Sequence
atgc intronic sequence ATGC exonic sequencegtatggattagaaatgctcttttttccttattcatgaatggatgcttatcataattccttaatatttcagCGGATGATGGCACTTTATGTTGCTTCCCATTACAAAAATTCACCCAATGACTTGCAACTAATGGCTGATGCGCCGGCTCATCACCTATTTGTATTGCTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os12g07300.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g07300.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv07s0031g01750.t01 (Vitis vinifera), 3'ss of exon 13
--------------gtatgg-attagaaatgctcttttttccttattc-atgaatggatgcttatcataattccttaatatttcagCGGATGATGGCACTTTATGTTGCTTCCCATTACAAAAATTCACCCAATGACTTGCAACTAATGGCTGATGCGCCGGCTCATCACCTATTTGTATTGCTTG
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gtaactacttgtcaatctggtaatgattctcattttttttccttattttgtgaaaaacttttgctcatgtattattaactttgcagCGAATGATGGCCCTTTATGTTGCTTCTCACTACAAAAATTCTCCAAATGATTTACAATTAATGGCTGATGCTCCAGCTCACCACTTGTTTGTGTTACTTG
upper sequence: LOC_Os12g07300.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S93_182V6.1 (Physcomitrella patens), 3'ss of exon 13
---------------------------------------------------------------gtatggattagaaatgctcttttttccttattcatgaatggatgcttatcataattccttaatatt-----------tcagCGGATGATGGCACTTTATGTTGCTTCCCATTACAAAAATTCACCCAATGACTTGCAACTAATGGCTGATGCGCCGGCTCATCACCTATTTGTATTGCTTG
| | | | || | | | || | | | | | | || ||| | | | |||| | |||||||| | ||||| ||||| ||||||||||| ||||||||||| |||| || ||| ||||||| || || ||||| || ||||| || ||||
gtaactcacctgaagttattatgcccaatttcttctagtcaacttggagaatcattcaatccgctttaatctgggaaatcgttgtgttgcatgcatgcacaccggctttaactatcgttcttggttttggtttgaggggatcagAGAATGATGGCGTTGTATGTCGCTTCACATTACAAAAACACACCCAATGACCTGCAGCTTATGTCTGATGCACCAGCACATCATCTGTTTGTTTTACTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctcttttttccttattcatgaatggatgcttatcataattccttaatatttcagCGGATGATGGCACTTTATGTTGCTTCCCATTACAAAAATTCACCCAATGACTTGCAACTAATGGCTGATGCGCCGGCTCATCACCTATTTGTATTGCTTG
ccttaat putative branch site (score: 4)
ttcctta CT-rich tract
ttatcataattcctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggattagaaatgctcttttttccttattcatgaatggatgcttatcataattccttaatatttcagCGGATGATGGCACTTTATGTTGCTTCCCATTACAAAAATTCACCCAATGACTTGCAACTAATGGCTGATGCGCCGGCTCATCACCTATTTGTATTGCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT