Sequence
atgc intronic sequence ATGC exonic sequence...gagcgctaagcacttcccgtctattcagctttgatacaaccatgttccatgtttccatgctgttatactgcctagttgattttccctttttcttaattagATAAGAGATACCAGTGTTCTGGTACGGTTGAGGCCTGCATGGGAGGATCTTCGGAGCTACTTAATTGCAAGAGGTCGCAAACGTTTTGAGGTATATGTGT
Basic information
species | Oryza sativa |
transcript | LOC_Os04g44710.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g44710.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G07800.1 (Glycine max), 3'ss of exon 2
---------gagcgctaagcacttcccgtctattcagctttgatacaaccatgttccatgtttccatgctgttatactgcctagttgattttccctttttcttaattagATAAGAGATACCAGTGTTCTGGTACGGTTGAGGCCTGCATGGGAGGATCTTCGGAGCTACTTAATTGCAAGAGGTCGCAAACGTTTTGAGGTATATGTGT
| | || || | || ||| | | || || ||||| | |||| || || | | ||| || | | || |||| | ||||| |||||||| || |||| || ||||||||||| ||||||||||||||| | | ||||||||| ||||| ||||||||||| | ||| |
aacatgaatggatgatacatggtttctgtagtttc--ttgtaattaaaacatgtag-acttttcagaatcattggtctaacaa--tgacttg----tgtctttggaaagATTCGTGATACTAGTGTTCTTGTGAGGTTAAGACCTGCATGGGAAGATCTTCGGAGCTACCTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTTTGTTT
upper sequence: LOC_Os04g44710.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA13G31510.1 (Glycine max), 3'ss of exon 2
--gagcgctaagcacttcccgtctattcagctttgatacaaccatgttccatgtttccatgctgttat-actgcctagttgattttccctttttcttaattagATAAGAGATACCAGTGTTCTGGTACGGTTGAGGCCTGCATGGGAGGATCTTCGGAGCTACTTAATTGCAAGAGGTCGCAAACGTTTTGAGGTATATGTGT
| | | | || | | ||| || || | ||||| | || || | || || | | | || |||| | ||||| |||||||| || ||||||| ||||||||||| ||||| ||||||||| | | ||||||||| ||||| ||||||||||| | ||| |
aacatgaatggatggtacatgttttctgtagtttcttataattaaa--acatgtagacttgtcagaatcattggtccaacaataa-cttgtgtctttggaaagATTCGTGATACTAGTGTTCTTGTGAGGTTGAGACCTGCATGGGAAGATCTCCGGAGCTACCTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTTTGTTT
upper sequence: LOC_Os04g44710.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA07G31430.1 (Glycine max), 3'ss of exon 2
---gagcgctaagcact-tcccgtctattcagctttga---tacaaccatgttccatgtttccatgctgttatactgcctagttgattttccctttttcttaattagATAAGAGATACCAGTGTTCTGGTACGGTTGAGGCCTGCATGGGAGGATCTTCGGAGCTACTTAATTGCAAGAGGTCGCAAACGTTTTGAGGTATATGTGT
| | ||||| | | |||||| | | ||||| || | | || | || ||| | ||| | || | | || | |||| | ||||| |||||||| || ||||||| ||||||||||| ||||||||||||||||| | ||||||||| ||||| ||||||||||| ||||| |
ataaatagataagctgtgttttatctattttatctaaaatatacaagca-gatagatttgtcagaatcatta----gtctaacaaaaatttgcgtgtt--tgggaagATTCGTGATACGAGTGTTCTTGTGAGGTTGAGACCTGCATGGGAAGATCTTCGGAGCTACTTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTATGTCT
upper sequence: LOC_Os04g44710.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA13G25010.1 (Glycine max), 3'ss of exon 2
---gagcgctaagcact-tcccgtctattcagctttga---tacaaccatgttccatgtttccatgctgttatactgcctagttgattttccctttttcttaattagATAAGAGATACCAGTGTTCTGGTACGGTTGAGGCCTGCATGGGAGGATCTTCGGAGCTACTTAATTGCAAGAGGTCGCAAACGTTTTGAGGTATATGTGT
| | ||||| | | |||||| | | | ||| | || | | || | || ||| || | | |||| | | || | |||| | ||||| |||||||| || ||||||| ||||||||||| ||||||||||||||| | | ||||||||| ||||| ||||||||||| ||||| |
ataaatagataagctgtgttttatctattttgtgtaaaatatactagca-gatagatttgtcagaatcattaatctaacaaa--aatttg----tgtgtttgacaagATTCGTGATACGAGTGTTCTTGTGAGGTTGAGACCTGCATGGGAAGATCTTCGGAGCTACCTTACTGCAAGAGGACGCAAGCGTTTTGAGGTTTATGTCT
upper sequence: LOC_Os04g44710.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv00s0370g00040.t01 (Vitis vinifera), 3'ss of exon 2
-gagcgctaagcacttcccgtctattcagctttgatacaaccatgttccatgtttccatgctgttatactgcctagt----tgattttccctttttcttaattagATAAGAGATACCAGTGTTCTGGTACGGTTGAGGCCTGCATGGGAGGATCTTCGGAGCTACTTAATTGCAAGAGGTCGCAAACGTTTTGAGGTATATGTGT
| | ||| ||||| || ||| | | | || | ||| | ||||| | | || |||| | || || | | |||| | ||||| ||||| || || || | || |||||||||||||| || ||||||||| ||| |||||| || ||||| ||||||||||| ||||| |
ataccacta--tacttcttgtttat---gtcatccaataagcctgtaaactcattccaagaaactggtttgtttagtgacacaaaatttttttatatctccacagATTCGTGATACAAGTGTACTTGTGAGGCTAAGACCTGCATGGGAGGACCTCCGGAGCTACCTAACTGCAAGGGGGCGCAAGCGTTTTGAGGTTTATGTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccatgtttccatgctgttatactgcctagttgattttccctttttcttaattagATAAGAGATACCAGTGTTCTGGTACGGTTGAGGCCTGCATGGGAGGATCTTCGGAGCTACTTAATTGCAAGAGGTCGCAAACGTTTTGAGGTATATGTGT
agttgat putative branch site (score: 5)
ttgattttcccttttt CT-rich tract
tttttcttaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gagcgctaagcacttcccgtctattcagctttgatacaaccatgttccatgtttccatgctgttatactgcctagttgattttccctttttcttaattagATAAGAGATACCAGTGTTCTGGTACGGTTGAGGCCTGCATGGGAGGATCTTCGGAGCTACTTAATTGCAAGAGGTCGCAAACGTTTTGAGGTATATGTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - -gcacttc
- - - - - - - - - - - -ttcagct
- - - - - - - - - - - - - - - - gatacaa
- - - - - - - - - - - - - - - - - - - - catgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - -tccatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tactgcc