Sequence
atgc intronic sequence ATGC exonic sequence...tttcatcagttccacatatggatagctgaatcctgaacagaaaatcaaacttcattaggtcacagttactagctcttaccttttacattcaacaggaaagTGAGGACTGAGCTGCTACAAAAGTACGGAAGGAATCGCAAGTTCTACCTTAAGCGAAAGCGGTATGGTAACTATCGATCAGAGATGGCTCGCTCCTTGTT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g01760.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g01760.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G035377_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------------------------------tttcatcagttccacatatggatagctgaatcctgaacagaaaatcaaacttcattaggtcacagttactagctct--taccttttacattcaacaggaaagTGAGGACTGAGCTGCTACAAAAGTACGGAAGGAATCGCAAGTTCTACCTTAAGCGAAAGCGGTATGGTAACTATCGATCAGAGATGGCTCGCTCCTTGTT
| | |||| | || | | | | | || | | | | || | | || || ||| | | | |||||||| ||||||||||| || |||||| | || || | ||||||||||||||||||||| ||||||||| | ||||| |||||||||||||| || ||
gtaagcatacaccacaagtccttgcttctccttttgtacatggattgattatggggtcattgctaggctaggctatgcttcattacacttagtagttaactgtttgtacaatgcatctgcttatgaataacaatatcttgaaactaaaccgaacatgacttcaataacttctccttataacagGAAGGTGAGGACTGAACTTCTACAACATTATGGCCGCAATCGCAAGTTCTACCTTAAGAGAAAGCGGTTCGACAACTACCGATCAGAGATGGCCCGGTCG-----
upper sequence: LOC_Os03g01760.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G113245_T01 (Zea mays), 3'ss of exon 2
----------------------------------------------------------------------------------------tttcatcagttccacatatggatagctgaatcctgaacagaaaatcaaacttcattaggtcaca-------gttactagctcttac----cttttacattcaacaggaaagTGAGGACTGAGCTGCTACAAAAGTACGGAAGGAATCGCAAGTTCTACCTTAAGCGAAAGCGGTATGGTAACTATCGATCAGAGATGGCTCGCTCCTTGTT
|||| | | ||| | | | | ||| | | | | | ||| | |||| | | ||| | | | |||||||| |||||||||||||| |||||| | || || | || |||||||||||||||||| ||||||||| | ||||| ||||||||||||||||| ||
gtaagcatatactggaaacccttgttcctcgtttagtcgcttcatctaacaattatccataatgacttgtatagggatcgatttgtggggtcattcctcattatctttagtagttaagtttttgccagtgctccttccacctatgaataacaagatcttgagactaaaccaaatatgacttctccttataacagGAAGGTGAGGACTGAGCTTCTACAACATTATGGTCGCAACCGCAAGTTCTACCTTAAGAGAAAGCGGTTCGACAACTACCGATCAGAGATGGCTCGGTCA----- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaacttcattaggtcacagttactagctcttaccttttacattcaacaggaaagTGAGGACTGAGCTGCTACAAAAGTACGGAAGGAATCGCAAGTTCTACCTTAAGCGAAAGCGGTATGGTAACTATCGATCAGAGATGGCTCGCTCCTTGTT
ctcttac putative branch site (score: 3)
ttttacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttcatcagttccacatatggatagctgaatcctgaacagaaaatcaaacttcattaggtcacagttactagctcttaccttttacattcaacaggaaagTGAGGACTGAGCTGCTACAAAAGTACGGAAGGAATCGCAAGTTCTACCTTAAGCGAAAGCGGTATGGTAACTATCGATCAGAGATGGCTCGCTCCTTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - gctgaat
- - - - - - - - - - - - - - - -cctgaac
- - - - - - - - - - - - - - - - - - - - -aaatcaa