Sequence
atgc intronic sequence ATGC exonic sequence...gttcgtttaggttggatttgggttaggatttgtgtggcataatgcggtggttggaattgccttcgggagttgtggttgatggtggtgaggtttggcgcagGGACGCGTATGGATTCGCGGTGCGGCCGCAGCATCTGCAGCGTTTCCGCGAGTATGCCAAGATTTACAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g17540.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g17540.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G095868_T03 (Zea mays), 3'ss of exon 1
---gttcgtttaggttggatttgggttaggatttgtgtggcataatgcggtggttggaattgccttcgggagttgtggttgatggtggtgaggtttggcgcagGGACGCGTATGGATTCGCGGTGCGGCCGCAGCATCTGCAGCGTTTCCGCGAGTATGCCAAGATTTACAAG
||||| || ||| ||| | || | | | | |||||| || ||||| || ||| |||||| ||||||||||| | ||||||||||||||||||||| ||||||||| ||||||||||||||||||||||||||||||||||||| |||||||||||||||
cttgttcggttcc-ttgtattcgtatt--gccccgggggtgctaatgccgttgttggggttccctccgggagctgtggttgatgctcctgaggtttggcgcagGGACGCTTATGGATTCACGGTGCGGCCGCAGCATCTGCAGCGTTTCCGCGAGTACGCCAAGATTTACAAG
upper sequence: LOC_Os03g17540.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G154883_T02 (Zea mays), 3'ss of exon 1
---------------------------------------------------------------------gttcgtttaggttggatttgggttaggattt--gtgtggcataatgcggtggttggaattgccttcgggagttgtggttgatggtggtgaggtttggcgcagGGACGCGTATGGATTCGCGGTGCGGCCGCAGCATCTGCAGCGTTTCCGCGAGTATGCCAAGATTTACAAG
|||| | | ||| | || | | | || ||||| | ||||| || ||| |||||| ||||||||||||| ||||||||||||||||||||| ||||| |||||||||||||| |||||||||||||||||||||||||| |||||||||||||||
gtaaatcccacaaaaaggcgggtccctttgcccatttcgcctgcctccttttctctgctatggtctcttgttctccgttccttgttttcatattggcctgaggagggggggaatgcctttgttggggttccctccgggagctgtggttgatggtcctgaggtttggcgcagGGACGCTTATGGTTTCGCGGTGCGGCCACAGCATCTGCAGCGTTTCCGCGAGTACGCCAAGATTTACAAG
upper sequence: LOC_Os03g17540.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G154883_T01 (Zea mays), 3'ss of exon 1
-gttcgtttaggttggatttgggttaggatttgt-gtggcataatgcggtggttggaattgccttcgggagttgtggttgatggtggtgaggtttggcgcagGGACGCGTATGGATTCGCGGTGCGGCCGCAGCATCTGCAGCGTTTCCGCGAGTATGCCAAGATTTACAAG
| |||| ||| || || | | | | || ||||| | ||||| || ||| |||||| ||||||||||||| ||||||||||||||||||||| ||||| |||||||||||||| |||||||||||||||||||||||||| |||||||||||||||
tctccgttc--cttgttttcatattggcctgaggagggggggaatgcctttgttggggttccctccgggagctgtggttgatggtcctgaggtttggcgcagGGACGCTTATGGTTTCGCGGTGCGGCCACAGCATCTGCAGCGTTTCCGCGAGTACGCCAAGATTTACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtggttggaattgccttcgggagttgtggttgatggtggtgaggtttggcgcagGGACGCGTATGGATTCGCGGTGCGGCCGCAGCATCTGCAGCGTTTCCGCGAGTATGCCAAGATTTACAAG
ggttgat putative branch site (score: 5)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcgtttaggttggatttgggttaggatttgtgtggcataatgcggtggttggaattgccttcgggagttgtggttgatggtggtgaggtttggcgcagGGACGCGTATGGATTCGCGGTGCGGCCGCAGCATCTGCAGCGTTTCCGCGAGTATGCCAAGATTTACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - tggcata
- - - - - - - - - - - - - - - - - - - - - - - gtggttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgatg