Sequence
atgc intronic sequence ATGC exonic sequencegtaatgtcaatcagttttgtagtgatcatctgctattctgaaactaggcatgcggtattagcagttatgttgaatgatcccttggggttgtacagAAGAATTCACAAGATGAGATGCATTTCAAGTGCTTACCAAAGTCCAGTGCCATAAAGCTGATAGATTTTGGTAGTACCGCCTTTGATAATCAGGAACATA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g40840.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G094039_T01 (Zea mays), 3'ss of exon 5
----gtaatgtcaatcagttttgtagtgatcatctgctattctgaaactaggcatgcggtattagcagttatgttgaatgatcccttggggttgtacagAAGAATTCACAAGATGAGATGCATTTCAAGTGCTTACCAAAGTCCAGTGCCATAAAGCTGATAGATTTTGGTAGTACCGCCTTTGATAATCAGGAACATA
|| | ||| || | || ||||||| ||||||||| |||||| || | ||||| |||||| | ||||||||| ||||||||||||||||||||||| |||| ||| ||||||||||||||||| || |||||||||||||||||||||||||||||||| ||||||||||||||||||| | | ||||
gtgcctattctcacccactcttttagtgattgtctgctatttctttactaggaatacagtatttgcagttttcttgaatgattgcttggggttgtacagAAGAATTCGCAAGGTGAAATGCATTTCAAGTGCTTGCCGAAGTCCAGTGCCATAAAGCTGATAGATTTTGGCAGTACCGCCTTTGATAATCGGAACCATA
upper sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G366935_T09 (Zea mays), 3'ss of exon 6
----gtaatgtcaatcagttttgtagtgatcatctgctattctgaaactaggcatgcggtattagcagttatgttgaatgatcccttggggttgtacagAAGAATTCACAAGATGAGATGCATTTCAAGTGCTTACCAAAGTCCAGTGCCATAAAGCTGATAGATTTTGGTAGTACCGCCTTTGATAATCAGGAACATA
|| | | | || |||| |||||| |||||||| ||||||||| ||||| |||||| | ||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| ||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||
gtacctattcttacccattttt--agtgattatctgctaaatctttactaggcatagagtatttgcagttttcttgaatgattgcttggggttgtacagAAGAATTCACAAGATGAGATGCATTTCAAGTGCTTGCCACAGTCCAGTGCCATAAAGCTGATAGATTTTGGTAGTACCGCCTTTGATAATCAGGACCATA
upper sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA06G08480.2 (Glycine max), 3'ss of exon 6
gtaatgtcaatcagttttgtagtgatcatctgctattctgaaactaggcatgcggtattagcagttatgttgaatgatcccttggggttgtacagAAGAATTCACAAGATGAGATGCATTTCAAGTGCTTACCAAAGTCCAGTGCCATAAAGCTGATAGATTTTGGTAGTACCGCCTTTGATAATCAGGAACATA
| | || | ||||| |||| | || | | | | | | ||| | ||| | | |||| | ||||||| | ||| |||||| ||||| |||| |||||| || ||||| ||||| || |||||||| |||||||||||||| || | |||||||||| | ||||
---gtatttattatttttg----gatc--caaacataataatgtttg-tagactcagttataatatatttaagggtaattattggattggtacagAGAATTTCCTCAGATGAAATGCAATTCAGGTGCTTGCCCAAGTCTAGTGCTATTAAGCTGATTGATTTTGGTAGTACTGCATATGATAATCAGAATCATA
upper sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT4G32660.2 (Arabidopsis thaliana), 3'ss of exon 7
------------gtaat--gtcaa--tcagttttgtagtgatcatctgctatt------ctgaaactaggcatgcggtatt--agcagttatgttgaatgatcccttgg-----ggttgta-----cagAAGAATTCACAAGATGAGATGCATTTCAAGTGCTTACCAAAGTCCAGTGCCATAAAGCTGATAGATTTTGGTAGTACCGCCTTTGATAATCAGGAACATA
| ||| || || | | |||| | |||| || ||||| | | || || || | | ||| |||| | || || |||| || | | | |||||| ||||||| ||||||||||||||| || ||||| || ||||| |||||||| ||||| | | |||||| | | |||
gtatctagaactgaaataggttaaggttgggtttgggtacactctctgtagttaaagttttgaaagaaaaagaaaaatcttcaagagtttgtactttttgacagtttggtatttgattttaaataacagAGGAGTGCTGCAAATGAGACACATTTCAGGTGCTTACCAAAGTCAAGCGCCATTAAACTGATTGATTTTGGCAGTACTGTTTGTGATAACCGGATTCATC
upper sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv04s0008g04220.t01 (Vitis vinifera), 3'ss of exon 7
gtaat--gtcaatcagttttgtagtgatcatctgctattctgaaactaggcatgcg-gtattagcagttatgttgaatgatcccttggggttgtacagAAGAATTCACAAGATGAGATGCATTTCAAGTGCTTACCAAAGTCCAGTGCCATAAAGCTGATAGATTTTGGTAGTACCGCCTTTGATAATCAGGAACATA
||| | | | | | ||| | ||||| | ||| || | | || || | ||| | | || || ||| | ||||| | ||||||| | ||| ||||| | || |||| |||||| |||||||| ||||| || |||||||| |||||||||||||| || | |||||||||| | ||||
gtatttggccttttacaattggaa-aatcatt--ccattttggatttgggtatagatgcatttataat-at-ttaaataaatgcttggaatggtacagAGGTTTTCTTCCGATGAAACTCACTTCAGGTGCTTGCCAAAGTCGAGTGCAATTAAGCTGATTGATTTTGGTAGTACTGCATATGATAATCAGAACCATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaactaggcatgcggtattagcagttatgttgaatgatcccttggggttgtacagAAGAATTCACAAGATGAGATGCATTTCAAGTGCTTACCAAAGTCCAGTGCCATAAAGCTGATAGATTTTGGTAGTACCGCCTTTGATAATCAGGAACATA
ttatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgtcaatcagttttgtagtgatcatctgctattctgaaactaggcatgcggtattagcagttatgttgaatgatcccttggggttgtacagAAGAATTCACAAGATGAGATGCATTTCAAGTGCTTACCAAAGTCCAGTGCCATAAAGCTGATAGATTTTGGTAGTACCGCCTTTGATAATCAGGAACATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT