||||||| ||||| ||||||||||||||||| |||||||| |||
gttcactttccttttgatttgga-----gttcttaattagttcttagtatataccgtaactgtaatggagtttttgtctggactcgattttccatcctc--gtgcagATAGAAGGTAATCTTGCCCAGGCTGAGGATGCCATTATGCTAGATAAGGATGGCTTTGTATCAGAAACAAACGCAACAAATATT
upper sequence: LOC_Os03g24460.3 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA10G29770.1 (Glycine max), 3'ss of exon 15
-------------------------------------------------------------------gtactttatcctttaga---------tttgtatagctgtccttacatacatttt-----tttaaatggagccctttattaattgtaatagcactaagttgctaatgcttttatgcagATAGAGGGTAACCTTGCACAGGCTGAGGATGCCATCATGCTAGATAAAGATGGTTTTGTATCAGAAACAAATGCAACAAACATT
|| | | | | || ||| || ||| | | | | | || | | | ||| || || | | | | |||| || | || ||| ||||| || ||||| |||| | || || ||||| |||||||| || ||||| |||| |||||| ||||| ||||||||||||||
gtattttttttcctctcgtgaatttttacatgtaattattacagcaaattgtatcaggtaatgaataatatgcaaccatgtggaaacggatgcttttaatggcttttcatgctaatatcctgtcattctgaataatatttcttgcagcttatcacaaaa--aagtctttatttctgtta--cagATTGAAGGTAATAATGCAAAAGCAGATGATGCAATCATGCTTGACAAAGACGGTTATGTATCTGAAACCAATGCAACAAACATG
upper sequence: LOC_Os03g24460.3 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv14s0128g00100.t01 (Vitis vinifera), 3'ss of exon 24
--gtactttatcctttagatttgtatagctgtccttacatacatttttttaaatggagccctttattaattgtaatagcactaagttgctaatgcttttatgcagATAGAGGGTAACCTTGCACAGGCTGAGGATGCCATCATGCTAGATAAAGATGGTTTTGTATCAGAAACAAATGCAACAAACATT
|| || || | | || | | ||||| | | || | | | | | | ||| ||| | | |||| | || | | |||||||| || || |||| | ||||| ||||| |||||||| || || ||||||| ||| || ||||||||||| |||||||||
tctggtggtagcccttcattgtccttatgcattcatacatgtacagatcta--ttatgtcttgt-tggattttaacttaaattagttatt--tggggtggtacagATAGAAGGGAATAATGCAAATGCTGATGATGCAATCATGCTTGACAAGGATGGTTATGTTTCTGAAACAAATGCTACAAACATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatggagccctttattaattgtaatagcactaagttgctaatgcttttatgcagATAGAGGGTAACCTTGCACAGGCTGAGGATGCCATCATGCTAGATAAAGATGGTTTTGTATCAGAAACAAATGCAACAAACATT
tgctaat putative branch site (score: 2)
tgctttt CT-rich tract
tttattaattgtaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactttatcctttagatttgtatagctgtccttacatacatttttttaaatggagccctttattaattgtaatagcactaagttgctaatgcttttatgcagATAGAGGGTAACCTTGCACAGGCTGAGGATGCCATCATGCTAGATAAAGATGGTTTTGTATCAGAAACAAATGCAACAAACATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG