Sequence
atgc intronic sequence ATGC exonic sequencegtatgttgttctctatgataatggaatttctgaaatttatagcctaactagcttaagtagcttgtatgttgtgtacaagtgaaataaggaaatcttatcaattaaatatgcagATTGCGCTGGGTAATATACTAAAGTTCCGCAAGAAGAATTGGCAGTTTGACACAATTGGTGGTTTTATCTACTTCATACTGGTATTCTCAATGTTCCCAC
Basic information
species | Oryza sativa |
transcript | LOC_Os07g01540.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g01540.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G135839_T01 (Zea mays), 3'ss of exon 11
gtatgttgttctctatgataatggaat--ttctgaaatttatagccta---actagcttaagtagcttgtatgttgtgtacaa------gtgaaataagga-aatcttatcaattaaatatgcagATTGCGCTGGGTAATATACTAAAGTTCCGCAAGAAGAATTGGCAGTTTGACACAATTGGTGGTTTTATCTACTTCATACTGGTATTCTCAATGTTCCCAC
||||||| || ||||| | ||| | | |||| | | ||| | | || ||| | | ||| | ||| | ||| | |||| || || | |||| || | ||||| |||||||| ||||||| ||| | ||||||||||| ||||||||||||||||||| ||||| |||||||| |||||||| |||| || |||||||||||||
gtatgttttttcctatgttgatgaagtaattcttgcttatttagttcagtgatcagtttatgaatcttttgtgtactataccatcaattgtgagatgagcacgatctgatttactaaattcacagATTGCATTGGGTAACATATTGAAGTTCCGCAAAAAGAATTGGCAGTTTGACATCATTGGCGGTTTTATATACTTCATTTTGGTGTTTTCAATGTTCCCAC
upper sequence: LOC_Os07g01540.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv18s0001g11060.t01 (Vitis vinifera), 3'ss of exon 11
----gtatgttgttctctatgataatggaatttctgaaatttatagcctaactagcttaagtagcttgtatgttgtgtacaagtga--aataaggaaatcttatcaattaaat-atgcagATTGCGCTGGGTAATATACTAAAGTTCCGCAAGAAGAATTGGCAGTTTGACACAATTGGTGGTTTTATCTACTTCATACTGGTATTCTCAATGTTCCCAC
| || ||| | || | || | | | | | | | ||| | ||| | | || | || | ||||| | | || | | | ||||||||||| |||| ||||| | |||||||| |||||||||||||||||||| |||||||| |||| || || || |||| || || ||||| ||||
gtaaatctgaaaatctacagttccattggcttgtcaataccaaaaatttcatt---ttatattcctttttttttccttttaatttctcaataatatggtgt-attggtcatttgatgcagATTGCATTGGGAAATATTTTGAAGTTCCGAAAGAAGAATTGGCAGTTTGATTTCATTGGTGGCATTATATATTTTGTATTGGTTTTTTCTATGTTTCCAC
upper sequence: LOC_Os07g01540.1 (Oryza sativa), 3'ss of exon 11
lower sequence: PP1S72_100V6.1 (Physcomitrella patens), 3'ss of exon 9
gtatgttgttctctatgataatggaatttctgaaatttatagcctaactagcttaagtagcttgtatgttgtgtacaagtgaaataaggaaatcttatcaattaaatatgcagATTGCGCTGGGTAATATACTAAAGTTCCGCAAGAAGAATTGGCAGTTTGACACAATTGGTGGTTTTATCTACTTCATACTGGTATTCTCAATGTTCCCAC
|||||| || | | | |||| || |||||||| |||| |||| | | | ||| | | || ||| |||| | | | | | | | | |||||||| ||| || || | ||||| || ||||||||||||| ||||| |||||||||| || | ||||| ||| |||| ||||||||||||||||
gtatgtaaatcataacattcttcaaattactcaaatttat-gcctgtctaggacatg-atattggacaaagcttatgagt-aaatttgtgtgtatggttaccttcct-tacagATTGCATGGGGAAACATCTTGAAGTTTCGAAAGAAGAATTGGCGTTTTGATGTAATTGGTGGTGTTGTATACTTTATATTGGTTTTCTCAATGTTCCCACMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|87009563|gb|CI309084.1|CI309084EST: CTACTTATGAGTGCAAGGCTGCGTATCCATCCTTCGATGACTCCAGCGGG ATTGCGCTGGGTAATATACTAAAGTTCCGCAAGAAGAATTGGCAGTTTGAC
genomic: CTACTTATGAGTGCAAGGCTGCGTATCCATCCTTCGATGACTCCAGCGGGgtatgttgtt ... aaatatgcagATTGCGCTGGGTAATATACTAAAGTTCCGCAAGAAGAATTGGCAGTTTGAC
EST:
gi|44677296|gb|CR290730.1|CR290730EST: CTACTTATGAGTGCAAGGCTGCGTATCCATCCTTCGATGACTCCAGCGGG ATTGCGCTGGGTAATATACTAAAGTTCCGCAAGAAGAATTGGCAGTTTGAC
genomic: CTACTTATGAGTGCAAGGCTGCGTATCCATCCTTCGATGACTCCAGCGGGgtatgttgtt ... aaatatgcagATTGCGCTGGGTAATATACTAAAGTTCCGCAAGAAGAATTGGCAGTTTGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcttgtatgttgtgtacaagtgaaataaggaaatcttatcaattaaatatgcagATTGCGCTGGGTAATATACTAAAGTTCCGCAAGAAGAATTGGCAGTTTGACACAATTGGTGGTTTTATCTACTTCATACTGGTATTCTCAATGTTCCCAC
aaataaggaaatctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttgttctctatgataatggaatttctgaaatttatagcctaactagcttaagtagcttgtatgttgtgtacaagtgaaataaggaaatcttatcaattaaatatgcagATTGCGCTGGGTAATATACTAAAGTTCCGCAAGAAGAATTGGCAGTTTGACACAATTGGTGGTTTTATCTACTTCATACTGGTATTCTCAATGTTCCCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG