Sequence
atgc intronic sequence ATGC exonic sequencegtagatttttaccattattggcattctgcttgctcatgattctcagactaatgtcattaactcatgaacaacaagcctacaaatctgcaattattccgtggctgaaagtttgcttcaccattgtttgtgcatgtattttgagcagTGGTGAGCACAACTTGCCAGACAGCCCGTTTGCTTCCTCTACCAAGTCGACCGCATTCTTTACCGCAACCGCTGCCACTGCCATTGGTAGCGAGGGAGAT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g21160.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g21160.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G819035_T02 (Zea mays), 3'ss of exon 6
gtagatttttaccattattggcattctgcttgctcatgattctcagactaatgtcattaactcatgaacaacaagcctacaaatctgcaattattccgtggctgaaagtttgcttcaccattgtttgtgcatgtattttgagcagTGGTGAGCACAACTTGCCAGACAGCCCGTTTGCTTCCTCTACCAAGTCGACCGCATTCTT-TACCGCAAC--CGCTGCCACTGCCATTGGTAGCGAGGGAGAT
||||||| || | | || | || | || | | | | || ||| || | | ||| | | | | ||| ||| | | | | |||||| || ||||||||||| |||||||| ||||| ||| |||||||||| || || | || || ||| ||||| | || | | |
-------------------------------aatcatgatcct-atatgtatattgata-ttaatcagttctag----aaagttcaacaacatttgagcatgtcaaaa----cctaatcgttgcctgttc-catgtc---aacagTGGAGATCACAACTTGCCGGACAGCCCATTTGCGTCCCCTACCAAGTCTGACGTGCTCGTGCACGACAGTTTCGCCGCCACGGAGCCTGAGAACACCGCG---
upper sequence: LOC_Os03g21160.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G003424_T01 (Zea mays), 3'ss of exon 6
gtagatt---tttaccattattggcattctgcttgctcatga-ttctcagactaatgtcattaactcatgaacaacaagcctacaaat--ctgcaattattccgtggctgaaagtt------tgcttcaccat---------tgtttgt-gcatgtattttga--gcagTGGTGAGCACAACTTGCCAGACAGCCCGTTTGCTTCCTCTACCAAGTCGACCGCATTCTT-TACCGCAAC--CGCTGCCACTGCCATTGGTAGCGAGGGAGAT
|| |||| |||| || |||||| ||| || | | || | | || | | ||||||| | | |||| | || || |||| || || ||||||| || | ||| || | || || ||| ||| |||||| |||||||||||||| |||||||| ||||| ||| |||||||||| |||| || | || || ||| ||||| | || | | |
gtggattaaacaacccatcatcatcattcttcttccttgttagttatgatacccacgcttgcctttcatgaatcatgatcctatagatatttgatattaatcagttctggaaagttgaacaacatttgagcatgtcaaaacctgatcgttgcctgttccatgacaacagTGGAGAGCACAACTTGCCGGACAGCCCATTTGCGTCCCCTACCAAGTCTGCCGCGCTCGTGCACGACAGTTTCGCCGCCACGGAGCCTGAGAACACCGCG---Mapped 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|88978350|gb|CI384758.1|CI384758EST: AAGGCGGATTCTGCCGGTGAGGTTACCCGCAATGCCGATAGTGACCAAAG TGGTGAGCACAACTTGCCAGACAGCCCGTTTGCTTCCTCTACCAAATCGAC
genomic: AAGGCGGATTCTGCCGGTGAGGTTACCCGCAATGCCGATAGTGACCAAAGgtagattttt ... ttttgagcagTGGTGAGCACAACTTGCCAGACAGCCCGTTTGCTTCCTCTACCAAGTCGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattccgtggctgaaagtttgcttcaccattgtttgtgcatgtattttgagcagTGGTGAGCACAACTTGCCAGACAGCCCGTTTGCTTCCTCTACCAAGTCGACCGCATTCTTTACCGCAACCGCTGCCACTGCCATTGGTAGCGAGGGAGAT
atgtatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagatttttaccattattggcattctgcttgctcatgattctcagactaatgtcattaactcatgaacaacaagcctacaaatctgcaattattccgtggctgaaagtttgcttcaccattgtttgtgcatgtattttgagcagTGGTGAGCACAACTTGCCAGACAGCCCGTTTGCTTCCTCTACCAAGTCGACCGCATTCTTTACCGCAACCGCTGCCACTGCCATTGGTAGCGAGGGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT