Sequence
atgc intronic sequence ATGC exonic sequencegtaatccttcacttatagagggtctaagcttcttggtaagaattttcttagcatttctcacagtgcaattaaaactcttgctcaatgcaattctagGTGATCCTGGACTAGGCAAGAGTCAACTGCTACAGGCTGCAGCAGCTGTTTCTCCACGGGGTATATATGTTTGTGGGAATACAACAACAAATGCTGGTCT
Basic information
species | Oryza sativa |
transcript | LOC_Os05g38850.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g38850.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G163658_T01 (Zea mays), 3'ss of exon 6
----gtaatccttcacttatagagggtctaagcttcttggtaag--aattttcttagcatttctcacagtgcaattaaaactcttgctcaatgcaattctagGTGATCCTGGACTAGGCAAGAGTCAACTGCTACAGGCTGCAGCAGCTGTTTCTCCACGGGGTATATATGTTTGTGGGAATACAACAACAAATGCTGGTCT
| || | | | | | || || ||||| | | ||| || | || ||| |||| |||||||| || || ||||||||| || |||||||| || ||||| || || ||||||||||||||||| ||||| || |||||||| ||||||||||| |||||||| ||||| ||
cttttttctctcttaatgaaatgatgtgcaactctcttgcatgttcagataaaatagtgttgcgcatggtgtgattatg-ctcttgcttaaaaca-ccacagGTGATCCAGGGCTAGGCAAAAGCCAACTCCTCCAAGCTGCAGCAGCTGTTTCCCCACGAGGAATATATGTATGTGGGAATACGACAACAAAGGCTGGCCT
upper sequence: LOC_Os05g38850.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA19G36230.1 (Glycine max), 3'ss of exon 6
--------------------------------------------------------------------------------------------gtaatccttca-cttatagagggtctaa--gcttcttggtaagaattttcttagcatttctcacagtgcaattaaaactcttgctcaatgcaattctagGTGATCCTGGACTAGGCAAGAGTCAACTGCTACAGGCTGCAGCAGCTGTTTCTCCACGGGGTATATATGTTTGTGGGAATACAACAACAAATGCTGGTCT
| | || || ||| || || ||| | | |||||||| || || | ||| | | || | | | | |||||||||||||||| ||||| ||||| || | ||||| || |||||||||||||||||||| ||||| ||||| ||||| ||| ||||||| | ||||| ||
gtatgcttaatgtcttttgcttaccttctaaacggaatcagaccttcagattttttattctttttacgaagaagtggatttatttgtcaaaaatgttactccagtttaaagttggcataacggagacaaggtaagaagttatggagatgagatgacaa-actactagtattgcaattt--cggttttctagGTGATCCTGGTCTAGGTAAGAGCCAGTTACTACAAGCAGCAGCAGCTGTTTCTCCACGTGGTATCTATGTCTGTGGTAATGCAACAACCAGAGCTGGCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttcttagcatttctcacagtgcaattaaaactcttgctcaatgcaattctagGTGATCCTGGACTAGGCAAGAGTCAACTGCTACAGGCTGCAGCAGCTGTTTCTCCACGGGGTATATATGTTTGTGGGAATACAACAACAAATGCTGGTCT
ttctcac putative branch site (score: 2)
aattaaaact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatccttcacttatagagggtctaagcttcttggtaagaattttcttagcatttctcacagtgcaattaaaactcttgctcaatgcaattctagGTGATCCTGGACTAGGCAAGAGTCAACTGCTACAGGCTGCAGCAGCTGTTTCTCCACGGGGTATATATGTTTGTGGGAATACAACAACAAATGCTGGTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG