Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgcctctataatctattgcaactatattgttattttcataattacaaataaaattgacgataaaagattttttgatgaaagtaaggtttatttatggtgatcagtgaatgttctattgttatgtccatcagAAATTTTTGACCGTGGAATGTATGCTGGACCTGTTGGTTGGTTTGGAGGAGCTGAAAGTGAGTTCGCTGTTGGGATTAGATCAGCACTACTAGGAAAA
Basic information
species | Oryza sativa |
transcript | LOC_Os09g19734.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g19734.2 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G022837_T02 (Zea mays), 3'ss of exon 10
gtatgtgcctctataatctattgcaactatattgttattttcataattacaaataaaattgacgataaaagattttttgatgaaagtaaggtttatttatggtgatcagtgaatgttctattgttatgtccatcagAAATTTTTGACCGTGGAATGTATGCTGGACCTGTTGGTTGGTTTGGAGGAGCTGAAAGTGAGTTCGCTGTTGGGATTAGATCAGCACTACTAGGAAAA
||| ||| | || || || ||| | || ||| || || | || | || | | || ||| | | | ||| || ||||||||||||||||||||||||||||||| |||||||| ||| ||||||||||||| | ||||||||||| |||||||||||||| |||| ||||||
----------------------------------gtatgctcaaatttgattattctgtt--cgaacatagcctttctg----aaattag----acacatactaactag-----gtttt-tggatat-tctgacagAAATTTTTGACCGTGGAATGTATGCTGGTCCTGTTGGCTGGCTTGGAGGAGCTGAGTGCGAGTTCGCTGTCGGGATTAGATCAGCGTTACTTGGAAAA
upper sequence: LOC_Os09g19734.2 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA03G17420.1 (Glycine max), 3'ss of exon 10
gtatgtgcctctataatctattgcaactatattgttattttcataattacaaataaaattgacgataaaagattttttgatgaaagtaaggtttatttatggtgatcagtgaatgttctattgttatgtccatcagAAATTTTTGACCGTGGAATGTATGCTGGACCTGTTGGTTGGTTTGGAGGAGCTGAAAGTGAGTTCGCTGTTGGGATTAGATCAGCACTACTAGGAAAA
|| | | | ||| || || ||||| || || | | || | |||| | | | || | | | | | ||| | |||| | |||| | ||||| || || |||||||||||||||||||||||||||||||||| || || ||||| || ||||| || || |||||| | | | |||
--------------------------ttaaactatctctttgatg-tttcaaatcctgtttacaacacaaagct-----atgactcctattcctttggataaactttacttact-ttcaaagacaatgtgc---agAAGTATTTGATCGAGGGATGTATGCTGGACCTGTTGGTTGGTTTGGAGGAGGAGAGAGCGAGTTTGCGGTTGGCATCAGGTCAGCATTGGTGGAAAAG
upper sequence: LOC_Os09g19734.2 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA01G25690.1 (Glycine max), 3'ss of exon 11
gtatgtgcctctataatctattgcaactatattgttattttcataattacaaataaaattgacgataaaagattttttgatgaaagtaaggtttatttatggtgatca-gtgaatgttctattgttatgtccatcagAAATTTTTGACCGTGGAATGTATGCTGGACCTGTTGGTTGGTTTGGAGGAGCTGAAAGTGAGTTCGCTGTTGGGATTAGATCAGCACTACTAGGAAAA
|| | | | ||| || || ||||| || || | | ||| || | | | || |||| || | ||||| | |||| | |||| | ||||| || |||||||||||||||||||||||||||||||| |||| || |||||||| |||||||| || || |||||| | | | |||
--------------------------ttaaactatctgtttgatg-tttcaaattctgtttacaacacaaggttct-------gactcctattcatttggataaattttacttactttctaaggcaatgtgc---agAAGTATTTGATCGAGGAATGTATGCTGGACCTGTTGGTTGGTTTGGTGGAGGAGAGAGTGAGTTTGCTGTTGGCATCAGGTCAGCATTGGTGGAAAAGMapped 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|66923198|gb|CX110046.1|CX110046EST: CGTTTGTGGTCTGCCCACTGAAGAGGCACGCCAATTCATACAAGATTATG AAATTTTTGACCGTGGAATGTATGCTGGACCTGTTGGTTGGTTTGGAAGAG
genomic: CGTTTGTGGTCTGCCCACTGAAGAGGCACGCCAATTCATACAAGATTATGgtatgtgcct ... tgtccatcagAAATTTTTGACCGTGGAATGTATGCTGGACCTGTTGGTTGGTTTGGAGGAG
EST:
gi|157651526|gb|EX451160.1|EX451160EST: CGTTTGTGGTCTGCCCACTGAAGAGGCACGCCAATTCATACAAGATTATG AAATTTTTGACCGTGGAATGTATGCTGGACCTGTTGGTTGGTTTGGAGGAG
genomic: CGTTTGTGGTCTGCCCACTGAAGAGGCACGCCAATTCATACAAGATTATGgtatgtgcct ... tgtccatcagAAATTTTTGACCGTGGAATGTATGCTGGACCTGTTGGTTGGTTTGGAGGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaagtaaggtttatttatggtgatcagtgaatgttctattgttatgtccatcagAAATTTTTGACCGTGGAATGTATGCTGGACCTGTTGGTTGGTTTGGAGGAGCTGAAAGTGAGTTCGCTGTTGGGATTAGATCAGCACTACTAGGAAAA
taaggtttatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgcctctataatctattgcaactatattgttattttcataattacaaataaaattgacgataaaagattttttgatgaaagtaaggtttatttatggtgatcagtgaatgttctattgttatgtccatcagAAATTTTTGACCGTGGAATGTATGCTGGACCTGTTGGTTGGTTTGGAGGAGCTGAAAGTGAGTTCGCTGTTGGGATTAGATCAGCACTACTAGGAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA