Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgttatggtcactctgttgacttggaccttgatgatttcagtaatatttacagtagtgagatgttcttgttttcacgtttttagGCTGTCAAAGACAAGTTGAGCCAAGTTGCACGCACCATTGGTCAATCTGCAGCTG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g22400.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g22400.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G044317_T03 (Zea mays), 3'ss of exon 5
--------------------------------------gtatgtgttatggtca-ctctgttgacttggaccttgatgatttcagtaatatttacagtagtgagatg-ttcttgttttcacgtttttagGCTGTCAAAGACAAGTTGAGCCAAGTTGCACGCACCATTGGTCAATCTGCAGCTG
| || | | ||| | | | |||| | || | || | || | | ||| | | |||| || || ||||||||| ||||| ||||||| |||||||| ||||||||||||||||| |||||||||||||||| ||
gtatagactttggcctctaatagaactgctgaggacttggatct-tcatgcttaacactgtacaactgcagtttttggccttt--tcctgtttgct-tcgtgaagtgatttttgttttcatgtttt-agGCTGTGAAAGACAAATTGAGCCAAGTTGCACGTTCCATTGGTCAATCTGCCAGTG
upper sequence: LOC_Os07g22400.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G130351_T01 (Zea mays), 3'ss of exon 5
------------gtatgtgttatggtca-ctctgttgacttggaccttgatgatttcagtaatatttacagtagtgagatgttcttgttttcacgtttttagGCTGTCAAAGACAAGTTGAGCCAAGTTGCACGCACCATTGGTCAATCTGCAGCTG
| || | | ||||| | | ||| | || | | | | ||| | | ||| | | | | || | || |||| || |||||||| |||||||||||||||||||||||||| |||| |||||||||||| ||
gtatagactttggcatct-tcatggttaacaatgtacaactgcagcgtttggctttt--tcctgtttgct-ttgcaaagtgattttcttttttgtgttctagGCTGTGAAAGACAAGTTGAGCCAAGTTGCACGTTCCATCGGTCAATCTGCAAATG
upper sequence: LOC_Os07g22400.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G044317_T04 (Zea mays), 3'ss of exon 5
--------------------------------------gtatgtgttatggtca-ctctgttgacttggaccttgatgatttcagtaatatttacagtagtgagatg-ttcttgttttcacgtttttagGCTGTCAAAGACAAGTTGAGCCAAGTTGCACGCACCATTGGTCAATCTGCAGCTG---------------------------------------------
| || | | ||| | | | |||| | || | || | || | | ||| | | |||| || || ||||||||| ||||| ||||||| |||||||| ||||||||||||||||| |||||||||||||||| ||
gtatagactttggcctctaatagaactgctgaggacttggatct-tcatgcttaacactgtacaactgcagtttttggccttt--tcctgtttgct-tcgtgaagtgatttttgttttcatgtttt-agGCTGTGAAAGACAAATTGAGCCAAGTTGCACGTTCCATTGGTCAATCTGCCAGTGGTATGCATAATTTGATATTGCCACTGTCTTCGCTCAATTTATTGCMapped 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|58665435|gb|CK054121.1|CK054121EST: TGAGTGAGTTTCGACTTCCATACAAAGCATTGCCACACTCGGAATTTGAG GCTGTCAAAGACAAGTTGAGCCAAGTTGCACGCACCATTGGTCAATCTGCA
genomic: TGAGTGAGTTTCGACTTCCATACAAAGCATTGCCACACTCGGAATTTGAGgtatgtgtta ... acgtttttagGCTGTCAAAGACAAGTTGAGCCAAGTTGCACGCACCATTGGTCAATCTGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatgatttcagtaatatttacagtagtgagatgttcttgttttcacgtttttagGCTGTCAAAGACAAGTTGAGCCAAGTTGCACGCACCATTGGTCAATCTGCAGCTG
ccttgat putative branch site (score: 5)
ttttcac putative PPT
atttcagtaatattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgttatggtcactctgttgacttggaccttgatgatttcagtaatatttacagtagtgagatgttcttgttttcacgtttttagGCTGTCAAAGACAAGTTGAGCCAAGTTGCACGCACCATTGGTCAATCTGCAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG