Sequence
atgc intronic sequence ATGC exonic sequence...tgcatatgattttgattactaactcatatttatttttcaatatttcattcattatatatatatatatattttgacaaacccaccattcaatttttattagGTCCGTGGTTTTCTTCTCAACTTTGGTGTGTACTATGCTACTAGAGCAGCACTGGGTCTTACATTCCAATGGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g38850.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g38850.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G113476_T03 (Zea mays), 3'ss of exon 4
-tgc-atatgattttgattactaactcatatttatttttcaatatttcattcattatatatatatatatattttgacaaacccaccattcaattttt---attagGTCCGTGGTTTTCTTCTCAACTTTGGTGTGTACTATGCTACTAGAGCAGCACTGGGTCTTACATTCCAATGGAG
||| |||| ||| || ||| | | ||| ||| | | || || || | ||| | ||| ||||||| |||||||||||||| |||| ||||||| |||||||| |||||||||||||| ||||||||||||||||| || ||||| ||||||||||||||||||||
atgctgcttgatcttgttttctagat----tctatgtttaataaacacaatccatacac-tatttgtatgttttgacgaacccaccattcaaattttttgattagGTTCGTGGTTTCCTTCTCAACTTTGGCGTGTACTATGCTACTAGGGCTGCACTAGGTCTTACATTCCAATGGAG
upper sequence: LOC_Os07g38850.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G26820.2 (Glycine max), 3'ss of exon 3
----------------------------------------------tgcatatgattttgattactaactcatatttatttttcaa--tatttcattcattatatatatatatatattttgacaaacccaccattcaatttttattagGTCCGTGGTTTTCTTCTCAACTTTGGTGTGTACTATGCTACTAGAGCAGCACTGGGTCTTACATTCCAATGGAG
| ||| |||| | | ||| ||| | |||| ||| ||| | | || | || | | | || | | |||| || |||||||| || |||||||||||||||||||| |||||||| || || || ||| |||| |||||||
gtatgatatgtcctcctttccacctaatattttcagtactaacaacaatttgtgaatttgttcttttttggggattaattcagtaggttattgaattttaagtatttgttgattaagttcaaaagattgacagaaaaggcatatacagGTTCGGGGTTTTCTCCTTAACTTTGGTGTGTACTATGCCACTAGAGCTGCCCTTGGGCTTGCATTTGAATGGAG
upper sequence: LOC_Os07g38850.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA09G15720.1 (Glycine max), 3'ss of exon 4
-----------------------------------------------------tgcatatgattttgattactaactcatatttatttt--------tcaatatttcattca---ttatatatatat--atatattttgacaaacccaccattcaatttttattagGTCCGTGGTTTTCTTCTCAACTTTGGTGTGTACTATGCTACTAGAGCAGCACTGGGTCTTACATTCCAATGGAG
| ||| | || ||| | || | ||| |||| ||| || ||| | ||| ||| | | ||||| || | | | || | || |||| ||||||||||| || |||||||||||||||||||| |||||||| | || || ||| |||| |||||||
gtatgatatatcctcctttcctcctaattttttcagttctaacaagtaacaacaatttgtgaatctgtttattttttctttttttttttggataaattcagtaggcaattgaattttaagtatttgttgatatagttgaaaagattgacagaagaggcttatgcagGTACGTGGTTTTCTCCTTAACTTTGGTGTGTACTATGCCACTAGAGCTTCCCTTGGGCTTGCATTTGAATGGAG
upper sequence: LOC_Os07g38850.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G11945.1 (Arabidopsis thaliana), 3'ss of exon 4
-tgcatatgatttt--gattactaactcatatttatttttcaa--tatttcattcattatatatatatatatattttgacaa----acccaccatt--caatttttattagGTCCGTGGTTTTCTTCTCAACTTTGGTGTGTACTATGCTACTAGAGCAGCACTGGGTCTTACATTCCAATGGAG
| || |||| | || ||| |||| | | ||| ||| | || || | | | |||| | || | | ||| || || |||| |||| || ||||| ||||| ||||||||||||||| ||||||| ||||| || || || ||| |||| || |||||
gtaaatgctgttttatgcttcttaatcaatatacaactatcaccttatgtgatatttttcgtggcttgggaacttttaataacataattctgtattgacatttcttatcagGTACGAGGTTTCCTTCTTAACTTTGGTGTGTACCATGCTACAAGAGCTGCTCTTGGACTTCCATTTCAGTGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattcattatatatatatatatattttgacaaacccaccattcaatttttattagGTCCGTGGTTTTCTTCTCAACTTTGGTGTGTACTATGCTACTAGAGCAGCACTGGGTCTTACATTCCAATGGAG
ttttgac putative branch site (score: 3)
tttttatt putative PPT
attatatatatatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgcatatgattttgattactaactcatatttatttttcaatatttcattcattatatatatatatatattttgacaaacccaccattcaatttttattagGTCCGTGGTTTTCTTCTCAACTTTGGTGTGTACTATGCTACTAGAGCAGCACTGGGTCTTACATTCCAATGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
tgcatat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccattca