Sequence
atgc intronic sequence ATGC exonic sequencegttagttttaaatctctaccaggaaataattcatactatgtgtaggctgtgaaataaccatctgatatttagGGCGAGGAAATATGTGTAGCACTTCAGACGCATATCAATGATGTGATGCTCCGCAGATATTCAAAAGCACGCTCTGCTACTAGCGCGGTTTCTCAAAACG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g57140.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 10
-------------gttagttttaaatctctac--caggaaataat-tcatactatgtgtaggctgtgaaataaccatctgatatttagGGCGAGGAAATATGTGTAGCACTTCAGACGCATATCAATGATGTGATGCTCCGCAGATATTCAAAAGCACGCTCTGCTACTAGCGCGGTTTCTCAAAACG
|| | | | || ||| || | | ||| || ||| | |||||| || | ||||||||||||||||||||||||||||||| || ||||| |||||||| ||||||||||||||||||||||||||||||| || ||| | || ||||| |
gtattctaaagcttcgaggcaatagtttataatacagccgatcctgttatatcatccatagctgttagaataacgatg-actttttagGGCGAGGAAATATGTGTAGCACTTCAAACACATATAAATGATGTCATGCTCCGCAGATATTCAAAAGCACGCTCTGGTAATAGTGTTACATCACAAAATG
upper sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 10
-----------gttagttttaaatctctaccaggaaa-taattc----atactatgtgtaggctgtgaaataaccatctgatatttagGGCGAGGAAATATGTGTAGCACTTCAGACGCATATCAATGATGTGATGCTCCGCAGATATTCAAAAGCACGCTCTGCTACTAGCGCGGTTTCTCAAAACG
|| | || | | | | | | || | ||| || | || | ||||||||| | | ||||||||||||||||||||||||||||||| || ||||| ||||| || |||||||||||||||||||||||||||||||||| ||| | | || ||||| |
gtattctaaagtttcgaggcaatagttcataatgcatctgatcctgttatatcatctataactgatagaataaccat--gttttttagGGCGAGGAAATATGTGTAGCACTTCAAACACATATAAATGACGTCATGCTCCGCAGATATTCAAAAGCACGCTCTGCTAATAGTGTGACATCGCAAAATG
upper sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 11
--------------------------------------------------gttagttttaaatctctaccaggaaataattcata--ctatgtgtaggctgtgaaataa-------ccatctgatatt---tagGGCGAGGAAATATGTGTAGCACTTCAGACGCATATCAATGATGTGATGCTCCGCAGATATTCAAAAGCACGCTCTGCTACTAGCGCGGTTTCTCAAAACG-
||||| | | ||| | | | | || | |||| | | | | | | | || || || |||| || ||||| ||||| || |||||||||||||| |||||||| ||| | || | ||||| |||||||| |||||| |||| | | | | | ||
gttcttaatcttttgagtttctatatgtatatatataacatttttagagttttagtctcttttttcttttatgtattccttgtttgcctatcaaaaaattattatttgatagagttctattccattttatgcagGGAGAAGAAATTTGTGTTGCTCTTCAGACGCATATAAATGATGTTATGTTGCGTCGCTATTCTAAAGCACGGTCTGCTGCTAGTG-GCTCTATGAATGGAGMapped 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|58671897|gb|CK060583.1|CK060583EST: AAATGAGAGTCGCTGGTGTTCTTCATATCTCCCAGCTTGAAACTAAGCAG GGCGAGGAAATATGTGTAGCACTTCAGACGCATATCAATGATGTGATGCTC
genomic: AAATGAGAGTCGCTGGTGTTCTTCATATCTTTCAGTTTGAAACTAAGCAGgttagtttta ... tgatatttagGGCGAGGAAATATGTGTAGCACTTCAGACGCATATCAATGATGTGATGCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.accaggaaataattcatactatgtgtaggctgtgaaataaccatctgatatttagGGCGAGGAAATATGTGTAGCACTTCAGACGCATATCAATGATGTGATGCTCCGCAGATATTCAAAAGCACGCTCTGCTACTAGCGCGGTTTCTCAAAACG
aaataattcatactat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagttttaaatctctaccaggaaataattcatactatgtgtaggctgtgaaataaccatctgatatttagGGCGAGGAAATATGTGTAGCACTTCAGACGCATATCAATGATGTGATGCTCCGCAGATATTCAAAAGCACGCTCTGCTACTAGCGCGGTTTCTCAAAACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT