Sequence
atgc intronic sequence ATGC exonic sequence...ctacggctagatcttctttgacaagcaggcatcagtttggtttattcccaaattaaacatcgccattttggttttgtgtaaaatgtgatatgttttgcagAACGAGGTATCCGTGCTGTCCCCTCGGGTGGCGTTTCTGGATCAGCAGCGGACGATCCTGACCGTCGGCAACAGCCACCTCAAGCAGCGGATCGCGGCTC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g55150.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g55150.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G027976_T01 (Zea mays), 3'ss of exon 2
-ctacggctagatcttctttgacaagcaggcatcagtttggtttattcccaaattaaacatcgc-cattttggttttgtgtaaaatgtgatatgttttgcagAACGAGGTATCCGTGCTGTCCCCTCGGGTGGCGTTTCTGGATCAGCAGCGGACGATCCTGACCGTCGGCAACAGCCACCTCAAGCAGCGGATCGCGGCTC
|| |||||| | ||| | || | ||| | | | || || | | | || | || | || | ||||||||||||| |||| |||||| || || ||||| ||||||||||||||||| || || |||||||||||||||||||||||||||||||||||||| ||||
aatagtttcggatctttgtcgac--ggagttgctcgcttgctctcagctagaactagaagctgtataattaaaaccgatcgtttgcgtcgtttgctgtgcagAACGAGGTGTCCGCGCTGTCTCCCCGTGTGGCATTTCTGGATCAGCAGCGTACCATACTGACCGTCGGCAACAGCCACCTCAAGCAGCGGATCGCAGCTC
upper sequence: LOC_Os01g55150.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G170079_T02 (Zea mays), 3'ss of exon 2
---------ctacggctagatcttctttgacaagcaggcatcagtttggtttattcccaaattaaacatcgccattttggttttgtgtaaaatgtgatatgttttgcagAACGAGGTATCCGTGCTGTCCCCTCGGGTGGCGTTTCTGGATCAGCAGCGGACGATCCTGACCGTCGGCAACAGCCACCTCAAGCAGCGGATCGCGGCTC
||| |||| || | | |||| | ||| || || | || | | || | | || |||| || ||||||||||||| || |||||||||||||| |||||||||||||| ||||||||||| || |||| |
gcttgcttgctattgctattgctattgctctgcg-aggcgagatgttgtgttgttgtaactttgtaaaccgaccgtctg--tttgccctgcgcctg------cctgcagAACGAGGTGTCGGTGCTGTCCCCTCGCGTGGCGTTTCTGGACCAGCAGCGGACCATACTGAGC------------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcccaaattaaacatcgccattttggttttgtgtaaaatgtgatatgttttgcagAACGAGGTATCCGTGCTGTCCCCTCGGGTGGCGTTTCTGGATCAGCAGCGGACGATCCTGACCGTCGGCAACAGCCACCTCAAGCAGCGGATCGCGGCTC
aattaaacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctacggctagatcttctttgacaagcaggcatcagtttggtttattcccaaattaaacatcgccattttggttttgtgtaaaatgtgatatgttttgcagAACGAGGTATCCGTGCTGTCCCCTCGGGTGGCGTTTCTGGATCAGCAGCGGACGATCCTGACCGTCGGCAACAGCCACCTCAAGCAGCGGATCGCGGCTC
- - - - - - - - - - - - gcaggca
- - - - - - - - - - - - - - - - - - - - - - - - - - - aaacatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgata