Sequence
atgc intronic sequence ATGC exonic sequenceTACTTGACGCTTATCTCAATCCTAAGATCTCAGATTTTGGGCTAGCTAAACTTTATGATGACAAGAAGACGCATGTTAGCACAAAAGTTGCTGGTACCTTgtaagttcattccatctttcgcaccttcatgtttacaaattattttcgtacctgtgctaacgggatttatggcttttcttttatctag
Basic information
species | Oryza sativa |
transcript | LOC_Os04g52606.2 |
intron # | 19 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g52606.2 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM2G155837_T02 (Zea mays), 5'ss of exon 18
TACTTGACGCTTATCTCAATCCTAAGATCTCAGATTTTGGGCTAGCTAAACTTTATGATGACAAGAAGACGCATGTTAGCACAAAAGTTGCTGGTACCTTgtaagttcattccatctttcgcaccttcatgtttacaaattattttcgtacctgtgctaacgg-gatttatggcttttcttttatctag
| ||||| || ||||||| ||||||||||| ||||| ||||| || |||||||| |||||||||||||| ||||| ||||| |||||||| ||||| |||||||| |||| | || | ||| | ||| |||||||| | || ||| | |||| | || |||| | |
TGCTTGATGCAAATCTCAACCCTAAGATCTCGGATTTCGGGCTCGCCAAACTTTACGATGACAAGAAGACTCATGTCAGCACCAAAGTTGCGGGTACATTgtaagtgcatttccatattgcctcctctacacc--caagttattttcaaatgtgagctggtgtcaatttcttactcttctgtgaag---
upper sequence: LOC_Os04g52606.2 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM2G126858_T02 (Zea mays), 5'ss of exon 20
TACTTGACGCTTATCTCAATCCTAAGATCTCAGATTTTGGGCTAGCTAAACTTTATGATGACAAGAAGACGCATGTTAGCACAAAAGTTGCTGGTACCTTgtaagttcattccatctttcgcaccttcatgtttacaaattattttc-----gtacctgtgctaacggga----tttatggcttttcttttatctag
||||||| || | | || |||||||| || ||||| ||||| || ||||||||||| || || ||||| |||||||||||||||||||||||||| ||||||| ||| | || | || | || ||||||| ||||| |||| | ||| ||||| || | || | |||| ||| | ||
TACTTGATGCCACTTTGAACCCTAAGATTTCGGATTTCGGGCTCGCCAAACTTTATGACGATAAAAAGACACATGTTAGCACAAAAGTTGCTGGTACATTgtaagggcatac-atgtctc-cccccatatgtttaataattagtttccactaatgtctgagctaatggaagttccttttcactttgatttcttgaag
upper sequence: LOC_Os04g52606.2 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM2G031536_T01 (Zea mays), 5'ss of exon 7
TACTTGACGCTTATCTCAATCCTAAGATCTCAGATTTTGGGCTAGCTAAACTTTATGATGACAAGAAGACGCATGTTAGCACAAAAGTTGCTGGTACCTTgtaagttcatt-ccatctttcgcaccttcatgtttacaaattattttcgtacctgtgctaacgg-gatttatggcttttcttttatctag
| |||||||| || |||| ||||||||||||||||||||||| || ||||||||||| ||||||||||| ||||| |||||||||||||| ||||| |||||||| |||| ||||||| || | || | | || ||||||||| | || |||| | |||| | ||| |||| | |
TGCTTGACGCAAATTTCAACCCTAAGATCTCAGATTTTGGGCTCGCCAAACTTTATGACGACAAGAAGACTCATGTCAGCACAAAAGTTGCGGGTACATTgtaagtacatttccatcttgtgc-cttttacaagtgcatattattttcacatgtgaactaatgccaatttcttgctcttctgtgaag---
upper sequence: LOC_Os04g52606.2 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM2G126858_T01 (Zea mays), 5'ss of exon 20
TACTTGACGCTTATCTCAATCCTAAGATCTCAGATTTTGGGCTAGCTAAACTTTATGATGACAAGAAGACGCATGTTAGCACAAAAGTTGCTGGTACCTTgtaagttcattccatctttcgcaccttcatgtttacaaattattttc-----gtacctgtgctaacggga----tttatggcttttcttttatctag-------------------------------------------------------------------------------------
||||||| || | | || |||||||| || ||||| ||||| || ||||||||||| || || ||||| |||||||||||||||||||||||||| ||||||| ||| | || | || | || ||||||| ||||| |||| | ||| ||||| || | || | |||| ||| | ||
TACTTGATGCCACTTTGAACCCTAAGATTTCGGATTTCGGGCTCGCCAAACTTTATGACGATAAAAAGACACATGTTAGCACAAAAGTTGCTGGTACATTgtaagggcatac-atgtctc-cccccatatgtttaataattagtttccactaatgtctgagctaatggaagttccttttcactttgatttcttgaagtggctatctttcacctgagtacgccatgagaggtcacatgactgagaaagttgatatttttgcttttggtgtggtcatgttggag
upper sequence: LOC_Os04g52606.2 (Oryza sativa), 5'ss of exon 19
lower sequence: Vv12s0055g00600.t01 (Vitis vinifera), 5'ss of exon 1
TACTTGACGCTTATCTCAATCCTAAGATCTCAGATTTTGGGCTAGCTAAACTTTATGATGACAAGAAGACGCATGTTAGCACAAAAGTTGCTGGTACCTTgtaagttcattccatctttcgcacct-----tcatgtttacaaattattttcgta-------cctgtgctaacgggatttatggcttttcttttatctag---------
| |||||| |||||||||||||||||| ||||||||||| | || |||| ||||||| || | ||| || | ||||| ||||| || || |||||| || | | | | ||| | |||||| | |||| | | | ||| | ||| || |||||||| |
TGCTTGACTATTATCTCAATCCTAAGATTTCAGATTTTGGTTTGGCCAAACAGTATGATGGCACAATGACTCACATAAGCACCCGTGTTGCAGGCACAATgtaagatcctcaaaagtcaaggccctatgttccttgtttattctcttttttgggatatttttcatgtatcctcaaagttttaaactggtcttttatgttactgatgtag
upper sequence: LOC_Os04g52606.2 (Oryza sativa), 5'ss of exon 19
lower sequence: Vv12s0055g00580.t01 (Vitis vinifera), 5'ss of exon 22
TACTTGACGCTTATCTCAATCCTAAGATCTCAGATTTTGGGCTAGCTAAACTTTATGATGACAAGAAGACGCATGTTAGCACAAAAGTTGCTGGTACCTTgtaagttcattccatctttcgcaccttcatgtttacaaattattttcgtacctgtgctaacgggatttatggcttttctt-ttatctag----------------------------------
| |||||| ||||||||| |||||||| ||||||||||| | || ||||| |||||||||| |||||| || | ||||| ||||| || || |||||| || || | | |||| | | || || | | | | |||||| | || | | ||| |
TGCTTGACTATTATCTCAACCCTAAGATTTCAGATTTTGGTTTGGCCAAACTGTATGATGACACGAAGACTCACATAAGCACCCGTGTTGCAGGCACAATgtaagatccttgagagtcaaggcccttagtcccttt--tttgttctgtttttctttttttttggattttttttttcaggtatcatcaaagtttcaaaactgagattttatgctactgatgtag
upper sequence: LOC_Os04g52606.2 (Oryza sativa), 5'ss of exon 19
lower sequence: Vv12s0055g00590.t01 (Vitis vinifera), 5'ss of exon 47
TACTTGACGCTTATCTCAATCCTAAGATCTCAGATTTTGGGCTAGCTAAACTTTATGATGACAAGAAGACGCATGTTAGCACAAAAGTTGCTGGTACCTTgtaagttcattccatctttcgcaccttcatgtttacaaattattttcgtacctgtgctaacgggatttatggcttttcttttatctag----------------------------------
| |||||| ||||||||| |||||||| ||||||||||| | || ||||| |||||||||| |||||| || | ||||| ||||| || || |||||| || || | | |||| || | || || | | | | | | ||| | | | | ||| |
TGCTTGACTATTATCTCAACCCTAAGATTTCAGATTTTGGTTTGGCCAAACTGTATGATGACACGAAGACTCACATAAGCACCCGTGTTGCAGGCACAATgtaagatccttgagagtcaaggccctt--agtcccctttttgttctgtttttttttttttttgaattcttttttcaggtatcatcaaagttttaaaactgagattttatgctactgatgtag
upper sequence: LOC_Os04g52606.2 (Oryza sativa), 5'ss of exon 19
lower sequence: Vv12s0055g00640.t01 (Vitis vinifera), 5'ss of exon 1
TACTTGACGCTTATCTCAATCCTAAGATCTCAGATTTTGGGCTAGCTAAACTTTATGATGACAAGAAGACGCATGTTAGCACAAAAGTTGCTGGTACCTTgtaagttcatt-----ccatctttcgcaccttcatgtttacaaattattttcgtacctgtgctaa-------cgggatttatggcttttcttttatctag---------
| |||||| |||||||||||||||||| ||||||||||| | || ||||| |||||||||| | ||| || | ||||| || || || || |||||| || | || | | | | |||||| | |||| | | | | | | |||| || ||||||| |
TGCTTGACTATTATCTCAATCCTAAGATTTCAGATTTTGGTTTGGCCAAACTGTATGATGACACAATGACTCACATAAGCACCCGTGTGGCAGGCACAATgtaagatcctcaaaagtcaaggcccttagttccttgtttattctcttttttgggatttttttcatttatccccaaagtttaaaactgggcttttatgttactgaagtagMapped 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|86479836|gb|CI122469.1|CI122469EST: CTTTATGATGACAAGAAGACGCATGTTAGCACAAAAGTTGCTGGTACCTT TGGTTATCTTGCACCTGAGTATGCTATGAGAGCTCGTTTGACCGAGAAAGT
genomic: CTTTATGATGACAAGAAGACGCATGTTAGCACAAAAGTTGCTGGTACCTTgtaagttcat ... ttttatctagTGGTTATCTTGCACCTGAGTATGCTATGAGAGGTCGTTTGACCGAGAAAGT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TACTTGACGCTTATCTCAATCCTAAGATCTCAGATTTTGGGCTAGCTAAACTTTATGATGACAAGAAGACGCATGTTAGCACAAAAGTTGCTGGTACCTTgtaagttcattccatctttcgcaccttcatgtttacaaattattttcgtacctgtgctaacgggatttatggcttttcttttatctag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG